diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_1.txt new file mode 100644 index 00000000000..c3f86ade180 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_1.txt @@ -0,0 +1,15 @@ +Getting an HPC Account +Getting ready to request an account +All users of AUGent can request +an +account on the HPC, which is part of the Flemish Supercomputing Centre (VSC). +See HPC policies for more information on who is entitled to an account. +The VSC, abbreviation of Flemish Supercomputer Centre, is a virtual +supercomputer centre. It is a partnership between the five Flemish +associations: the Association KU Leuven, Ghent University Association, +Brussels University Association, Antwerp University Association and the +University Colleges-Limburg. The VSC is funded by the Flemish +Government. +There are two methods for connecting to HPC-UGent infrastructure: +- Using a terminal to connect via SSH. +- Using the web portal diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_10.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_10.txt new file mode 100644 index 00000000000..7b0a39279e4 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_10.txt @@ -0,0 +1,18 @@ +After you have uploaded your public key you will receive an e-mail with +a link to confirm your e-mail address. After confirming your e-mail +address the VSC staff will review and if applicable approve your +account. +Welcome e-mail +Within one day, you should receive a Welcome e-mail with your VSC +account details. +Dear (Username), +Your VSC-account has been approved by an administrator. +Your vsc-username is vsc40000 +Your account should be fully active within one hour. +To check or update your account information please visit +https://account.vscentrum.be/ +For further info please visit https://www.vscentrum.be/user-portal +Kind regards, +-- The VSC administrators +Now, you can start using the HPC. You can always look up your VSC id later +by visiting . diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_10_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_10_metadata.json new file mode 100644 index 00000000000..e417029c16f --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_10_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Welcome-e-mail", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "", + "previous_title": "account_paragraph_9", + "next_title": "account_paragraph_11", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/account/#welcome-e-mail" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_12.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_12.txt new file mode 100644 index 00000000000..7ecd78e5c9f --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_12.txt @@ -0,0 +1,14 @@ +Computation Workflow on the HPC +A typical Computation workflow will be: +1. Connect to the HPC +2. Transfer your files to the HPC +3. Compile your code and test it +4. Create a job script +5. Submit your job +6. Wait while + 1. your job gets into the queue + 2. your job gets executed + 3. your job finishes +7. Move your results +We'll take you through the different tasks one by one in the following +chapters. \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_12_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_12_metadata.json new file mode 100644 index 00000000000..e43e729aa74 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_12_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Computation-Workflow-on-the-HPC", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 2, + "directory": "account", + "parent_title": "", + "previous_title": "account_paragraph_11", + "next_title": null, + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/account/#computation-workflow-on-the-hpc" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_1_metadata.json new file mode 100644 index 00000000000..52a3ef55568 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_1_metadata.json @@ -0,0 +1,16 @@ +{ + "main_title": "account", + "subtitle": "Getting-ready-to-request-an-account", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 2, + "directory": "account", + "links": { + "0": "https://docs.hpc.ugent.be/sites/hpc_policies", + "1": "https://docs.hpc.ugent.be/web_portal" + }, + "parent_title": "", + "previous_title": null, + "next_title": "account_paragraph_2", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/account/#getting-ready-to-request-an-account" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_2.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_2.txt new file mode 100644 index 00000000000..9614ed1447c --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_2.txt @@ -0,0 +1,9 @@ +The web portal offers a convenient way to upload files and gain shell access to the HPC-UGent infrastructure from a standard web browser (no software installation or configuration required). +If you would like use a terminal with SSH as this gives you more flexibility continue reading. +However if you prefer to use the web portal, you can skip ahead to the following section: Applying for the account. +Once you have successfully obtained an account, you can then delve into the details of utilizing the HPC-UGent web portal by reading Using the HPC-UGent web portal. +The HPC-UGent infrastructure clusters use public/private key pairs for user authentication +(rather than passwords). Technically, the private key is stored on your +local computer and always stays there; the public key is stored on the HPC. +Access to the HPC is granted to anyone who can prove to have access to the +corresponding private key on his local computer. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_2_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_2_metadata.json new file mode 100644 index 00000000000..a41a1993674 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_2_metadata.json @@ -0,0 +1,16 @@ +{ + "main_title": "account", + "subtitle": "Getting-ready-to-request-an-account", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 2, + "directory": "account", + "links": { + "0": "https://docs.hpc.ugent.be/account/#applying-for-the-account", + "1": "https://docs.hpc.ugent.be/web_portal" + }, + "parent_title": "", + "previous_title": "account_paragraph_1", + "next_title": "account_paragraph_3", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/account/#getting-ready-to-request-an-account" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_3.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_3.txt new file mode 100644 index 00000000000..963b35c090b --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_3.txt @@ -0,0 +1,15 @@ +How do SSH keys work? +- an SSH public/private key pair can be seen as a lock and a key +- the SSH public key is equivalent with a lock: you give it to the + VSC and they put it on the door that gives access to your account. +- the SSH private key is like a physical key: you don't hand it out + to other people. +- anyone who has the key (and the optional password) can unlock the + door and log in to the account. +- the door to your VSC account is special: it can have multiple + locks (SSH public keys) attached to it, and you only need to open + one lock with the corresponding key (SSH private key) to open + the door (log in to the account). +Since all VSC clusters use Linux as their main operating system, you +will need to get acquainted with using the command-line interface and +using the terminal (see tutorial). diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_3_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_3_metadata.json new file mode 100644 index 00000000000..4df622cc4aa --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_3_metadata.json @@ -0,0 +1,15 @@ +{ + "main_title": "account", + "subtitle": "How-do-SSH-keys-work", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "links": { + "0": "https://docs.hpc.ugent.be/linux-tutorial" + }, + "parent_title": "", + "previous_title": "account_paragraph_2", + "next_title": "account_paragraph_4", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/account/#how-do-ssh-keys-work" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_8.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_8.txt new file mode 100644 index 00000000000..6c5695dfff3 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_8.txt @@ -0,0 +1,14 @@ +Applying for the account +Visit +You will be redirected to our WAYF (Where Are You From) service where +you have to select your "Home Organisation". +Select "UGent" in the dropdown box and optionally select "Save my preference" +and "permanently". +Click "Confirm" +You will now be taken to the authentication page of your institute. +You will now have to log in with CAS using your UGent account. +You either have a login name of maximum 8 characters, or a (non-UGent) +email address if you are an external user. In case of problems with your +UGent password, please visit: . After +logging in, you may be requested to share your information. Click "Yes, +continue". diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_8_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_8_metadata.json new file mode 100644 index 00000000000..6a77c48dbd1 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_8_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Applying-for-the-account", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 2, + "directory": "account", + "parent_title": "", + "previous_title": "account_paragraph_7", + "next_title": "account_paragraph_9", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/account/#applying-for-the-account" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_1.txt new file mode 100644 index 00000000000..db1afd43e68 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_1.txt @@ -0,0 +1,10 @@ +Compiling and testing your software on the HPC +All nodes in the HPC cluster are running the "RHEL 8.8 (accelgor, doduo, donphan, gallade, joltik, skitty)" +Operating system, which is a specific version of Red Hat Enterprise Linux. This means that all the +software programs +(executable) that the end-user wants to run on the HPC first must be +compiled for RHEL 8.8 (accelgor, doduo, donphan, gallade, joltik, skitty). It also means that you first have to install all the +required external software packages on the HPC. +Most commonly used compilers are already pre-installed on the HPC and can be +used straight away. Also, many popular external software packages, which +are regularly used in the scientific community, are also pre-installed. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_10.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_10.txt new file mode 100644 index 00000000000..d49ba76b01a --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_10.txt @@ -0,0 +1,19 @@ +The "mpi_hello.c" program is a simple source file, written in C with MPI +library calls. +Then, check the command line options for *"mpicc" (GNU C-Compiler with +MPI extensions)*, then we compile and list the contents of the directory +again: +mpicc --help +mpicc -o mpihello mpihello.c +ls -l +A new file "hello" has been created. Note that this program has +"execute" rights. +Let's test this program on the "login" node first: +$ ./mpihello +Hello World from Node 0. +It seems to work, now run it on the HPC. +qsub mpihello.pbs +Compiling a parallel program in Intel Parallel Studio Cluster Edition +We will now compile the same program, but using the Intel Parallel +Studio Cluster Edition compilers. We stay in the examples directory for +this chapter: diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_10_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_10_metadata.json new file mode 100644 index 00000000000..ca0d7d80669 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_10_metadata.json @@ -0,0 +1,11 @@ +{ + "main_title": "compiling_your_software", + "subtitle": "Compiling-a-parallel-program-in-Intel-Parallel-Studio-Cluster-Edition", + "title_depth": 3, + "directory": "compiling_your_software", + "parent_title": "", + "previous_title": "compiling_your_software_paragraph_9", + "next_title": "compiling_your_software_paragraph_11", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#compiling-a-parallel-program-in-intel-parallel-studio-cluster-edition" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_11.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_11.txt new file mode 100644 index 00000000000..be02d069ac7 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_11.txt @@ -0,0 +1,20 @@ +cd ~/examples/Compiling-and-testing-your-software-on-the-HPC +We will compile this C/MPI -file into an executable with the Intel +Parallel Studio Cluster Edition. First, clear the modules (purge) and +then load the latest "intel" module: +module purge +module load intel +Then, compile and list the contents of the directory again. The Intel +equivalent of mpicc is mpiicc. +mpiicc -o mpihello mpihello.c +ls -l +Note that the old "mpihello" file has been overwritten. Let's test this +program on the "login" node first: +$ ./mpihello +Hello World from Node 0. +It seems to work, now run it on the HPC. +qsub mpihello.pbs +Note: The AUGent only has a license for the Intel Parallel Studio Cluster +Edition for a fixed number of users. As such, it might happen that you +have to wait a few minutes before a floating license becomes available +for your use. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_11_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_11_metadata.json new file mode 100644 index 00000000000..808331a3f9d --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_11_metadata.json @@ -0,0 +1,11 @@ +{ + "main_title": "compiling_your_software", + "subtitle": "Compiling-a-parallel-program-in-Intel-Parallel-Studio-Cluster-Edition", + "title_depth": 3, + "directory": "compiling_your_software", + "parent_title": "", + "previous_title": "compiling_your_software_paragraph_10", + "next_title": "compiling_your_software_paragraph_12", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#compiling-a-parallel-program-in-intel-parallel-studio-cluster-edition" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_12.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_12.txt new file mode 100644 index 00000000000..1d37014a426 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_12.txt @@ -0,0 +1,9 @@ +Note: The Intel Parallel Studio Cluster Edition contains equivalent +compilers for all GNU compilers. Hereafter the overview for C, C++ and +Fortran compilers. +| | Sequential Program | | **Parallel Program (with MPI)** | | +|-------------|------------------------|-----------|---------------------------------|-----------| +| | GNU | Intel | GNU | Intel | +| C | gcc | icc | mpicc | mpiicc | +| **C++** | g++ | icpc | mpicxx | mpiicpc | +| Fortran | gfortran | ifort | mpif90 | mpiifort | \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_12_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_12_metadata.json new file mode 100644 index 00000000000..d032428daf1 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_12_metadata.json @@ -0,0 +1,11 @@ +{ + "main_title": "compiling_your_software", + "subtitle": "Compiling-a-parallel-program-in-Intel-Parallel-Studio-Cluster-Edition", + "title_depth": 3, + "directory": "compiling_your_software", + "parent_title": "", + "previous_title": "compiling_your_software_paragraph_11", + "next_title": null, + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#compiling-a-parallel-program-in-intel-parallel-studio-cluster-edition" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_1_metadata.json new file mode 100644 index 00000000000..ec4b55c9a4d --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_1_metadata.json @@ -0,0 +1,11 @@ +{ + "main_title": "compiling_your_software", + "subtitle": "Compiling-and-testing-your-software-on-the-HPC", + "title_depth": 1, + "directory": "compiling_your_software", + "parent_title": "", + "previous_title": null, + "next_title": "compiling_your_software_paragraph_2", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#compiling-and-testing-your-software-on-the-hpc" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_2.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_2.txt new file mode 100644 index 00000000000..b52639b649d --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_2.txt @@ -0,0 +1,13 @@ +Check the pre-installed software on the HPC +In order to check all the available modules and their version numbers, +which are pre-installed on the HPC enter: +When your required application is not available on the HPC please contact +any HPC member. Be aware of potential "License Costs". "Open Source" +software is often preferred. +Porting your code +To port a software-program is to translate it from the operating system in +which it was developed (e.g., Windows 7) to another operating system +(e.g., Red Hat Enterprise Linux on our HPC) so that it can be used there. Porting implies some +degree of effort, but not nearly as much as redeveloping the program in +the new environment. It all depends on how "portable" you wrote your +code. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_2_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_2_metadata.json new file mode 100644 index 00000000000..00750c81d97 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_2_metadata.json @@ -0,0 +1,11 @@ +{ + "main_title": "compiling_your_software", + "subtitle": "Porting-your-code", + "title_depth": 2, + "directory": "compiling_your_software", + "parent_title": "", + "previous_title": "compiling_your_software_paragraph_1", + "next_title": "compiling_your_software_paragraph_3", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#porting-your-code" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_3.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_3.txt new file mode 100644 index 00000000000..f994f0bc148 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_3.txt @@ -0,0 +1,13 @@ +In the simplest case the file or files may simply be copied from one +machine to the other. However, in many cases the software is installed +on a computer in a way, which depends upon its detailed hardware, +software, and setup, with device drivers for particular devices, using +installed operating system and supporting software components, and using +different directories. +In some cases software, usually described as "portable software" is +specifically designed to run on different computers with compatible +operating systems and processors without any machine-dependent +installation; it is sufficient to transfer specified directories and +their contents. Hardware- and software-specific information is often +stored in configuration files in specified locations (e.g., the registry +on machines running MS Windows). diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_3_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_3_metadata.json new file mode 100644 index 00000000000..90e7d236beb --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_3_metadata.json @@ -0,0 +1,11 @@ +{ + "main_title": "compiling_your_software", + "subtitle": "Porting-your-code", + "title_depth": 2, + "directory": "compiling_your_software", + "parent_title": "", + "previous_title": "compiling_your_software_paragraph_2", + "next_title": "compiling_your_software_paragraph_4", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#porting-your-code" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_4.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_4.txt new file mode 100644 index 00000000000..f7bf4172b71 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_4.txt @@ -0,0 +1,15 @@ +Software, which is not portable in this sense, will have to be +transferred with modifications to support the environment on the +destination machine. +Whilst programming, it would be wise to stick to certain standards +(e.g., ISO/ANSI/POSIX). This will ease the porting of your code to other +platforms. +Porting your code to the RHEL 8.8 (accelgor, doduo, donphan, gallade, joltik, skitty) platform is the responsibility of the end-user. +Compiling and building on the HPC +Compiling refers to the process of translating code written in some +programming language, e.g., Fortran, C, or C++, to machine code. +Building is similar, but includes gluing together the machine code +resulting from different source files into an executable (or library). +The text below guides you through some basic problems typical for small +software projects. For larger projects it is more appropriate to use +makefiles or even an advanced build system like CMake. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_4_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_4_metadata.json new file mode 100644 index 00000000000..b7c9ef0f71b --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_4_metadata.json @@ -0,0 +1,11 @@ +{ + "main_title": "compiling_your_software", + "subtitle": "Compiling-and-building-on-the-HPC", + "title_depth": 2, + "directory": "compiling_your_software", + "parent_title": "", + "previous_title": "compiling_your_software_paragraph_3", + "next_title": "compiling_your_software_paragraph_5", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#compiling-and-building-on-the-hpc" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_5.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_5.txt new file mode 100644 index 00000000000..342262b9264 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_5.txt @@ -0,0 +1,16 @@ +All the HPC nodes run the same version of the Operating System, i.e. RHEL 8.8 (accelgor, doduo, donphan, gallade, joltik, skitty). So, +it is sufficient to compile your program on any compute node. Once you +have generated an executable with your compiler, this executable should +be able to run on any other compute-node. +A typical process looks like: +1. Copy your software to the login-node of the HPC +2. Start an interactive session on a compute node; +3. Compile it; +4. Test it locally; +5. Generate your job scripts; +6. Test it on the HPC +7. Run it (in parallel); +We assume you've copied your software to the HPC. The next step is to request +your private compute node. +$ qsub -I +qsub: waiting for job 123456 to start diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_5_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_5_metadata.json new file mode 100644 index 00000000000..02a8fad0ae2 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_5_metadata.json @@ -0,0 +1,11 @@ +{ + "main_title": "compiling_your_software", + "subtitle": "Compiling-and-building-on-the-HPC", + "title_depth": 2, + "directory": "compiling_your_software", + "parent_title": "", + "previous_title": "compiling_your_software_paragraph_4", + "next_title": "compiling_your_software_paragraph_6", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#compiling-and-building-on-the-hpc" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_6.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_6.txt new file mode 100644 index 00000000000..7ebde664878 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_6.txt @@ -0,0 +1,30 @@ +Compiling a sequential program in C +Go to the examples for chapter +Compiling and testing your software on the HPC and load the +foss module: +cd ~/examples/Compiling-and-testing-your-software-on-the-HPC +module load foss +We now list the directory and explore the contents of the "hello.c" +program: +$ ls -l +total 512 +-rw-r--r-- 1 vsc40000 214 Sep 16 09:42 hello.c +-rw-r--r-- 1 vsc40000 130 Sep 16 11:39 hello.pbs* +-rw-r--r-- 1 vsc40000 359 Sep 16 13:55 mpihello.c +-rw-r--r-- 1 vsc40000 304 Sep 16 13:55 mpihello.pbs +/* + * VSC : Flemish Supercomputing Centre + * Tutorial : Introduction to HPC + * Description: Print 500 numbers, whilst waiting 1 second in between + */ +#include "stdio.h" +int main( int argc, char *argv[] ) +{ + int i; + for (i=0; i<500; i++) + { + printf("Hello #%d\n", i); + fflush(stdout); + sleep(1); + } +} diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_6_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_6_metadata.json new file mode 100644 index 00000000000..16942249583 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_6_metadata.json @@ -0,0 +1,14 @@ +{ + "main_title": "compiling_your_software", + "subtitle": "Compiling-a-sequential-program-in-C", + "title_depth": 3, + "directory": "compiling_your_software", + "links": { + "0": "https://docs.hpc.ugent.be/compiling_your_software/#compiling-and-building-on-the-hpc" + }, + "parent_title": "", + "previous_title": "compiling_your_software_paragraph_5", + "next_title": "compiling_your_software_paragraph_7", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#compiling-a-sequential-program-in-c" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_7.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_7.txt new file mode 100644 index 00000000000..1d58d0d6ae4 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_7.txt @@ -0,0 +1,15 @@ +The "hello.c" program is a simple source file, written in C. It'll print +500 times "Hello #<num>", and waits one second between 2 printouts. +We first need to compile this C-file into an executable with the +gcc-compiler. +First, check the command line options for *"gcc" (GNU C-Compiler)*, then +we compile. the O2 option enables a moderate level of optimization when compiling the code. +It instructs the compiler to optimize the code for better performance without significantly increasing compilation time. +Finally, list the contents of the directory again: +$ gcc -help +$ gcc -O2 -o hello hello.c +$ ls -l +total 512 +-rwxrwxr-x 1 vsc40000 7116 Sep 16 11:43 hello* +-rw-r--r-- 1 vsc40000 214 Sep 16 09:42 hello.c +-rwxr-xr-x 1 vsc40000 130 Sep 16 11:39 hello.pbs* diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_7_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_7_metadata.json new file mode 100644 index 00000000000..e5f3161c3f2 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_7_metadata.json @@ -0,0 +1,11 @@ +{ + "main_title": "compiling_your_software", + "subtitle": "Compiling-a-sequential-program-in-C", + "title_depth": 3, + "directory": "compiling_your_software", + "parent_title": "", + "previous_title": "compiling_your_software_paragraph_6", + "next_title": "compiling_your_software_paragraph_8", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#compiling-a-sequential-program-in-c" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_8.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_8.txt new file mode 100644 index 00000000000..5ca5de1e6d4 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_8.txt @@ -0,0 +1,19 @@ +A new file "hello" has been created. Note that this file has "execute" +rights, i.e., it is an executable. More often than not, calling gcc -- +or any other compiler for that matter -- will provide you with a list of +errors and warnings referring to mistakes the programmer made, such as +typos, syntax errors. You will have to correct them first in order to +make the code compile. Warnings pinpoint less crucial issues that may +relate to performance problems, using unsafe or obsolete language +features, etc. It is good practice to remove all warnings from a +compilation process, even if they seem unimportant so that a code change +that produces a warning does not go unnoticed. +Let's test this program on the local compute node, which is at your +disposal after the qsub --I command: +$ ./hello +Hello #0 +Hello #1 +Hello #2 +Hello #3 +Hello #4 +... diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_8_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_8_metadata.json new file mode 100644 index 00000000000..942949951d1 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_8_metadata.json @@ -0,0 +1,11 @@ +{ + "main_title": "compiling_your_software", + "subtitle": "Compiling-a-sequential-program-in-C", + "title_depth": 3, + "directory": "compiling_your_software", + "parent_title": "", + "previous_title": "compiling_your_software_paragraph_7", + "next_title": "compiling_your_software_paragraph_9", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#compiling-a-sequential-program-in-c" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_9.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_9.txt new file mode 100644 index 00000000000..28982d2bd95 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_9.txt @@ -0,0 +1,32 @@ +It seems to work, now run it on the HPC +qsub hello.pbs +Compiling a parallel program in C/MPI +cd ~/examples/Compiling-and-testing-your-software-on-the-HPC +List the directory and explore the contents of the "mpihello.c" +program: +$ ls -l +total 512 +total 512 +-rw-r--r-- 1 vsc40000 214 Sep 16 09:42 hello.c +-rw-r--r-- 1 vsc40000 130 Sep 16 11:39 hello.pbs* +-rw-r--r-- 1 vsc40000 359 Sep 16 13:55 mpihello.c +-rw-r--r-- 1 vsc40000 304 Sep 16 13:55 mpihello.pbs +/* + * VSC : Flemish Supercomputing Centre + * Tutorial : Introduction to HPC + * Description: Example program, to compile with MPI + */ +#include +#include +main(int argc, char **argv) +{ + int node, i, j; + float f; + MPI_Init(&argc,&argv); + MPI_Comm_rank(MPI_COMM_WORLD, &node); + + printf("Hello World from Node %d.\n", node); + for (i=0; i<=100000; i++) + f=i*2.718281828*i+i+i*3.141592654; + MPI_Finalize(); +} diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_9_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_9_metadata.json new file mode 100644 index 00000000000..fe51e423a96 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_9_metadata.json @@ -0,0 +1,11 @@ +{ + "main_title": "compiling_your_software", + "subtitle": "Compiling-a-parallel-program-in-CMPI", + "title_depth": 3, + "directory": "compiling_your_software", + "parent_title": "", + "previous_title": "compiling_your_software_paragraph_8", + "next_title": "compiling_your_software_paragraph_10", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#compiling-a-parallel-program-in-cmpi" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_1.txt new file mode 100644 index 00000000000..bc5a1f80140 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_1.txt @@ -0,0 +1,18 @@ +Connecting to the HPC infrastructure +Before you can really start using the HPC clusters, there are several things +you need to do or know: +1. You need to log on to the cluster using an SSH client to one of + the login nodes or by using the HPC web portal. + This will give you command-line access. + A standard web browser like Firefox or Chrome for the web portal will suffice. +2. Before you can do some work, you'll have to transfer the files + that you need from your desktop computer to the cluster. At the end + of a job, you might want to transfer some files back. +3. Optionally, if you wish to use programs with a **graphical user + interface**, you will need an X-server on your client system and log + in to the login nodes with X-forwarding enabled. +4. Often several versions of software packages and libraries are + installed, so you need to select the ones you need. To manage + different versions efficiently, the VSC clusters use so-called + modules, so you will need to select and load the modules that + you need. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_10.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_10.txt new file mode 100644 index 00000000000..5c715d218a1 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_10.txt @@ -0,0 +1,24 @@ +You can exit the connection at anytime by entering: +$ exit +logout +Connection to login.hpc.ugent.be closed. + tip "tip: Setting your Language right" + You may encounter a warning message similar to the following one during connecting: + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LC_CTYPE = "UTF-8", + LANG = (unset) + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + or any other error message complaining about the locale. + This means that the correct "locale" has not yet been properly specified on your local machine. Try: + LANG= + LC_COLLATE="C" + LC_CTYPE="UTF-8" + LC_MESSAGES="C" + LC_MONETARY="C" + LC_NUMERIC="C" + LC_TIME="C" + LC_ALL= diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_10_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_10_metadata.json new file mode 100644 index 00000000000..96a1f9cee80 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_10_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "First-Time-connection-to-the-HPC-infrastructure", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 2, + "directory": "connecting", + "parent_title": "", + "previous_title": "connecting_paragraph_9", + "next_title": "connecting_paragraph_11", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/connecting/#first-time-connection-to-the-hpc-infrastructure" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_15.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_15.txt new file mode 100644 index 00000000000..df00d4ed2a4 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_15.txt @@ -0,0 +1,7 @@ +Fast file transfer for large datasets +See the section on rsync in chapter 5 of the Linux intro manual. +Changing login nodes +It can be useful to have control over which login node you are on. However, when you connect to the HPC (High-Performance Computing) system, you are directed to a random login node, which might not be the one where you already have an active session. To address this, there is a way to manually switch your active login node. +For instance, if you want to switch to the login node named gligar07.gastly.os, you can use the following command while you are connected to the gligar08.gastly.os login node on the HPC: +ssh gligar07.gastly.os +This is also possible the other way around. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_15_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_15_metadata.json new file mode 100644 index 00000000000..74ea0125d71 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_15_metadata.json @@ -0,0 +1,15 @@ +{ + "main_title": "connecting", + "subtitle": "Changing-login-nodes", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 2, + "directory": "connecting", + "links": { + "0": "https://docs.hpc.ugent.be/linux-tutorial/uploading_files/#copying-faster-with-rsync" + }, + "parent_title": "", + "previous_title": "connecting_paragraph_14", + "next_title": "connecting_paragraph_16", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/connecting/#changing-login-nodes" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_16.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_16.txt new file mode 100644 index 00000000000..dd4f3269fb5 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_16.txt @@ -0,0 +1,11 @@ +If you want to find out which login host you are connected to, you can use the hostname command. +$ hostname +gligar07.gastly.os +$ ssh gligar08.gastly.os +$ hostname +gligar08.gastly.os +Rather than always starting a new session on the HPC, you can also use a terminal multiplexer like screen or tmux. +These can make sessions that 'survives' across disconnects. +You can find more information on how to use these tools here (or on other online sources): +- screen +- tmux \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_16_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_16_metadata.json new file mode 100644 index 00000000000..623be877f5b --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_16_metadata.json @@ -0,0 +1,16 @@ +{ + "main_title": "connecting", + "subtitle": "Changing-login-nodes", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 2, + "directory": "connecting", + "links": { + "0": "https://www.howtogeek.com/662422/how-to-use-linuxs-screen-command/", + "1": "https://www.howtogeek.com/671422/how-to-use-tmux-on-linux-and-why-its-better-than-screen/" + }, + "parent_title": "", + "previous_title": "connecting_paragraph_15", + "next_title": null, + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/connecting/#changing-login-nodes" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_1_metadata.json new file mode 100644 index 00000000000..783e60c1ab5 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_1_metadata.json @@ -0,0 +1,15 @@ +{ + "main_title": "connecting", + "subtitle": "Connecting-to-the-HPC-infrastructure", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 1, + "directory": "connecting", + "links": { + "0": "https://docs.hpc.ugent.be/web_portal" + }, + "parent_title": "", + "previous_title": null, + "next_title": "connecting_paragraph_2", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/connecting/#connecting-to-the-hpc-infrastructure" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_2.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_2.txt new file mode 100644 index 00000000000..49c4572f3b2 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_2.txt @@ -0,0 +1,18 @@ +Connection restrictions +Since March 20th 2020, restrictions are in place that limit from where +you can connect to the VSC HPC infrastructure, in response to security +incidents involving several European HPC centres. +VSC login nodes are only directly accessible from within university +networks, and from (most) Belgian commercial internet providers. +All other IP domains are blocked by default. If you are connecting from +an IP address that is not allowed direct access, you have the following +options to get access to VSC login nodes: +- Use an VPN connection to connect to UGent the network (recommended). See for more information. +- Whitelist your IP address automatically by accessing + and log in with your UGent account. + - While this web connection is active new SSH sessions can be + started. + - Active SSH sessions will remain active even when this web page + is closed. +- Contact your HPC support team (via hpc@ugent.be) and ask them to whitelist your + IP range (e.g., for industry access, automated processes). diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_2_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_2_metadata.json new file mode 100644 index 00000000000..10f3e042d9a --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_2_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "Connection-restrictions", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 2, + "directory": "connecting", + "parent_title": "", + "previous_title": "connecting_paragraph_1", + "next_title": "connecting_paragraph_3", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/connecting/#connection-restrictions" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_3.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_3.txt new file mode 100644 index 00000000000..db490973b7f --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_3.txt @@ -0,0 +1,9 @@ +Trying to establish an SSH connection from an IP address that does not +adhere to these restrictions will result in an immediate failure to +connect, with an error message like: +ssh_exchange_identification: read: Connection reset by peer +First Time connection to the HPC infrastructure +The remaining content in this chapter is primarily focused for people utilizing a terminal with SSH. +If you are instead using the web portal, the corresponding chapter might be more helpful: Using the HPC-UGent web portal. +If you have any issues connecting to the HPC after you've followed these +steps, see Issues connecting to login node to troubleshoot. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_3_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_3_metadata.json new file mode 100644 index 00000000000..8d6b1696e08 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_3_metadata.json @@ -0,0 +1,16 @@ +{ + "main_title": "connecting", + "subtitle": "First-Time-connection-to-the-HPC-infrastructure", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 2, + "directory": "connecting", + "links": { + "0": "https://docs.hpc.ugent.be/web_portal", + "1": "https://docs.hpc.ugent.be/troubleshooting/#issues-connecting-to-login-node" + }, + "parent_title": "", + "previous_title": "connecting_paragraph_2", + "next_title": "connecting_paragraph_4", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/connecting/#first-time-connection-to-the-hpc-infrastructure" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_6.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_6.txt new file mode 100644 index 00000000000..862e6952252 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_6.txt @@ -0,0 +1,14 @@ +Congratulations, you're on the HPC infrastructure now! +To find out where you have landed you can print the current working directory: +$ pwd +/user/home/gent/vsc400/vsc40000 +Your new private home directory is "/user/home/gent/vsc400/vsc40000". Here you can create your own +subdirectory structure, copy and prepare your applications, compile and +test them and submit your jobs on the HPC. +$ cd /apps/gent/tutorials +$ ls +Intro-HPC/ +This directory currently contains all training material for the Introduction to the HPC. More +relevant training material to work with the HPC can always be added later in +this directory. +You can now explore the content of this directory with the "ls --l" (lists long) and the "cd" (change directory) commands: diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_6_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_6_metadata.json new file mode 100644 index 00000000000..66b2a89fbb1 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_6_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "First-Time-connection-to-the-HPC-infrastructure", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 2, + "directory": "connecting", + "parent_title": "", + "previous_title": "connecting_paragraph_5", + "next_title": "connecting_paragraph_7", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/connecting/#first-time-connection-to-the-hpc-infrastructure" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_7.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_7.txt new file mode 100644 index 00000000000..aa590b9b269 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_7.txt @@ -0,0 +1,21 @@ +As we are interested in the use of the HPC, move further to Intro-HPC and explore the +contents up to 2 levels deep: +$ cd Intro-HPC +$ tree -L 2 +. +'-- examples + |-- Compiling-and-testing-your-software-on-the-HPC + |-- Fine-tuning-Job-Specifications + |-- Multi-core-jobs-Parallel-Computing + |-- Multi-job-submission + |-- Program-examples + |-- Running-batch-jobs + |-- Running-jobs-with-input + |-- Running-jobs-with-input-output-data + |-- example.pbs + '-- example.sh +9 directories, 5 files +This directory contains: +1. This HPC Tutorial (in either a Mac, Linux or Windows version). +2. An examples subdirectory, containing all the examples that you need in this + Tutorial, as well as examples that might be useful for your specific applications. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_7_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_7_metadata.json new file mode 100644 index 00000000000..6e3f90fbe8a --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_7_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "First-Time-connection-to-the-HPC-infrastructure", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 2, + "directory": "connecting", + "parent_title": "", + "previous_title": "connecting_paragraph_6", + "next_title": "connecting_paragraph_8", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/connecting/#first-time-connection-to-the-hpc-infrastructure" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_8.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_8.txt new file mode 100644 index 00000000000..634df6034b1 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_8.txt @@ -0,0 +1,12 @@ +cd examples + tip + Typing cd ex followed by tab (the Tab-key) will generate the cd examples + command. Command-line completion (also tab completion) is a common feature of the bash command + line interpreter, in which the program automatically fills in partially + typed commands. + tip + For more exhaustive tutorials about Linux usage, see Appendix Useful Linux Commands +The first action is to copy the contents of the HPC examples directory to +your home directory, so that you have your own personal copy and that +you can start using the examples. The "-r" option of the copy command +will also copy the contents of the sub-directories "recursively". diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_8_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_8_metadata.json new file mode 100644 index 00000000000..38f265cfdcd --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_8_metadata.json @@ -0,0 +1,15 @@ +{ + "main_title": "connecting", + "subtitle": "First-Time-connection-to-the-HPC-infrastructure", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 2, + "directory": "connecting", + "links": { + "0": "https://docs.hpc.ugent.be/useful_linux_commands" + }, + "parent_title": "", + "previous_title": "connecting_paragraph_7", + "next_title": "connecting_paragraph_9", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/connecting/#first-time-connection-to-the-hpc-infrastructure" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_9.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_9.txt new file mode 100644 index 00000000000..ad2fee7457f --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_9.txt @@ -0,0 +1,19 @@ +cp -r /apps/gent/tutorials/Intro-HPC/examples ~/ +Go to your home directory, check your own private examples directory, ... and start working. +cd +ls -l +Upon connecting you will see a login message containing your last login time stamp and a basic overview of the current cluster utilisation. +Last login: Thu Mar 18 13:15:09 2021 from gligarha02.gastly.os + STEVIN HPC-UGent infrastructure status on Mon, 19 Feb 2024 10:00:01 + cluster - full - free - part - total - running - queued + nodes nodes free nodes jobs jobs + ------------------------------------------------------------------------- + skitty 39 0 26 68 1839 5588 + joltik 6 0 1 10 29 18 + doduo 22 0 75 128 1397 11933 + accelgor 4 3 2 9 18 1 + donphan 0 0 16 16 16 13 + gallade 2 0 5 16 19 136 +For a full view of the current loads and queues see: +https://hpc.ugent.be/clusterstate/ +Updates on current system status and planned maintenance can be found on https://www.ugent.be/hpc/en/infrastructure/status diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_9_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_9_metadata.json new file mode 100644 index 00000000000..bd1d462e614 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/generic/connecting/connecting_paragraph_9_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "First-Time-connection-to-the-HPC-infrastructure", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 2, + "directory": "connecting", + "parent_title": "", + "previous_title": "connecting_paragraph_8", + "next_title": "connecting_paragraph_10", + "OS": "generic", + "reference_link": "https://docs.hpc.ugent.be/connecting/#first-time-connection-to-the-hpc-infrastructure" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_11.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_11.1.txt new file mode 100644 index 00000000000..dfc59211792 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_11.1.txt @@ -0,0 +1,17 @@ +Adding multiple SSH public keys (optional) +In case you are connecting from different computers to the login nodes, +it is advised to use separate SSH public keys to do so. You should +follow these steps. +1. Create a new public/private SSH key pair from the new computer. + Repeat the process described in + section Generate a public/private key pair with OpenSSH. +2. Go to +3. Upload the new SSH public key using the Add public key section. Make sure that your + public key is actually saved, because a public key will be refused + if it is too short, wrong type, or in a wrong format. +4. (optional) If you lost your key, you can delete the old key on the + same page. You should keep at least one valid public SSH key in your + account. +5. Take into account that it will take some time before the new SSH + public key is active in your account on the system; waiting for + 15-30 minutes should be sufficient. \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_11.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_11.1_metadata.json new file mode 100644 index 00000000000..ffdeaf550e0 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_11.1_metadata.json @@ -0,0 +1,15 @@ +{ + "main_title": "account", + "subtitle": "Adding-multiple-SSH-public-keys-(optional)", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Applying-for-the-account", + "links": { + "0": "https://docs.hpc.ugent.be/account/#generate-a-publicprivate-key-pair-with-openssh" + }, + "previous_title": "account_paragraph_10", + "next_title": "account_paragraph_12", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/account/#adding-multiple-ssh-public-keys-optional" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.1.txt new file mode 100644 index 00000000000..caaaea5ee91 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.1.txt @@ -0,0 +1,14 @@ +How do SSH keys work +Launch a terminal from your desktop's application menu and you will see +the bash shell. There are other shells, but most Linux distributions use +bash by default. +Test OpenSSH +Secure Shell (ssh) is a cryptographic network protocol for secure data +communication, remote command-line login, remote command execution, and +other secure network services between two networked computers. In short, +ssh provides a secure connection between 2 computers via insecure +channels (Network, Internet, telephone lines, ...). +"Secure" means that: +1. the User is authenticated to the System; and +2. the System is authenticated to the User; and +3. all data is encrypted during transfer. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.1_metadata.json new file mode 100644 index 00000000000..7654a65253a --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Test-OpenSSH", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_paragraph_4", + "next_title": "account_linux_paragraph_5.2", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/account/#test-openssh" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.2.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.2.txt new file mode 100644 index 00000000000..318f913fba3 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.2.txt @@ -0,0 +1,14 @@ +OpenSSH is a FREE implementation of the SSH connectivity protocol. comes +with its own implementation of OpenSSH, so you don't need to install any +third-party software to use it. Just open a terminal window and jump in! +On all popular Linux distributions, the OpenSSH software is readily +available, and most often installed by default. You can check whether +the OpenSSH software is installed by opening a terminal and typing: +$ ssh -V +OpenSSH_7.4p1, OpenSSL 1.0.2k-fips 26 Jan 2017 +To access the clusters and transfer your files, you will use the +following commands: +1. ssh-keygen: to generate the SSH key pair (public + private key); +2. ssh: to open a shell on a remote machine; +3. sftp: a secure equivalent of ftp; +4. scp: a secure equivalent of the remote copy command rcp. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.2_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.2_metadata.json new file mode 100644 index 00000000000..32f1120307f --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.2_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Test-OpenSSH", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_linux_paragraph_5.1", + "next_title": "account_linux_paragraph_5.3", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/account/#test-openssh" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.3.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.3.txt new file mode 100644 index 00000000000..5df90a3dd7c --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.3.txt @@ -0,0 +1,16 @@ +Generate a public/private key pair with OpenSSH +A key pair might already be present in the default location inside your +home directory. Therefore, we first check if a key is available with the +"list short" ("ls") command: +ls ~/.ssh +If a key-pair is already available, you would normally get: +authorized_keys id_rsa id_rsa.pub known_hosts +Otherwise, the command will show: +ls: .ssh: No such file or directory +You can recognise a public/private key pair when a pair of files has the +same name except for the extension ".pub" added to one of them. In this +particular case, the private key is "id_rsa" and public key is +"id_rsa.pub". You may have multiple keys (not necessarily in the +directory "~/.ssh") if you or your operating system requires this. Be +aware that your existing key pair might be too short, or not the right +type. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.3_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.3_metadata.json new file mode 100644 index 00000000000..722ba1a2ad4 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.3_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Generate-a-publicprivate-key-pair-with-OpenSSH", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_linux_paragraph_5.2", + "next_title": "account_linux_paragraph_5.4", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/account/#generate-a-publicprivate-key-pair-with-openssh" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.4.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.4.txt new file mode 100644 index 00000000000..d29d61d27d9 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.4.txt @@ -0,0 +1,13 @@ +You will need to generate a new key pair, when: +1. you don't have a key pair yet +2. you forgot the passphrase protecting your private key +3. your private key was compromised +4. your key pair is too short or not the right type +For extra security, the private key itself can be encrypted using a +"passphrase", to prevent anyone from using your private key even when +they manage to copy it. You have to "unlock" the private key by typing +the passphrase. Be sure to never give away your private key, it is +private and should stay private. You should not even copy it to one of +your other machines, instead, you should create a new public/private key +pair for each machine. +ssh-keygen -t rsa -b 4096 diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.4_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.4_metadata.json new file mode 100644 index 00000000000..4f65f6ebf36 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.4_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Generate-a-publicprivate-key-pair-with-OpenSSH", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_linux_paragraph_5.3", + "next_title": "account_linux_paragraph_5.5", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/account/#generate-a-publicprivate-key-pair-with-openssh" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.5.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.5.txt new file mode 100644 index 00000000000..78c142e82e0 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.5.txt @@ -0,0 +1,6 @@ +This will ask you for a file name to store the private and public key, +and a passphrase to protect your private key. It needs to be emphasised +that you really should choose the passphrase wisely! The system will ask +you for it every time you want to use the private key that is every time +you want to access the cluster or transfer your files. +Without your key pair, you won't be able to apply for a personal VSC account. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.5_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.5_metadata.json new file mode 100644 index 00000000000..468fb5d0938 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_5.5_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Generate-a-publicprivate-key-pair-with-OpenSSH", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_linux_paragraph_5.4", + "next_title": "account_paragraph_6", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/account/#generate-a-publicprivate-key-pair-with-openssh" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_6.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_6.1.txt new file mode 100644 index 00000000000..c3b395b5296 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_6.1.txt @@ -0,0 +1 @@ +Using an SSH agent (optional) \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_6.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_6.1_metadata.json new file mode 100644 index 00000000000..fb82c40a7d7 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_6.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Using-an-SSH-agent-(optional", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_paragraph_5", + "next_title": "account_paragraph_7", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/account/#using-an-ssh-agent-optional" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_7.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_7.1.txt new file mode 100644 index 00000000000..8e8429c1642 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_7.1.txt @@ -0,0 +1,14 @@ +Using an SSH agent (optional) +Most recent Unix derivatives include by default an SSH agent ("gnome-keyring-daemon" in most cases) +to keep and manage the user SSH keys. If you use one of these derivatives you must include the new keys into +the SSH manager keyring to be able to connect to the HPC cluster. If +not, SSH client will display an error message (see Connecting) similar to this: +Agent admitted failure to sign using the key. +Permission denied (publickey,gssapi-keyex,gssapi-with-mic). +This could be fixed using the ssh-add command. You can include the new +private keys' identities in your keyring with: +ssh-add + tip + Without extra options ssh-add adds any key located at $HOME/.ssh + directory, but you can specify the private key location path as + argument, as example: ssh-add /path/to/my/id_rsa. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_7.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_7.1_metadata.json new file mode 100644 index 00000000000..2b3633d71e7 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_7.1_metadata.json @@ -0,0 +1,15 @@ +{ + "main_title": "account", + "subtitle": "Using-an-SSH-agent-(optional)", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "links": { + "0": "https://docs.hpc.ugent.be/connecting" + }, + "previous_title": "account_paragraph_6", + "next_title": "account_linux_paragraph_7.2", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/account/#using-an-ssh-agent-optional" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_7.2.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_7.2.txt new file mode 100644 index 00000000000..c227dbbb6e2 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_7.2.txt @@ -0,0 +1,8 @@ +Check that your key is available from the keyring with: +ssh-add -l +After these changes the key agent will keep your SSH key to connect to +the clusters as usual. + tip + You should execute ssh-add command again if you generate a new SSH + key. +Visit for more information. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_7.2_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_7.2_metadata.json new file mode 100644 index 00000000000..de9700c7a5b --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_7.2_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Using-an-SSH-agent-(optional)", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_linux_paragraph_7.1", + "next_title": "account_paragraph_8", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/account/#using-an-ssh-agent-optional" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_9.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_9.1.txt new file mode 100644 index 00000000000..815c414e059 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_9.1.txt @@ -0,0 +1,7 @@ +Applying for the account +After you log in using your UGent login and password, you will be asked to +upload the file that contains your public key, i.e., the file +"id_rsa.pub" which you have generated earlier. Make sure that your +public key is actually accepted for upload, because if it is in a wrong +format, wrong type or too short, then it will be refused. +This file has been stored in the directory "~/.ssh/". diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_9.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_9.1_metadata.json new file mode 100644 index 00000000000..31c14d853b3 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/account/account_linux_paragraph_9.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Applying-for-the-account", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 2, + "directory": "account", + "parent_title": "account", + "previous_title": "account_paragraph_8", + "next_title": "account_paragraph_10", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/account/#applying-for-the-account" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_11.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_11.1.txt new file mode 100644 index 00000000000..1d912924535 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_11.1.txt @@ -0,0 +1,37 @@ +First Time connection to the HPC infrastructure + A locale is a set of parameters that defines the user's language, country and + any special variant preferences that the user wants to see in their user + interface. Usually a locale identifier consists of at least a language + identifier and a region identifier. + Note + If you try to set a non-supported locale, then it will be automatically + set to the default. Currently the default is en_US.UFT-8 or en_US, + depending on whether your originally (non-supported) locale was UTF-8 or not. + Open the .bashrc on your local machine with your favourite editor and + add the following lines: + + $ nano ~/.bashrc + ... + export LANGUAGE="en_US.UTF-8" + export LC_ALL="en_US.UTF-8" + export LC_CTYPE="en_US.UTF-8" + export LANG="en_US.UTF-8" + ... + + tip "tip: vi" + To start entering text in vi: move to the place you want to start + entering text with the arrow keys and type "i" to switch to insert mode. You can easily exit vi by entering: ""ESC" :wq" + To exit vi without saving your changes, enter ""ESC":q!" + + + or alternatively (if you are not comfortable with the Linux editors), + again on your local machine: + + echo "export LANGUAGE=\"en_US.UTF-8\"" >> ~/.profile + echo "export LC_ALL=\"en_US.UTF-8\"" >> ~/.profile + echo "export LC_CTYPE=\"en_US.UTF-8\"" >> ~/.profile + echo "export LANG=\"en_US.UTF-8\"" >> ~/.profile + + You can now log out, open a new terminal/shell on your local machine and + reconnect to the login node, and you should not get these warnings anymore. + \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_11.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_11.1_metadata.json new file mode 100644 index 00000000000..ef14b084e5f --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_11.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "First-Time-connection-to-the-HPC-infrastructure", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 2, + "directory": "connecting", + "parent_title": "Connecting-to-the-HPC-infrastructure", + "previous_title": "connecting_paragraph_10", + "next_title": "connecting_paragraph_12", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/connecting/#first-time-connection-to-the-hpc-infrastructure" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_12.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_12.1.txt new file mode 100644 index 00000000000..d872c89a0f8 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_12.1.txt @@ -0,0 +1,6 @@ +Transfer Files to/from the HPC +Before you can do some work, you'll have to transfer the files you need from your desktop or department to the cluster. At the end of a job, you might want to transfer some files back. +The preferred way to transfer files is by using an scp or sftp via the +secure OpenSSH protocol. ships with an implementation of OpenSSH, so you +don't need to install any third-party software to use it. Just open a +terminal window and jump in! diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_12.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_12.1_metadata.json new file mode 100644 index 00000000000..081156a5d16 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_12.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "Transfer-Files-tofrom-the-HPC", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 2, + "directory": "connecting", + "parent_title": "Connecting-to-the-HPC-infrastructure", + "previous_title": "connecting_paragraph_11", + "next_title": "connecting_paragraph_13", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/connecting/#transfer-files-tofrom-the-hpc" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.1.txt new file mode 100644 index 00000000000..8d0031fcca9 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.1.txt @@ -0,0 +1,12 @@ +Transfer Files tofrom the HPC +Using scp +Secure copy or SCP is a tool (command) for securely transferring files between a local +host (= your computer) and a remote host (the HPC). It is based on the +Secure Shell (SSH) protocol. The scp command is the equivalent of the cp (i.e., +copy) command, but can copy files to or from remote machines. +It's easier to copy files directly to $VSC_DATA and $VSC_SCRATCH if +you have symlinks to them in your home directory. See +the chapter titled "Uploading/downloading/editing files", section "Symlinks for data/scratch" in the intro to Linux + for how to do this. +Open an additional terminal window and check that you're working on your +local machine. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.1_metadata.json new file mode 100644 index 00000000000..6b70790e1e3 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.1_metadata.json @@ -0,0 +1,15 @@ +{ + "main_title": "connecting", + "subtitle": "Using-scp", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "Transfer-Files-tofrom-the-HPC", + "links": { + "0": "https://docs.hpc.ugent.be/localhost:8000/Gent//intro-Linux/uploading_files/#symlinks-for-datascratch" + }, + "previous_title": "connecting_paragraph_12", + "next_title": "connecting_linux_paragraph_13.2", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/connecting/#using-scp" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.2.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.2.txt new file mode 100644 index 00000000000..f1da0677a67 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.2.txt @@ -0,0 +1,17 @@ +$ hostname + +If you're still using the terminal that is connected to the HPC, close the +connection by typing "exit" in the terminal window. +For example, we will copy the (local) file "localfile.txt" to your +home directory on the HPC cluster. We first generate a small dummy +"localfile.txt", which contains the word "Hello". Use your own VSC +account, which is something like "vsc40000". Don't forget the colon (:) at the +end: if you forget it, it will just create a file named vsc40000@login.hpc.ugent.be on your +local filesystem. You can even specify where to save the file on the +remote filesystem by putting a path after the colon. +$ echo "Hello" > localfile.txt +$ ls -l +... +-rw-r--r-- 1 user staff 6 Sep 18 09:37 localfile.txt +$ scp localfile.txt vsc40000@login.hpc.ugent.be: +localfile.txt 100% 6 0.0KB/s 00:00 diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.2_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.2_metadata.json new file mode 100644 index 00000000000..43affa4e36c --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.2_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "Using-scp", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "Transfer-Files-tofrom-the-HPC", + "previous_title": "connecting_linux_paragraph_13.1", + "next_title": "connecting_linux_paragraph_13.3", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/connecting/#using-scp" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.3.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.3.txt new file mode 100644 index 00000000000..9585900e356 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.3.txt @@ -0,0 +1,22 @@ +Connect to the HPC via another terminal, print the working directory (to +make sure you're in the home directory) and check whether the file has +arrived: +$ pwd +/user/home/gent/vsc400/vsc40000 +$ ls -l +total 1536 +drwxrwxr-x 2 +drwxrwxr-x 2 +drwxrwxr-x 10 +-rw-r--r-- 1 +$ cat localfile.txt +Hello +The scp command can also be used to copy files from the cluster to your +local machine. Let us copy the remote file "intro-HPC--Gent.pdf" from your "docs" +subdirectory on the cluster to your local computer. +First, we will confirm that the file is indeed in the "docs" +subdirectory. In the terminal on the login node, enter: +$ cd ~/docs +$ ls -l +total 1536 +-rw-r--r-- 1 vsc40000 Sep 11 09:53 intro-HPC--Gent.pdf diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.3_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.3_metadata.json new file mode 100644 index 00000000000..ccc74bb5b94 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.3_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "Using-scp", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "Transfer-Files-tofrom-the-HPC", + "previous_title": "connecting_linux_paragraph_13.2", + "next_title": "connecting_linux_paragraph_13.4", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/connecting/#using-scp" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.4.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.4.txt new file mode 100644 index 00000000000..d09b69552ef --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.4.txt @@ -0,0 +1,14 @@ +Now we will copy the file to the local machine. On the terminal on your +own local computer, enter: +$ scp vsc40000@login.hpc.ugent.be:./docs/intro-HPC--Gent.pdf . +intro-HPC--Gent.pdf 100% 725KB 724.6KB/s 00:01 +$ ls -l +total 899 +-rw-r--r-- 1 user staff 741995 Sep 18 09:53 +-rw-r--r-- 1 user staff 6 Sep 18 09:37 localfile.txt +The file has been copied from the HPC to your local computer. +It's also possible to copy entire directories (and their contents) with +the -r flag. For example, if we want to copy the local directory +dataset to $VSC_SCRATCH, we can use the following command (assuming +you've created the scratch symlink): +scp -r dataset vsc40000@login.hpc.ugent.be:scratch diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.4_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.4_metadata.json new file mode 100644 index 00000000000..9ffcc4121f4 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.4_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "Using-scp", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "Transfer-Files-tofrom-the-HPC", + "previous_title": "connecting_linux_paragraph_13.3", + "next_title": "connecting_linux_paragraph_13.5", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/connecting/#using-scp" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.5.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.5.txt new file mode 100644 index 00000000000..532d57bb4a5 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.5.txt @@ -0,0 +1,14 @@ +If you don't use the -r option to copy a directory, you will run into +the following error: +$ scp dataset vsc40000@login.hpc.ugent.be:scratch +dataset: not a regular file +Using sftp +The SSH File Transfer Protocol (also Secure File Transfer Protocol, or SFTP) is a network protocol that provides file access, file +transfer and file management functionalities over any reliable data +stream. It was designed as an extension of the Secure Shell protocol +(SSH) version 2.0. This protocol assumes that it is run over a secure +channel, such as SSH, that the server has already authenticated the +client, and that the identity of the client user is available to the +protocol. +The sftp is an equivalent of the ftp command, with the difference that +it uses the secure ssh protocol to connect to the clusters. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.5_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.5_metadata.json new file mode 100644 index 00000000000..8e3b4056b6b --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.5_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "Using-sftp", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "Transfer-Files-tofrom-the-HPC", + "previous_title": "connecting_linux_paragraph_13.4", + "next_title": "connecting_linux_paragraph_13.6", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/connecting/#using-sftp" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.6.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.6.txt new file mode 100644 index 00000000000..1ef13b80c6f --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.6.txt @@ -0,0 +1,18 @@ +One easy way of starting a sftp session is +sftp vsc40000@login.hpc.ugent.be +Typical and popular commands inside an sftp session are: +| | | +|:--------------------------|:-------------------------------------------------------------------------------------| +| cd ~/exmples/fibo | Move to the examples/fibo subdirectory on the (i.e., the HPC remote machine) | +| ls | Get a list of the files in the current directory on the HPC. | +| get fibo.py | Copy the file "fibo.py" from the HPC | +| get tutorial/HPC.pdf | Copy the file "HPC.pdf" from the HPC, which is in the "tutorial" subdirectory. | +| lcd test | Move to the "test" subdirectory on your local machine. | +| lcd .. | Move up one level in the local directory. | +| lls | Get local directory listing. | +| put test.py | Copy the local file test.py to the HPC. | +| put test1.py test2.py | Copy the local file test1.py to the and rename it to test2.py. | +| bye | Quit the sftp session | +| **mget *.cc** | Copy all the remote files with extension ".cc" to the local directory. | +| **mput *.h** | Copy all the local files with extension ".h" to the HPC. | +| | | diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.6_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.6_metadata.json new file mode 100644 index 00000000000..c7fe6bf6a44 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_13.6_metadata.json @@ -0,0 +1,16 @@ +{ + "main_title": "connecting", + "subtitle": "Using-sftp", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "Transfer-Files-tofrom-the-HPC", + "links": { + "0": "https://docs.hpc.ugent.be/", + "1": "https://docs.hpc.ugent.be/" + }, + "previous_title": "connecting_linux_paragraph_13.5", + "next_title": "connecting_linux_paragraph_13.7", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/connecting/#using-sftp" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_14.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_14.1.txt new file mode 100644 index 00000000000..a0496edfb14 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_14.1.txt @@ -0,0 +1,10 @@ +Transfer Files tofrom the HPC +Using a GUI +If you prefer a GUI to transfer files back and forth to the HPC, you can +use your file browser. Open your file browser and press +++"Ctrl"+"l"++ +This should open up a address bar where you can enter a URL. +Alternatively, look for the "connect to server" option in your file +browsers menu. +Enter: sftp://vsc40000@login.hpc.ugent.be/ and press enter. +You should now be able to browse files on the HPC in your file browser. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_14.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_14.1_metadata.json new file mode 100644 index 00000000000..e3c48fe4829 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_14.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "Using-a-GUI", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "Transfer-Files-tofrom-the-HPC", + "previous_title": "connecting_paragraph_13", + "next_title": "connecting_paragraph_15", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/connecting/#using-a-gui" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_5.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_5.1.txt new file mode 100644 index 00000000000..27ae3fb7bd4 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_5.1.txt @@ -0,0 +1,12 @@ +First Time connection to the HPC infrastructure +Connect +Open up a terminal and enter the following command to connect to the HPC. +ssh vsc40000@login.hpc.ugent.be +Here, user vsc40000 wants to make a connection to the "hpcugent" cluster at UGent via the login +node "login.hpc.ugent.be", so replace vsc40000 with your own VSC id in the above command. +The first time you make a connection to the login node, you will be +asked to verify the authenticity of the login node. Please check +Warning message when first connecting to new host on how to do this. +A possible error message you can get if you previously saved your +private key somewhere else than the default location +($HOME/.ssh/id_rsa): diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_5.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_5.1_metadata.json new file mode 100644 index 00000000000..66c5dc4aeff --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_5.1_metadata.json @@ -0,0 +1,15 @@ +{ + "main_title": "connecting", + "subtitle": "Connect", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "First-Time-connection-to-the-HPC-infrastructure", + "links": { + "0": "https://docs.hpc.ugent.be/troubleshooting/#warning-message-when-first-connecting-to-new-host" + }, + "previous_title": "connecting_paragraph_4", + "next_title": "connecting_linux_paragraph_5.2", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/connecting/#connect" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_5.2.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_5.2.txt new file mode 100644 index 00000000000..be01e09bba0 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_5.2.txt @@ -0,0 +1,4 @@ +Permission denied (publickey,gssapi-keyex,gssapi-with-mic). +In this case, use the -i option for the ssh command to specify the +location of your private key. For example: +ssh -i /home/example/my_keys diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_5.2_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_5.2_metadata.json new file mode 100644 index 00000000000..21b63518804 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/linux/connecting/connecting_linux_paragraph_5.2_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "Connect", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "First-Time-connection-to-the-HPC-infrastructure", + "previous_title": "connecting_linux_paragraph_5.1", + "next_title": "connecting_paragraph_6", + "OS": "linux", + "reference_link": "https://docs.hpc.ugent.be/Linux/connecting/#connect" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_11.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_11.1.txt new file mode 100644 index 00000000000..dfc59211792 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_11.1.txt @@ -0,0 +1,17 @@ +Adding multiple SSH public keys (optional) +In case you are connecting from different computers to the login nodes, +it is advised to use separate SSH public keys to do so. You should +follow these steps. +1. Create a new public/private SSH key pair from the new computer. + Repeat the process described in + section Generate a public/private key pair with OpenSSH. +2. Go to +3. Upload the new SSH public key using the Add public key section. Make sure that your + public key is actually saved, because a public key will be refused + if it is too short, wrong type, or in a wrong format. +4. (optional) If you lost your key, you can delete the old key on the + same page. You should keep at least one valid public SSH key in your + account. +5. Take into account that it will take some time before the new SSH + public key is active in your account on the system; waiting for + 15-30 minutes should be sufficient. \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_11.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_11.1_metadata.json new file mode 100644 index 00000000000..d9d3c33f876 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_11.1_metadata.json @@ -0,0 +1,15 @@ +{ + "main_title": "account", + "subtitle": "Adding-multiple-SSH-public-keys-(optional)", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Applying-for-the-account", + "links": { + "0": "https://docs.hpc.ugent.be/account/#generate-a-publicprivate-key-pair-with-openssh" + }, + "previous_title": "account_paragraph_10", + "next_title": "account_paragraph_12", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/account/#adding-multiple-ssh-public-keys-optional" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.1.txt new file mode 100644 index 00000000000..d96c80b42a2 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.1.txt @@ -0,0 +1,15 @@ +How do SSH keys work +To open a Terminal window in macOS, open the Finder and choose +*\>\> Applications \> Utilities \> Terminal* +Before requesting an account, you need to generate a pair of ssh keys. +One popular way to do this on is using the OpenSSH client included with , which you can then also use to log on to the clusters. +Test OpenSSH +Secure Shell (ssh) is a cryptographic network protocol for secure data +communication, remote command-line login, remote command execution, and +other secure network services between two networked computers. In short, +ssh provides a secure connection between 2 computers via insecure +channels (Network, Internet, telephone lines, ...). +"Secure" means that: +1. the User is authenticated to the System; and +2. the System is authenticated to the User; and +3. all data is encrypted during transfer. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.1_metadata.json new file mode 100644 index 00000000000..028d9d25f7f --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Test-OpenSSH", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_paragraph_4", + "next_title": "account_macos_paragraph_5.2", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/account/#test-openssh" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.2.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.2.txt new file mode 100644 index 00000000000..318f913fba3 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.2.txt @@ -0,0 +1,14 @@ +OpenSSH is a FREE implementation of the SSH connectivity protocol. comes +with its own implementation of OpenSSH, so you don't need to install any +third-party software to use it. Just open a terminal window and jump in! +On all popular Linux distributions, the OpenSSH software is readily +available, and most often installed by default. You can check whether +the OpenSSH software is installed by opening a terminal and typing: +$ ssh -V +OpenSSH_7.4p1, OpenSSL 1.0.2k-fips 26 Jan 2017 +To access the clusters and transfer your files, you will use the +following commands: +1. ssh-keygen: to generate the SSH key pair (public + private key); +2. ssh: to open a shell on a remote machine; +3. sftp: a secure equivalent of ftp; +4. scp: a secure equivalent of the remote copy command rcp. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.2_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.2_metadata.json new file mode 100644 index 00000000000..dfec6f6fd5a --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.2_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Test-OpenSSH", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_macos_paragraph_5.1", + "next_title": "account_macos_paragraph_5.3", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/account/#test-openssh" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.3.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.3.txt new file mode 100644 index 00000000000..5df90a3dd7c --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.3.txt @@ -0,0 +1,16 @@ +Generate a public/private key pair with OpenSSH +A key pair might already be present in the default location inside your +home directory. Therefore, we first check if a key is available with the +"list short" ("ls") command: +ls ~/.ssh +If a key-pair is already available, you would normally get: +authorized_keys id_rsa id_rsa.pub known_hosts +Otherwise, the command will show: +ls: .ssh: No such file or directory +You can recognise a public/private key pair when a pair of files has the +same name except for the extension ".pub" added to one of them. In this +particular case, the private key is "id_rsa" and public key is +"id_rsa.pub". You may have multiple keys (not necessarily in the +directory "~/.ssh") if you or your operating system requires this. Be +aware that your existing key pair might be too short, or not the right +type. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.3_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.3_metadata.json new file mode 100644 index 00000000000..5a10e780b45 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.3_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Generate-a-publicprivate-key-pair-with-OpenSSH", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_macos_paragraph_5.2", + "next_title": "account_macos_paragraph_5.4", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/account/#generate-a-publicprivate-key-pair-with-openssh" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.4.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.4.txt new file mode 100644 index 00000000000..d29d61d27d9 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.4.txt @@ -0,0 +1,13 @@ +You will need to generate a new key pair, when: +1. you don't have a key pair yet +2. you forgot the passphrase protecting your private key +3. your private key was compromised +4. your key pair is too short or not the right type +For extra security, the private key itself can be encrypted using a +"passphrase", to prevent anyone from using your private key even when +they manage to copy it. You have to "unlock" the private key by typing +the passphrase. Be sure to never give away your private key, it is +private and should stay private. You should not even copy it to one of +your other machines, instead, you should create a new public/private key +pair for each machine. +ssh-keygen -t rsa -b 4096 diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.4_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.4_metadata.json new file mode 100644 index 00000000000..8da465c1f24 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.4_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Generate-a-publicprivate-key-pair-with-OpenSSH", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_macos_paragraph_5.3", + "next_title": "account_macos_paragraph_5.5", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/account/#generate-a-publicprivate-key-pair-with-openssh" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.5.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.5.txt new file mode 100644 index 00000000000..78c142e82e0 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.5.txt @@ -0,0 +1,6 @@ +This will ask you for a file name to store the private and public key, +and a passphrase to protect your private key. It needs to be emphasised +that you really should choose the passphrase wisely! The system will ask +you for it every time you want to use the private key that is every time +you want to access the cluster or transfer your files. +Without your key pair, you won't be able to apply for a personal VSC account. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.5_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.5_metadata.json new file mode 100644 index 00000000000..9d6f7b1a741 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_5.5_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Generate-a-publicprivate-key-pair-with-OpenSSH", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_macos_paragraph_5.4", + "next_title": "account_paragraph_6", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/account/#generate-a-publicprivate-key-pair-with-openssh" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_6.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_6.1.txt new file mode 100644 index 00000000000..c3b395b5296 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_6.1.txt @@ -0,0 +1 @@ +Using an SSH agent (optional) \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_6.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_6.1_metadata.json new file mode 100644 index 00000000000..17a34a2f80b --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_6.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Using-an-SSH-agent-(optional", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_paragraph_5", + "next_title": "account_paragraph_7", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/account/#using-an-ssh-agent-optional" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_7.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_7.1.txt new file mode 100644 index 00000000000..1069ebd9fbd --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_7.1.txt @@ -0,0 +1,14 @@ +Using an SSH agent (optional) +Most recent Unix derivatives include by default an SSH agent +to keep and manage the user SSH keys. If you use one of these derivatives you must include the new keys into +the SSH manager keyring to be able to connect to the HPC cluster. If +not, SSH client will display an error message (see Connecting) similar to this: +Agent admitted failure to sign using the key. +Permission denied (publickey,gssapi-keyex,gssapi-with-mic). +This could be fixed using the ssh-add command. You can include the new +private keys' identities in your keyring with: +ssh-add + tip + Without extra options ssh-add adds any key located at $HOME/.ssh + directory, but you can specify the private key location path as + argument, as example: ssh-add /path/to/my/id_rsa. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_7.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_7.1_metadata.json new file mode 100644 index 00000000000..18b3b3675de --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_7.1_metadata.json @@ -0,0 +1,15 @@ +{ + "main_title": "account", + "subtitle": "Using-an-SSH-agent-(optional)", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "links": { + "0": "https://docs.hpc.ugent.be/connecting" + }, + "previous_title": "account_paragraph_6", + "next_title": "account_macos_paragraph_7.2", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/account/#using-an-ssh-agent-optional" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_7.2.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_7.2.txt new file mode 100644 index 00000000000..c880ee4a228 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_7.2.txt @@ -0,0 +1,7 @@ +Check that your key is available from the keyring with: +ssh-add -l +After these changes the key agent will keep your SSH key to connect to +the clusters as usual. + tip + You should execute ssh-add command again if you generate a new SSH + key. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_7.2_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_7.2_metadata.json new file mode 100644 index 00000000000..072a43cb3e4 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_7.2_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Using-an-SSH-agent-(optional)", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_macos_paragraph_7.1", + "next_title": "account_paragraph_8", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/account/#using-an-ssh-agent-optional" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_9.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_9.1.txt new file mode 100644 index 00000000000..5a5a52da062 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_9.1.txt @@ -0,0 +1,12 @@ +Applying for the account +After you log in using your UGent login and password, you will be asked to +upload the file that contains your public key, i.e., the file +"id_rsa.pub" which you have generated earlier. Make sure that your +public key is actually accepted for upload, because if it is in a wrong +format, wrong type or too short, then it will be refused. +This file has been stored in the directory "~/.ssh/". + tip + As ".ssh" is an invisible directory, the Finder will not show it by + default. The easiest way to access the folder, is by pressing ++cmd+shift+g++ (or ++cmd+shift+"."++), + which will allow you to enter the name of a directory, which you would + like to open in Finder. Here, type "~/.ssh" and press enter. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_9.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_9.1_metadata.json new file mode 100644 index 00000000000..86c8c2048bf --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/account/account_macos_paragraph_9.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Applying-for-the-account", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 2, + "directory": "account", + "parent_title": "account", + "previous_title": "account_paragraph_8", + "next_title": "account_paragraph_10", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/account/#applying-for-the-account" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_11.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_11.1.txt new file mode 100644 index 00000000000..1d912924535 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_11.1.txt @@ -0,0 +1,37 @@ +First Time connection to the HPC infrastructure + A locale is a set of parameters that defines the user's language, country and + any special variant preferences that the user wants to see in their user + interface. Usually a locale identifier consists of at least a language + identifier and a region identifier. + Note + If you try to set a non-supported locale, then it will be automatically + set to the default. Currently the default is en_US.UFT-8 or en_US, + depending on whether your originally (non-supported) locale was UTF-8 or not. + Open the .bashrc on your local machine with your favourite editor and + add the following lines: + + $ nano ~/.bashrc + ... + export LANGUAGE="en_US.UTF-8" + export LC_ALL="en_US.UTF-8" + export LC_CTYPE="en_US.UTF-8" + export LANG="en_US.UTF-8" + ... + + tip "tip: vi" + To start entering text in vi: move to the place you want to start + entering text with the arrow keys and type "i" to switch to insert mode. You can easily exit vi by entering: ""ESC" :wq" + To exit vi without saving your changes, enter ""ESC":q!" + + + or alternatively (if you are not comfortable with the Linux editors), + again on your local machine: + + echo "export LANGUAGE=\"en_US.UTF-8\"" >> ~/.profile + echo "export LC_ALL=\"en_US.UTF-8\"" >> ~/.profile + echo "export LC_CTYPE=\"en_US.UTF-8\"" >> ~/.profile + echo "export LANG=\"en_US.UTF-8\"" >> ~/.profile + + You can now log out, open a new terminal/shell on your local machine and + reconnect to the login node, and you should not get these warnings anymore. + \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_11.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_11.1_metadata.json new file mode 100644 index 00000000000..323292b910e --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_11.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "First-Time-connection-to-the-HPC-infrastructure", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 2, + "directory": "connecting", + "parent_title": "Connecting-to-the-HPC-infrastructure", + "previous_title": "connecting_paragraph_10", + "next_title": "connecting_paragraph_12", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/connecting/#first-time-connection-to-the-hpc-infrastructure" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_12.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_12.1.txt new file mode 100644 index 00000000000..d872c89a0f8 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_12.1.txt @@ -0,0 +1,6 @@ +Transfer Files to/from the HPC +Before you can do some work, you'll have to transfer the files you need from your desktop or department to the cluster. At the end of a job, you might want to transfer some files back. +The preferred way to transfer files is by using an scp or sftp via the +secure OpenSSH protocol. ships with an implementation of OpenSSH, so you +don't need to install any third-party software to use it. Just open a +terminal window and jump in! diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_12.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_12.1_metadata.json new file mode 100644 index 00000000000..8a420f36c2b --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_12.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "Transfer-Files-tofrom-the-HPC", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 2, + "directory": "connecting", + "parent_title": "Connecting-to-the-HPC-infrastructure", + "previous_title": "connecting_paragraph_11", + "next_title": "connecting_paragraph_13", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/connecting/#transfer-files-tofrom-the-hpc" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.1.txt new file mode 100644 index 00000000000..8d0031fcca9 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.1.txt @@ -0,0 +1,12 @@ +Transfer Files tofrom the HPC +Using scp +Secure copy or SCP is a tool (command) for securely transferring files between a local +host (= your computer) and a remote host (the HPC). It is based on the +Secure Shell (SSH) protocol. The scp command is the equivalent of the cp (i.e., +copy) command, but can copy files to or from remote machines. +It's easier to copy files directly to $VSC_DATA and $VSC_SCRATCH if +you have symlinks to them in your home directory. See +the chapter titled "Uploading/downloading/editing files", section "Symlinks for data/scratch" in the intro to Linux + for how to do this. +Open an additional terminal window and check that you're working on your +local machine. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.1_metadata.json new file mode 100644 index 00000000000..79157005600 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.1_metadata.json @@ -0,0 +1,15 @@ +{ + "main_title": "connecting", + "subtitle": "Using-scp", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "Transfer-Files-tofrom-the-HPC", + "links": { + "0": "https://docs.hpc.ugent.be/localhost:8000/Gent//intro-Linux/uploading_files/#symlinks-for-datascratch" + }, + "previous_title": "connecting_paragraph_12", + "next_title": "connecting_macos_paragraph_13.2", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/connecting/#using-scp" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.2.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.2.txt new file mode 100644 index 00000000000..f1da0677a67 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.2.txt @@ -0,0 +1,17 @@ +$ hostname + +If you're still using the terminal that is connected to the HPC, close the +connection by typing "exit" in the terminal window. +For example, we will copy the (local) file "localfile.txt" to your +home directory on the HPC cluster. We first generate a small dummy +"localfile.txt", which contains the word "Hello". Use your own VSC +account, which is something like "vsc40000". Don't forget the colon (:) at the +end: if you forget it, it will just create a file named vsc40000@login.hpc.ugent.be on your +local filesystem. You can even specify where to save the file on the +remote filesystem by putting a path after the colon. +$ echo "Hello" > localfile.txt +$ ls -l +... +-rw-r--r-- 1 user staff 6 Sep 18 09:37 localfile.txt +$ scp localfile.txt vsc40000@login.hpc.ugent.be: +localfile.txt 100% 6 0.0KB/s 00:00 diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.2_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.2_metadata.json new file mode 100644 index 00000000000..dc57de365bf --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.2_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "Using-scp", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "Transfer-Files-tofrom-the-HPC", + "previous_title": "connecting_macos_paragraph_13.1", + "next_title": "connecting_macos_paragraph_13.3", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/connecting/#using-scp" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.3.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.3.txt new file mode 100644 index 00000000000..9585900e356 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.3.txt @@ -0,0 +1,22 @@ +Connect to the HPC via another terminal, print the working directory (to +make sure you're in the home directory) and check whether the file has +arrived: +$ pwd +/user/home/gent/vsc400/vsc40000 +$ ls -l +total 1536 +drwxrwxr-x 2 +drwxrwxr-x 2 +drwxrwxr-x 10 +-rw-r--r-- 1 +$ cat localfile.txt +Hello +The scp command can also be used to copy files from the cluster to your +local machine. Let us copy the remote file "intro-HPC--Gent.pdf" from your "docs" +subdirectory on the cluster to your local computer. +First, we will confirm that the file is indeed in the "docs" +subdirectory. In the terminal on the login node, enter: +$ cd ~/docs +$ ls -l +total 1536 +-rw-r--r-- 1 vsc40000 Sep 11 09:53 intro-HPC--Gent.pdf diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.3_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.3_metadata.json new file mode 100644 index 00000000000..5a4623c650d --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.3_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "Using-scp", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "Transfer-Files-tofrom-the-HPC", + "previous_title": "connecting_macos_paragraph_13.2", + "next_title": "connecting_macos_paragraph_13.4", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/connecting/#using-scp" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.4.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.4.txt new file mode 100644 index 00000000000..d09b69552ef --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.4.txt @@ -0,0 +1,14 @@ +Now we will copy the file to the local machine. On the terminal on your +own local computer, enter: +$ scp vsc40000@login.hpc.ugent.be:./docs/intro-HPC--Gent.pdf . +intro-HPC--Gent.pdf 100% 725KB 724.6KB/s 00:01 +$ ls -l +total 899 +-rw-r--r-- 1 user staff 741995 Sep 18 09:53 +-rw-r--r-- 1 user staff 6 Sep 18 09:37 localfile.txt +The file has been copied from the HPC to your local computer. +It's also possible to copy entire directories (and their contents) with +the -r flag. For example, if we want to copy the local directory +dataset to $VSC_SCRATCH, we can use the following command (assuming +you've created the scratch symlink): +scp -r dataset vsc40000@login.hpc.ugent.be:scratch diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.4_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.4_metadata.json new file mode 100644 index 00000000000..54b3fe19d58 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.4_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "Using-scp", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "Transfer-Files-tofrom-the-HPC", + "previous_title": "connecting_macos_paragraph_13.3", + "next_title": "connecting_macos_paragraph_13.5", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/connecting/#using-scp" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.5.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.5.txt new file mode 100644 index 00000000000..532d57bb4a5 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.5.txt @@ -0,0 +1,14 @@ +If you don't use the -r option to copy a directory, you will run into +the following error: +$ scp dataset vsc40000@login.hpc.ugent.be:scratch +dataset: not a regular file +Using sftp +The SSH File Transfer Protocol (also Secure File Transfer Protocol, or SFTP) is a network protocol that provides file access, file +transfer and file management functionalities over any reliable data +stream. It was designed as an extension of the Secure Shell protocol +(SSH) version 2.0. This protocol assumes that it is run over a secure +channel, such as SSH, that the server has already authenticated the +client, and that the identity of the client user is available to the +protocol. +The sftp is an equivalent of the ftp command, with the difference that +it uses the secure ssh protocol to connect to the clusters. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.5_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.5_metadata.json new file mode 100644 index 00000000000..0b9ba08e3b1 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.5_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "Using-sftp", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "Transfer-Files-tofrom-the-HPC", + "previous_title": "connecting_macos_paragraph_13.4", + "next_title": "connecting_macos_paragraph_13.6", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/connecting/#using-sftp" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.6.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.6.txt new file mode 100644 index 00000000000..1ef13b80c6f --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.6.txt @@ -0,0 +1,18 @@ +One easy way of starting a sftp session is +sftp vsc40000@login.hpc.ugent.be +Typical and popular commands inside an sftp session are: +| | | +|:--------------------------|:-------------------------------------------------------------------------------------| +| cd ~/exmples/fibo | Move to the examples/fibo subdirectory on the (i.e., the HPC remote machine) | +| ls | Get a list of the files in the current directory on the HPC. | +| get fibo.py | Copy the file "fibo.py" from the HPC | +| get tutorial/HPC.pdf | Copy the file "HPC.pdf" from the HPC, which is in the "tutorial" subdirectory. | +| lcd test | Move to the "test" subdirectory on your local machine. | +| lcd .. | Move up one level in the local directory. | +| lls | Get local directory listing. | +| put test.py | Copy the local file test.py to the HPC. | +| put test1.py test2.py | Copy the local file test1.py to the and rename it to test2.py. | +| bye | Quit the sftp session | +| **mget *.cc** | Copy all the remote files with extension ".cc" to the local directory. | +| **mput *.h** | Copy all the local files with extension ".h" to the HPC. | +| | | diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.6_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.6_metadata.json new file mode 100644 index 00000000000..9b08fbde549 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_13.6_metadata.json @@ -0,0 +1,16 @@ +{ + "main_title": "connecting", + "subtitle": "Using-sftp", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "Transfer-Files-tofrom-the-HPC", + "links": { + "0": "https://docs.hpc.ugent.be/", + "1": "https://docs.hpc.ugent.be/" + }, + "previous_title": "connecting_macos_paragraph_13.5", + "next_title": "connecting_macos_paragraph_13.7", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/connecting/#using-sftp" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_14.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_14.1.txt new file mode 100644 index 00000000000..20a4acb40a8 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_14.1.txt @@ -0,0 +1,15 @@ +Transfer Files tofrom the HPC +Using a GUI (Cyberduck) +Cyberduck is a graphical alternative to the scp command. It can be +installed from . +This is the one-time setup you will need to do before connecting: +1. After starting Cyberduck, the Bookmark tab will show up. To add a + new bookmark, click on the "+" sign on the bottom left of the + window. A new window will open. +2. In the drop-down menu on top, select "SFTP (SSH File Transfer Protocol)". +3. In the "Server" field, type in login.hpc.ugent.be. In the "Username" field, type in + your VSC account id (this looks like vsc40000). +4. Select the location of your SSH private key in the "SSH Private Key" field. +5. Finally, type in a name for the bookmark in the "Nickname" field and + close the window by pressing on the red circle in the top left + corner of the window. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_14.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_14.1_metadata.json new file mode 100644 index 00000000000..694b7682aa9 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_14.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "Using-a-GUI-(Cyberduck)", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "Transfer-Files-tofrom-the-HPC", + "previous_title": "connecting_paragraph_13", + "next_title": "connecting_macos_paragraph_14.2", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/connecting/#using-a-gui-cyberduck" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_14.2.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_14.2.txt new file mode 100644 index 00000000000..1d20edf411f --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_14.2.txt @@ -0,0 +1,3 @@ +To open the connection, click on the "Bookmarks" icon (which +resembles an open book) and double-click on the bookmark you just +created. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_14.2_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_14.2_metadata.json new file mode 100644 index 00000000000..e32b1ab4c58 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_14.2_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "Using-a-GUI-(Cyberduck)", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "Transfer-Files-tofrom-the-HPC", + "previous_title": "connecting_macos_paragraph_14.1", + "next_title": "connecting_paragraph_15", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/connecting/#using-a-gui-cyberduck" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_5.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_5.1.txt new file mode 100644 index 00000000000..1e22cfc8b1f --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_5.1.txt @@ -0,0 +1,10 @@ +First Time connection to the HPC infrastructure +Connect +Open up a terminal and enter the following command to connect to the HPC. +You can open a terminal by navigation to Applications and then Utilities in the finder and open Terminal.app, or enter Terminal in Spotlight Search. +ssh vsc40000@login.hpc.ugent.be +Here, user vsc40000 wants to make a connection to the "hpcugent" cluster at UGent via the login +node "login.hpc.ugent.be", so replace vsc40000 with your own VSC id in the above command. +The first time you make a connection to the login node, you will be +asked to verify the authenticity of the login node. Please check +Warning message when first connecting to new host on how to do this. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_5.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_5.1_metadata.json new file mode 100644 index 00000000000..f928fbfcdd6 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_5.1_metadata.json @@ -0,0 +1,15 @@ +{ + "main_title": "connecting", + "subtitle": "Connect", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "First-Time-connection-to-the-HPC-infrastructure", + "links": { + "0": "https://docs.hpc.ugent.be/troubleshooting/#warning-message-when-first-connecting-to-new-host" + }, + "previous_title": "connecting_paragraph_4", + "next_title": "connecting_macos_paragraph_5.2", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/connecting/#connect" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_5.2.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_5.2.txt new file mode 100644 index 00000000000..f3f5ac6e775 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_5.2.txt @@ -0,0 +1,7 @@ +A possible error message you can get if you previously saved your +private key somewhere else than the default location +($HOME/.ssh/id_rsa): +Permission denied (publickey,gssapi-keyex,gssapi-with-mic). +In this case, use the -i option for the ssh command to specify the +location of your private key. For example: +ssh -i /home/example/my_keys diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_5.2_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_5.2_metadata.json new file mode 100644 index 00000000000..047d5863361 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/macos/connecting/connecting_macos_paragraph_5.2_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "Connect", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "First-Time-connection-to-the-HPC-infrastructure", + "previous_title": "connecting_macos_paragraph_5.1", + "next_title": "connecting_paragraph_6", + "OS": "macos", + "reference_link": "https://docs.hpc.ugent.be/macOS/connecting/#connect" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_11.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_11.1.txt new file mode 100644 index 00000000000..ca00a8a0f65 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_11.1.txt @@ -0,0 +1,17 @@ +Adding multiple SSH public keys (optional) +In case you are connecting from different computers to the login nodes, +it is advised to use separate SSH public keys to do so. You should +follow these steps. +1. Create a new public/private SSH key pair from Putty. Repeat the + process described in + section Generate a public/private key pair. +2. Go to +3. Upload the new SSH public key using the Add public key section. Make sure that your + public key is actually saved, because a public key will be refused + if it is too short, wrong type, or in a wrong format. +4. (optional) If you lost your key, you can delete the old key on the + same page. You should keep at least one valid public SSH key in your + account. +5. Take into account that it will take some time before the new SSH + public key is active in your account on the system; waiting for + 15-30 minutes should be sufficient. \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_11.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_11.1_metadata.json new file mode 100644 index 00000000000..4614c053f2c --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_11.1_metadata.json @@ -0,0 +1,15 @@ +{ + "main_title": "account", + "subtitle": "Adding-multiple-SSH-public-keys-(optional)", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Applying-for-the-account", + "links": { + "0": "https://docs.hpc.ugent.be/account/#generate-a-publicprivate-key-pair" + }, + "previous_title": "account_paragraph_10", + "next_title": "account_paragraph_12", + "OS": "windows", + "reference_link": "https://docs.hpc.ugent.be/Windows/account/#adding-multiple-ssh-public-keys-optional" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.1.txt new file mode 100644 index 00000000000..93ca7ac9da5 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.1.txt @@ -0,0 +1,18 @@ +How do SSH keys work +A typical Windows environment does not come with pre-installed software +to connect and run command-line executables on a HPC. Some tools need to be +installed on your Windows machine first, before we can start the actual +work. +Get PuTTY: A free telnet/SSH client +We recommend to use the PuTTY tools package, which is freely available. +You do not need to install PuTTY, you can download the PuTTY and +PuTTYgen executable and run it. This can be useful in situations where +you do not have the required permissions to install software on the +computer you are using. Alternatively, an installation package is also +available. +You can download PuTTY from the official address: +. You +probably want the 64-bits version. If you can install software on your +computer, you can use the "Package files", if not, you can download and +use putty.exe and puttygen.exe in the "Alternative binary files" +section. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.1_metadata.json new file mode 100644 index 00000000000..e0024f40d55 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Get-PuTTY-A-free-telnetSSH-client", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_paragraph_3", + "next_title": "account_windows_paragraph_4.2", + "OS": "windows", + "reference_link": "https://docs.hpc.ugent.be/Windows/account/#get-putty-a-free-telnetssh-client" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.2.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.2.txt new file mode 100644 index 00000000000..cebd1da3baf --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.2.txt @@ -0,0 +1,13 @@ +The PuTTY package consists of several components, but we'll only use +two: +1. PuTTY: the Telnet and SSH client itself (to login, see Open a terminal) +2. PuTTYgen: an RSA and DSA key generation utility (to generate a key pair, + see Generate a public/private key pair) +Generating a public/private key pair +Before requesting a VSC account, you need to generate a pair of ssh +keys. You need 2 keys, a public and a private key. You can visualise the +public key as a lock to which only you have the key (your private key). +You can send a copy of your lock to anyone without any problems, because +only you can open it, as long as you keep your private key secure. To +generate a public/private key pair, you can use the PuTTYgen key +generator. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.2_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.2_metadata.json new file mode 100644 index 00000000000..534ebda0a1c --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.2_metadata.json @@ -0,0 +1,16 @@ +{ + "main_title": "account", + "subtitle": "Generating-a-publicprivate-key-pair", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "links": { + "0": "https://docs.hpc.ugent.be/connecting/#open-a-terminal", + "1": "https://docs.hpc.ugent.be/account/#generating-a-publicprivate-key-pair" + }, + "previous_title": "account_windows_paragraph_4.1", + "next_title": "account_windows_paragraph_4.3", + "OS": "windows", + "reference_link": "https://docs.hpc.ugent.be/Windows/account/#generating-a-publicprivate-key-pair" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.3.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.3.txt new file mode 100644 index 00000000000..6e65300562d --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.3.txt @@ -0,0 +1,30 @@ +Start PuTTYgen.exe it and follow these steps: +1. In "Parameters" (at the bottom of the window), choose "RSA" and set the number of + bits in the key to 4096. +2. Click on "Generate". To generate the key, you must move the mouse cursor over + the PuTTYgen window (this generates some random data that PuTTYgen + uses to generate the key pair). Once the key pair is generated, your + public key is shown in the field "Public key for pasting into OpenSSH authorized_keys file". +3. Next, it is advised to fill in the "Key comment" field to make it easier + identifiable afterwards. +4. Next, you should specify a passphrase in the "Key passphrase" field and retype it in + the "Confirm passphrase" field. Remember, the passphrase protects the private key against + unauthorised use, so it is best to choose one that is not too easy + to guess but that you can still remember. Using a passphrase is not + required, but we recommend you to use a good passphrase unless you + are certain that your computer's hard disk is encrypted with a + decent password. (If you are not sure your disk is encrypted, it + probably isn't.) +5. Save both the public and private keys in a folder on your personal + computer (We recommend to create and put them in the folder + "C:\\Users\\%USERNAME%\\AppData\\Local\\PuTTY\\.ssh") with the + buttons "Save public key" and "Save private key". We recommend using the name "id_rsa.pub" for the public key, and + "id_rsa.ppk" for the private key. +6. Finally, save an "OpenSSH" version of your private key (in + particular for later "X2Go" usage, see x2go) by entering the + "Conversions" menu and selecting "Export OpenSSH key" (do not select the + "force new file format" variant). Save the file in the same location + as in the previous step with filename "id_rsa". (If there is no + "Conversions" menu, you must update your "puttygen" version. If you + want to do this conversion afterwards, you can start with loading an + existing "id_rsa.ppk" and only do this conversions export.) diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.3_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.3_metadata.json new file mode 100644 index 00000000000..4555638639d --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.3_metadata.json @@ -0,0 +1,15 @@ +{ + "main_title": "account", + "subtitle": "Generating-a-publicprivate-key-pair", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "links": { + "0": "https://docs.hpc.ugent.be/" + }, + "previous_title": "account_windows_paragraph_4.2", + "next_title": "account_windows_paragraph_4.4", + "OS": "windows", + "reference_link": "https://docs.hpc.ugent.be/Windows/account/#generating-a-publicprivate-key-pair" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.4.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.4.txt new file mode 100644 index 00000000000..d0425d6738f --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.4.txt @@ -0,0 +1,2 @@ +If you use another program to generate a key pair, please remember that +they need to be in the OpenSSH format to access the HPC clusters. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.4_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.4_metadata.json new file mode 100644 index 00000000000..ebd55060657 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_4.4_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Generating-a-publicprivate-key-pair", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_windows_paragraph_4.3", + "next_title": "account_paragraph_5", + "OS": "windows", + "reference_link": "https://docs.hpc.ugent.be/Windows/account/#generating-a-publicprivate-key-pair" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.1.txt new file mode 100644 index 00000000000..b8dba743c0a --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.1.txt @@ -0,0 +1,13 @@ +Using an SSH agent (optional) +It is possible to setup a SSH agent in Windows. This is an optional +configuration to help you to keep all your SSH keys (if you have +several) stored in the same key ring to avoid to type the SSH key +password each time. The SSH agent is also necessary to enable SSH hops +with key forwarding from Windows. +Pageant is the SSH authentication agent used in windows. This agent should be +available from the PuTTY installation package + or as +stand alone binary package. +After the installation just start the Pageant application in Windows, +this will start the agent in background. The agent icon will be visible +from the Windows panel. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.1_metadata.json new file mode 100644 index 00000000000..5fd697066b6 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Using-an-SSH-agent-(optional)", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_paragraph_5", + "next_title": "account_windows_paragraph_6.2", + "OS": "windows", + "reference_link": "https://docs.hpc.ugent.be/Windows/account/#using-an-ssh-agent-optional" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.2.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.2.txt new file mode 100644 index 00000000000..62ac04dd9aa --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.2.txt @@ -0,0 +1,11 @@ +At this point the agent does not contain any private key. You should +include the private key(s) generated in the previous section Generating a public/private key pair. +1. Click on "Add key" +2. Select the private key file generated in Generating a public/private key pair ("id_rsa.ppk" by default). +3. Enter the same SSH key password used to generate the key. After this + step the new key will be included in Pageant to manage the SSH + connections. +4. You can see the SSH key(s) available in the key ring just clicking + on "View Keys". +5. You can change PuTTY setup to use the SSH agent. Open PuTTY and check + Connection > SSH > Auth > Allow agent forwarding. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.2_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.2_metadata.json new file mode 100644 index 00000000000..11c69338029 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.2_metadata.json @@ -0,0 +1,16 @@ +{ + "main_title": "account", + "subtitle": "Using-an-SSH-agent-(optional)", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "links": { + "0": "https://docs.hpc.ugent.be/account/#generating-a-publicprivate-key-pair", + "1": "https://docs.hpc.ugent.be/account/#generating-a-publicprivate-key-pair" + }, + "previous_title": "account_windows_paragraph_6.1", + "next_title": "account_windows_paragraph_6.3", + "OS": "windows", + "reference_link": "https://docs.hpc.ugent.be/Windows/account/#using-an-ssh-agent-optional" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.3.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.3.txt new file mode 100644 index 00000000000..17c94975dec --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.3.txt @@ -0,0 +1,5 @@ +Now you can connect to the login nodes as usual. The SSH agent will know +which SSH key should be used and you do not have to type the SSH +passwords each time, this task is done by Pageant agent automatically. +It is also possible to use WinSCP with Pageant, see + for more details. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.3_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.3_metadata.json new file mode 100644 index 00000000000..e33d002d248 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_6.3_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Using-an-SSH-agent-(optional)", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 3, + "directory": "account", + "parent_title": "Getting-ready-to-request-an-account", + "previous_title": "account_windows_paragraph_6.2", + "next_title": "account_paragraph_7", + "OS": "windows", + "reference_link": "https://docs.hpc.ugent.be/Windows/account/#using-an-ssh-agent-optional" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_9.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_9.1.txt new file mode 100644 index 00000000000..9fd23612756 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_9.1.txt @@ -0,0 +1,8 @@ +Applying for the account +After you log in using your UGent login and password, you will be asked to +upload the file that contains your public key, i.e., the file +"id_rsa.pub" which you have generated earlier. Make sure that your +public key is actually accepted for upload, because if it is in a wrong +format, wrong type or too short, then it will be refused. +This file should have been stored in the directory +"C:\\Users\\%USERNAME%\\AppData\\Local\\PuTTY\\.ssh" diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_9.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_9.1_metadata.json new file mode 100644 index 00000000000..87cda41283f --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/account/account_windows_paragraph_9.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "account", + "subtitle": "Applying-for-the-account", + "source_file": "../../mkdocs/docs/HPC/account.md", + "title_depth": 2, + "directory": "account", + "parent_title": "account", + "previous_title": "account_paragraph_8", + "next_title": "account_paragraph_10", + "OS": "windows", + "reference_link": "https://docs.hpc.ugent.be/Windows/account/#applying-for-the-account" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_11.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_11.1.txt new file mode 100644 index 00000000000..5aa8ca03374 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_11.1.txt @@ -0,0 +1,9 @@ +First Time connection to the HPC infrastructure + A locale is a set of parameters that defines the user's language, country and + any special variant preferences that the user wants to see in their user + interface. Usually a locale identifier consists of at least a language + identifier and a region identifier. + Note + If you try to set a non-supported locale, then it will be automatically + set to the default. Currently the default is en_US.UFT-8 or en_US, + depending on whether your originally (non-supported) locale was UTF-8 or not. \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_11.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_11.1_metadata.json new file mode 100644 index 00000000000..d4b02dbc9fb --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_11.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "First-Time-connection-to-the-HPC-infrastructure", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 2, + "directory": "connecting", + "parent_title": "Connecting-to-the-HPC-infrastructure", + "previous_title": "connecting_paragraph_10", + "next_title": "connecting_paragraph_12", + "OS": "windows", + "reference_link": "https://docs.hpc.ugent.be/Windows/connecting/#first-time-connection-to-the-hpc-infrastructure" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.1.txt new file mode 100644 index 00000000000..67e5e454852 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.1.txt @@ -0,0 +1,22 @@ +Transfer Files to/from the HPC +Before you can do some work, you'll have to transfer the files you need from your desktop or department to the cluster. At the end of a job, you might want to transfer some files back. +WinSCP +To transfer files to and from the cluster, we recommend the use of +WinSCP, a graphical file management tool which can transfer files using +secure protocols such as SFTP and SCP. WinSCP is freely available from +. +To transfer your files using WinSCP, +1. Open the program +2. The "Login" menu is shown automatically (if it is closed, click "New Session" to open it again). Fill in the necessary fields under "Session" + 1. Click "New Site". + 2. Enter "login.hpc.ugent.be" in the "Host name" field. + 3. Enter your "vsc-account" in the "User name" field. + 4. Select "SCP" as the "file" protocol. + 5. Note that the password field remains empty. + + 6. Click "Advanced...". + 7. Click "SSH > Authentication". + 8. Select your private key in the field "Private key file". +3. Press the "Save" button, to save the session under "Session > Sites" for future access. +4. Finally, when clicking on "Login", you will be asked for your key passphrase. + diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.1_metadata.json new file mode 100644 index 00000000000..a4bbaee0f59 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.1_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "WinSCP", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "First-Time-connection-to-the-HPC-infrastructure", + "previous_title": "connecting_paragraph_11", + "next_title": "connecting_windows_paragraph_12.2", + "OS": "windows", + "reference_link": "https://docs.hpc.ugent.be/Windows/connecting/#winscp" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.2.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.2.txt new file mode 100644 index 00000000000..82c71ac4129 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.2.txt @@ -0,0 +1,11 @@ +The first time you make a connection to the login node, a Security +Alert will appear and you will be asked to verify the authenticity of the +login node. +Make sure the fingerprint in the alert matches one of the following: +- ssh-rsa 2048 10:2f:31:21:04:75:cb:ed:67:e0:d5:0c:a1:5a:f4:78 +- ssh-rsa 2048 SHA256:W8Wz0/FkkCR2ulN7+w8tNI9M0viRgFr2YlHrhKD2Dd0 +- ssh-ed25519 255 19:28:76:94:52:9d:ff:7d:fb:8b:27:b6:d7:69:42:eb +- ssh-ed25519 256 SHA256:8AJg3lPN27y6i+um7rFx3xoy42U8ZgqNe4LsEycHILA +- ssh-ecdsa 256 e6:d2:9c:d8:e7:59:45:03:4a:1f:dc:96:62:29:9c:5f +- ssh-ecdsa 256 SHA256:C8TVx0w8UjGgCQfCmEUaOPxJGNMqv2PXLyBNODe5eOQ +If it does, press Yes, if it doesn't, please contact hpc@ugent.be. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.2_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.2_metadata.json new file mode 100644 index 00000000000..80a8ef763a1 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.2_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "WinSCP", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "First-Time-connection-to-the-HPC-infrastructure", + "previous_title": "connecting_windows_paragraph_12.1", + "next_title": "connecting_windows_paragraph_12.3", + "OS": "windows", + "reference_link": "https://docs.hpc.ugent.be/Windows/connecting/#winscp" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.3.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.3.txt new file mode 100644 index 00000000000..c0ffe6b4602 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.3.txt @@ -0,0 +1,6 @@ +Note: it is possible that the ssh-ed25519 fingerprint starts with ssh-ed25519 255 +rather than ssh-ed25519 256 (or vice versa), depending on the PuTTY version you are using. +It is safe to ignore this 255 versus 256 difference, but the part after should be +identical. +Now, try out whether you can transfer an arbitrary file from your local +machine to the HPC and back. diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.3_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.3_metadata.json new file mode 100644 index 00000000000..07760730d56 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_12.3_metadata.json @@ -0,0 +1,12 @@ +{ + "main_title": "connecting", + "subtitle": "WinSCP", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "First-Time-connection-to-the-HPC-infrastructure", + "previous_title": "connecting_windows_paragraph_12.2", + "next_title": "connecting_paragraph_13", + "OS": "windows", + "reference_link": "https://docs.hpc.ugent.be/Windows/connecting/#winscp" +} \ No newline at end of file diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_4.1.txt b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_4.1.txt new file mode 100644 index 00000000000..e45f4e63b85 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_4.1.txt @@ -0,0 +1,42 @@ +First Time connection to the HPC infrastructure +Open a Terminal +You've generated a public/private key pair with PuTTYgen and have an +approved account on the VSC clusters. The next step is to setup the +connection to (one of) the HPC. +In the screenshots, we show the setup for user +"vsc20167" +to the HPC cluster via the login node "login.hpc.ugent.be". +1. Start the PuTTY executable putty.exe in your directory + C:\Program Files (x86)\PuTTY and the configuration screen will pop + up. As you will often use the PuTTY tool, we recommend adding a + shortcut on your desktop. +2. Within the category , in the field , enter the name of the + login node of the cluster (i.e., "login.hpc.ugent.be") you want to connect to. + +3. In the category "Connection > Data", in the field "Auto-login username", put in , which is your VSC + username that you have received by e-mail after your request was + approved. + +4. In the category "Connection > SSH > Auth", in the field "Private key file for authentication" click on "Browse" and select the private key + (i.e., "id_rsa.ppk") that you generated and saved above. +5. In the category "Connection > SSH > X11", click the "Enable X11 Forwarding" checkbox. +6. Now go back to , and fill in "hpcugent" in the "Saved Sessions" field and press "Save" to + store the session information. + +7. Now pressing "Open", will open a terminal window and asks for you + passphrase. + +8. If this is your first time connecting, you will be asked to verify + the authenticity of the login node. Please see + section Warning message when first connecting to new host + on how to do this. +9. After entering your correct passphrase, you will be connected to the + login-node of the HPC. +10. To check you can now "Print the Working Directory" (pwd) and check + the name of the computer, where you have logged in (hostname): + $ pwd + /user/home/gent/vsc400/vsc40000 + $ hostname -f + gligar07.gastly.os +11. For future PuTTY sessions, just select your saved session (i.e. "hpcugent") + from the list, "Load" it and press "Open". diff --git a/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_4.1_metadata.json b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_4.1_metadata.json new file mode 100644 index 00000000000..d3b7d581c94 --- /dev/null +++ b/scripts/HPC_chatbot_preprocessor/parsed_mds/os_specific/windows/connecting/connecting_windows_paragraph_4.1_metadata.json @@ -0,0 +1,15 @@ +{ + "main_title": "connecting", + "subtitle": "Open-a-Terminal", + "source_file": "../../mkdocs/docs/HPC/connecting.md", + "title_depth": 3, + "directory": "connecting", + "parent_title": "First-Time-connection-to-the-HPC-infrastructure", + "links": { + "0": "https://docs.hpc.ugent.be/troubleshooting/#warning-message-when-first-connecting-to-new-host" + }, + "previous_title": "connecting_paragraph_3", + "next_title": "connecting_paragraph_5", + "OS": "windows", + "reference_link": "https://docs.hpc.ugent.be/Windows/connecting/#open-a-terminal" +} \ No newline at end of file diff --git a/scripts/README.md b/scripts/README.md deleted file mode 100644 index eed5a73e4d5..00000000000 --- a/scripts/README.md +++ /dev/null @@ -1,3 +0,0 @@ -Scripts that can be used to automatically generate markdown files, can be found here. - -* [`available_software`](available_software): script to generate overview of available environment modules; \ No newline at end of file