Merge branch 'main' of https://github.com/UPPMAX/HPC-python

Author: richelbilderbeek

docs/day2/evaluation.rst

@@ -2,4 +2,4 @@
 Evaluation
 ==========
 
-The evaluation form can be found here: https://forms.office.com/e/LFA8rPncbF
+The evaluation form can be found here: https://forms.office.com/e/rartwsGrvY

docs/day2/use_isolated_environments.rst

@@ -420,7 +420,7 @@ Breakout room according to grouping
 
             - `Python <https://lunarc-documentation.readthedocs.io/en/latest/guides/applications/Python/>`_
 
-            UPPMAX
+            UPPMAX (only Pelle)
 
             - `Python venv <https://docs.uppmax.uu.se/software/python_venv/>`_
             - `Video By Richel <https://www.youtube.com/watch?v=lj_Q-5l0BqU>`_
@@ -430,7 +430,7 @@ Breakout room according to grouping
             - `Venv <https://docs.hpc2n.umu.se/software/userinstalls/#venv>`_
             - `Video by Richel <https://www.youtube.com/watch?v=_ev3g5Zvn9g>`_
 
-         .. tab: conda
+         .. tab:: conda
 
             NSC:
 
@@ -520,7 +520,7 @@ Breakout room according to grouping
 
          - Check that the above packages are there by ``conda list``. 
 
-        2. Let's make a Jupyter installation based on Python 3.11.7
+         2. Let's make a Jupyter installation based on Python 3.11.7
 
          .. code-block:: console
 
@@ -558,9 +558,9 @@ Breakout room according to grouping
 
       .. tab:: UPPMAX
 
-         1. Let's make a Spyder installation in a `conda environment <https://saturncloud.io/blog/how-to-ensure-that-spyder-runs-within-a-conda-environment/#step-2-create-a-conda-environment>`_ 
+         Let's make a Spyder installation in a `conda environment <https://saturncloud.io/blog/how-to-ensure-that-spyder-runs-within-a-conda-environment/#step-2-create-a-conda-environment>`_ 
 
-         .. tabs:::
+         .. tabs::
 
             .. tab:: Bianca
 
@@ -576,7 +576,7 @@ Breakout room according to grouping
                   which python  # should point to the conda environment!
                   python -V     # should give python version 3.12.X
 
-           .. tab:: Pelle
+            .. tab:: Pelle
 
                .. code-block:: 
          
@@ -749,10 +749,24 @@ Breakout room according to grouping
             which python  # should point to the conda environment!
             python -V     # should give python version 3.12.X
     
-      .. tab:: UPPMAX: Pelle
+      .. tab:: UPPMAX: Bianca
 
-         .. code-block:: console
+          .. code-block:: 
          
+             ml conda
+             export CONDA_PKG_DIRS=/proj/hpc-python-uppmax/$USER
+             export CONDA_ENVS_PATH=/proj/hpc-python-uppmax/$USER
+             conda create --prefix $CONDA_ENVS_PATH/example python=3.12 -c conda-forge
+             source activate example
+             # A prompt "(/path-to/example/)" should show up
+             # double-check we are using python from the Conda environment!
+             which python  # should point to the conda environment!
+             python -V     # should give python version 3.12.X
+   
+      .. tab:: UPPMAX: Pelle
+   
+         .. code-block:: 
+            
             ml Miniforge3/24.11.3-0
             export CONDA_PKG_DIRS=/proj/hpc-python-uppmax/$USER  #only needed once per session
             export CONDA_ENVS_PATH=/proj/hpc-python-uppmax/$USER  #only needed once per session
@@ -762,7 +776,7 @@ Breakout room according to grouping
             # double-check we are using python from the Conda environment!
             which python  # should point to the conda environment!
             python -V     # should give python version 3.12.X
-
+   
       .. tab:: HPC2N
 
          Skip this exercise
@@ -777,6 +791,9 @@ Breakout room according to grouping
 
 
 
+
+
+
 .. challenge:: (optional) 5. Make a test environment and spread (venv)
 
    Read `here <https://uppmax.github.io/HPC-python/extra/isolated_deeper.html#creator-developer>`_ 

docs/day3/evaluation.rst

@@ -2,4 +2,4 @@
 Evaluation
 ==========
 
-The evaluation form can be found here: https://forms.office.com/e/GCB2xjM7zx  
+The evaluation form can be found here: https://forms.office.com/e/6RPcNSWC6E 

docs/day4/evaluation.rst

@@ -2,4 +2,4 @@
 Evaluation
 ==========
 
-The evaluation form can be found here: https://forms.office.com/e/KL2EEU3x2M 
+The evaluation form can be found here: https://forms.office.com/e/i9FE60VZhV 

docs/day4/parallel.rst

@@ -434,23 +434,30 @@ in Python rather than learning to write those codes.
    Optional flags for ``srun`` for writing output and error files are ``-o output_%j.out -e error_%j.err`` instead 
    of writing on the terminal screen.
 
-   **Data dependencied**
+   .. warning::
 
-   In general, one cannot parallelize an serial algorithm; let's take the case of:
+      **Data dependencies**
 
+      In general, one cannot parallelize a serial algorithm; let's take the case of:
 
-   .. code-block:: python
+      .. code-block:: python
 
-      a[0] = 0
-      for i in range(1, N):
-         a[i] = a[i-1] + i
+         a[0] = 0
+         for i in range(1, N):
+            a[i] = a[i-1] + i
 
-   Here, the iteration *i* depends on the previous iteration *i-1*. One needs to transform this algorithm:
+      Let's say we have the elements :code:`a[0], a[1],..., a[5]` and only two processes. Process number one
+      takes the elements :code:`a[0], a[1], a[2]` and process number two :code:`a[3], a[4], a[5]`.
+      Because in the loop the iteration ``i`` depends on the previous iteration ``i-1``, process two will have
+      conflicts computing :code:`a[3]` because it depends on :code:`a[2]` which is owned by process one.
+      
+      One can avoid data dependencies by transforming the initial algorithm to a more suitable algorithm for
+      parallelization:
 
-   .. code-block:: python
+      .. code-block:: python
 
-      for i in range(N):
-         a[i] = 0.5 * i * (i + 1)
+         for i in range(N):
+            a[i] = 0.5 * i * (i + 1)