Permission Denied error when submitting job

[pradeepjasal]

I am getting permission denied error when running simple hello world snakemake example with local htcondor cluster.

condor_version
$CondorVersion: 23.10.1 2024-10-03 BuildID: 759508 PackageID: 23.10.1-1+ubu22 GitSHA: acedc362 $
$CondorPlatform: X86_64-Ubuntu_22.04 $

snakemake --version
8.28.0

snakefile example

rule all:
    input:
        "hello_world.txt"
        
rule say_hello_world:
    output:
        "hello_world.txt"
    shell:
        """
        echo "hello world" > {output}
        """

snakemake log

Submitted job 1 with external jobid '1_1b4b3bad-7b9c-4978-90cf-83528660da14_Submitted 1 jobs into cluster 96,0 :'.
[Wed Mar 26 17:34:10 2025]
Error in rule say_hello_world:
    message: For further error details see the cluster/cloud log and the log files of the involved rule(s).
    jobid: 1
    output: hello_world.txt
    shell:
        
        echo "hello world" > hello_world.txt
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    external_jobid: 1_1b4b3bad-7b9c-4978-90cf-83528660da14_Submitted 1 jobs into cluster 96,0 :

Trying to restart job 1.
Select jobs to execute...
Execute 1 jobs...

condor err
/var/lib/condor/execute/dir_3566455/bash: /home/hpc/Desktop/condor_test/.snakemake/tmp.dn6i_0ra/snakejob.say_hello_world.1.sh: Permission denied

condor log

	CondorScratchDir = "/var/lib/condor/execute/dir_3561107"
	Cpus = 1
	Disk = 8644886
	GPUs = 0
	Memory = 1986
...
040 (096.000.000) 2025-03-26 17:30:08 Finished transferring output files
...
004 (096.000.000) 2025-03-26 17:30:08 Job was evicted.
	(0) Job terminated and was requeued
		Usr 0 00:00:00, Sys 0 00:00:00  -  Run Remote Usage
		Usr 0 00:00:00, Sys 0 00:00:00  -  Run Local Usage
	0  -  Run Bytes Sent By Job
	1396520  -  Run Bytes Received By Job
	(1) Normal termination (return value 126)
	The job attribute OnExitRemove expression 'NumJobCompletions > JobMaxRetries || ExitCode =?= 0' evaluated to FALSE

Could you please suggest how to resolve this ?

[jheuel]

Looks like the htcondor worker doesn’t have permissions to read the files in your condor_test directory.
Can you authenticate as your user in the htcondor jobs or move the files somewhere where the workers have the necessary permissions?

[pradeepjasal]

Is it possible to use htcondor's file transfer mechanism rather than shared file system

[jheuel]

At the moment we only support the shared file system setup. I guess everyone who used it until now was at CERN or contributing institutes with the default HTCondor setup with a shared file system.

However, we are always open for a PR.