Command 'ps' required by nextflow to collect task metrics cannot be found

[pouya-codes]

Bug report

(Please follow this template replacing the text between parentheses with the requested information)

Expected behavior and actual behavior

I am training to get the log of my job execution by using the -with-report flag, but I'm getting the following error.
I am using slurm executor to submit the jobs, and all the excitation nodes have ps installed.

Steps to reproduce the problem

(Provide a test case that reproduces the problem either with a self-contained script or GitHub repository)

Program output

Command exit status:
1

Command output:
(empty)

Command error:
Command 'ps' required by nextflow to collect task metrics cannot be found

Work dir:
/projects/ovcare/classification/cPathPortal/works/pipeline/91/d436a25b21b9ccc1ca7b7c2fc6ea6b

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

Environment

• Nextflow version: [22.05.0-edge build 5704]
• Java version: [11.0.15]
• Operating system: [Linux]
• Bash version: 4.4.20

Additional context

I am using the head node of the slurm cluster to execute my jobs on the executor nodes. All the processes execute by using a singularity environment.

[tbugfinder]

Typically the singularity container lacks the ps command. Did you check it being installed?

[pouya-codes]

Installing ps on the container solve the error thanks :)

[IvanWoo22]

Hi, I met the same error when running nf-core's workflow. When I independently run command -v ps, I got a /usr/bin/ps as result. I think ps is installed on our lsf sys, but I don't know how to check it in the singularity container. Could you give me some help?

[mribeirodantas]

You should be able to interactively enter your singularity container with singularity shell container.sif

[TKNsama]

Hi, I met the same error too.
I checked the ps command in singularity shell .sif. the ps is presented. but still nextflow can not found the ps command.

Command error:
  .command.run: line 147: /dev/null: Permission denied
  Command 'ps' required by nextflow to collect task metrics cannot be found
  cp: '.command.out' and '.command.out' are the same file
  cp: '.command.err' and '.command.err' are the same file
  cp: '.command.trace' and '.command.trace' are the same file

could you please give me some help?