Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

Tracing a Singularity container

See original GitHub issue

Hi,

I’m trying to use reprozip to monitor a workflow of mine, but getting a non-very-descriptive error message below when doing this. I’m able to run simpler commands, such as echo hello, but my current command (which happens to be a Python tool which launches Singularity containers) returns the following response each time. I’m not sure what the issue with the executable I’m currently trying to run is, or why reprozip seems incompatible with it, but am eager to see if you may know why this is happening.

Thanks for your help!

$ reprozip trace -w --dir=/mydir/ command arg1 arg2 arg3 arg4 ...
[REPROZIP] 15:14:44.630 CRITICAL: cleaning up, 4 processes to kill...
Traceback (most recent call last):
  File "/project/6008063/gkiar/computing/env/closh/lib/python3.6/site-packages/reprozip/main.py", line 390, in main
    status = args.func(args)
  File "/project/6008063/gkiar/computing/env/closh/lib/python3.6/site-packages/reprozip/main.py", line 206, in trace
    args.verbosity)
  File "/project/6008063/gkiar/computing/env/closh/lib/python3.6/site-packages/reprozip/tracer/trace.py", line 341, in trace
    c = _pytracer.execute(binary, argv, database.path, verbosity)
_pytracer.Error: Error occurred

Issue Analytics

State:
Created 5 years ago
Comments:13 (6 by maintainers)

Top GitHub Comments

1reaction

remram44commented, May 11, 2018

I have fixed the original bug and added a warning (#296) when a set-uid executable is encountered, so that users know why the program is failing.

Unfortunately I don’t see what else the Singularity team or us can do, since we cannot work around Linux security features. I am going to go ahead with the release, please don’t hesitate to let us know if you hit any other issue or roadblock in the future!

0reactions

gkiarcommented, May 11, 2018

Thank you very much!

Top Results From Across the Web

Quick Start — Singularity container 3.0 documentation

This guide is intended for running Singularity on a computer where you have root ... You can use the search command to locate...

Is there a way to track singularity containers like "docker ps ...

As such, tracking down Singularity processes can be done using the standard shell tools.

install - Singularity Hub Container Tools

This module is a singularity container wrapper for ghcr.io/autamus/lmod. The Persistence of Vision Ray Tracer, most commonly acronymed as POV-Ray, ...

Introduction to Singularity Containers - Bioinformatics Workbook

First go to Singularity Hub and locate the container you want through the search box located on the left side just below the...

Singularity containers — Nextflow 21.10.6 documentation

Nextflow is able to transparently pull remote container images stored in the Singularity-Hub, Singularity Library, or any Docker compatible registry. Note. This ...