CHTC — Center for High Throughput Computing
CHTC — Center for High Throughput Computing
UW-Madison College of Computing, Data & Information SciencesMorgridge Institute for Research

Known Issues on the HTC

This page documents some common and known issues encountered on the HTC system. While this page can be beneficial in troubleshooting, it does not contain a comprehensive list of errors.

General

When submitting a job, it doesn't run / goes on hold and shows the error "Job credentials are not available".

Cause:

This is a complicated bug that can strike randomly. We're working on a fix.

Solution:

To work around this issue, run the following command on the access point before resubmitting the job.

echo | condor_store_cred add-oauth -s scitokens -i -

My job exits with an "Illegal instructions" error.

Cause:

The instructions for communicating with the processor does not match between software and hardware.

Solution:

In the submit file, try adding one of the following to your requirements line:

requirements = (has_avx || has_avx2)
requirements = has_avx2
requirements = (Microarch > x86-64-v3)

Then resubmit and check if this resolves the issue.


Containers

When building an Apptainer, "apt" commands in the %post block fail to run.

Example error message:
Couldn't create temporary file /tmp/apt.conf.9vQdLs for passing config to apt-key
Cause:

The container needs global read/write permissions in order to update or install packages using the apt command.

Solution:

Add chmod 777 /tmp to the front of your %post block. See the example below:

Bootstrap: docker
From: ubuntu:22.04

%post
    chmod 777 /tmp
    apt-get update -y

We also recommend using the -y option to prevent installation from hanging due to interactive prompts.

After submitting a job with a Docker container, it goes on hold with a message like, "Cannot pull image user/repo:tag".

Cause:

The Docker container is likely built on an Apple computer using an ARM processor, which is incompatible with Linux machines.

Solution:

To resolve this, when building your Docker container, use the command:

docker build --platform linux/amd64 .

My interactive Apptainer job is failing with the error message, "Can't open master pty Bad file descriptor".

Cause:

Interactive Apptainer jobs are incompatible with CentOS7 machines.

Solution:

To your submit file, add the following line and resubmit:

requirements = (OpSysMajorVer > 7)

Can't find your issue?

Visit our Get Help page.

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