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I wanted to run a program called trinity, which is written in partly in perl using the high performance cluster at my institute. I used conda to install trinity and tried to run it by submitting the job .sh file in slurm. But the job would abort within one minute. The slurm exit code I received was 25. I could not find any information on this exit code. When I checked the stderr file I saw this:


perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LANG = "en_IN"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").

I tried resolving this by adding the following lines to my script but the error prevailed.

export LANGUAGE=en_IN
export LC_ALL=en_IN
export LANG=en_IN

I also checked in locales -a en_IN was indeed in the list so I did not have to do locale-gen (which I couldn't do even if I wanted to do because I do not have administrator privileges)

I am lost with this at the moment and I am a beginner to using slurm. How do I solve this? I have stuck with this for months. Do you have any idea on the slurm error code 25? I found no information for this in the documentation. I assume it has something to do with the locale warning.

Edit: Removed the last line in the error message I could solve it if I wanted to. That happened when I was troubleshooting the locale warning. The original error message was the locale warning. I installed Trinity using conda. I am running it by submitting a .sh file to slurm which activates the conda environment and then runs Trinity. But the job fails with error code 25 after a minute or so and the warning comes in the stderr

user21777965
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  • The warnings are only just warnings. The actual error is unrelated to your locale settings. How are you submitting the job and how exactly did you install the software you are trying to run? – tripleee Apr 30 '23 at 07:16
  • Please [edit] to only focus on one problem. You should update the title, too, unless the problem you want to focus on are the Perl locale warnings (which is probably a duplicate question anyway). – tripleee Apr 30 '23 at 07:17
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    @triplee It is not a duplicate question. The other questions related to locale setting warning were all in the context of running Perl on a local machine where the usage has administrator privileges. But here I am running the program on an HPC via slurm. – user21777965 May 01 '23 at 08:47
  • You don't need admin, you just need to run with a locale which is configured on the remote host. If `en_IN` is not installed, probably try `en_US`. If you need output in civilized units, you'll need to persuade the system administrator to install `en_IN` (or perhaps at least `en_IE` which is used in some organizations where the work language is English but they want SI units. But the cases where the locale is significant are corner cases; you probably don't need to worry about this, especially if your software produces only machine-readable output). – tripleee May 01 '23 at 10:25
  • Even though many answers on the canonical suggest to install missing locales, there are also answers like https://stackoverflow.com/a/50060181/874188 which document your other options. – tripleee May 01 '23 at 10:44

1 Answers1

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Regarding

Can't open perl script "Trinity": No such file or directory

it seems like Trinity is missing in the current working directory from where you start Perl. (updated after Ikegami's comment)

------ Reasoning

A simple search for Can't open Perl script led me to

--> https://perldoc.perl.org/perldiag#Can't-open-perl-script-%22%25s%22%3a-%25s

Can't open perl script "%s": %s (F)

The script you specified can't be opened for the indicated reason.

LanX
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  • @ikegami: you are right `-S` gives another message `Can't find Trinity on PATH.` The diagnostics are confusing. I'll update the reply unless you want post on yourself. – LanX Apr 30 '23 at 18:19
  • I updated the question. I could fix that error. But the locale setting warning persists and the job still gets terminated with the slurm error code 25. Any idea on the error code? I found no information in this – user21777965 May 01 '23 at 08:49
  • I don't think the specific error code is going to add useful information. If you haven't installed the software where it can be found, end of story. If the software itself fails with this error code, check _its_ documentation. I'm fairly confident it's completely unrelated to the locale warning. – tripleee May 01 '23 at 10:29
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    Moving the goalposts by changing the question after receiving answers is problematic. Going forward, please only ask one question per question, and don't change it in ways which invalidate existing answers. – tripleee May 01 '23 at 10:50