Ah, thanks so much. I'm still a slurm newbie and I've barely used srun. I'm not sure how long it would have taken me to find and understand those parameters from the docs. Thanks!
________________________________ From: slurm-users <slurm-users-boun...@lists.schedmd.com> on behalf of Jeffrey T Frey <f...@udel.edu> Sent: Wednesday, February 8, 2023 10:01 AM To: Slurm User Community List <slurm-users@lists.schedmd.com> Subject: Re: [slurm-users] slurm and singularity You don't often get email from f...@udel.edu. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> You may need srun to allocate a pty for the command. The InteractiveStepOptions we use (that are handed to srun when no explicit command is given to salloc) are: --interactive --pty --export=TERM E.g. without those flags a bare srun gives a promptless session: [(it_nss:frey)@login00.darwin ~]$ salloc -p idle srun /opt/shared/singularity/3.10.0/bin/singularity shell /opt/shared/singularity/prebuilt/postgresql/13.2.simg salloc: Granted job allocation 3953722 salloc: Waiting for resource configuration salloc: Nodes r1n00 are ready for job ls -l total 437343 -rw-r--r-- 1 frey it_nss 180419 Oct 26 16:56 amd.cache -rw-r--r-- 1 frey it_nss 72 Oct 26 16:52 amd.conf -rw-r--r-- 1 frey everyone 715 Nov 12 23:39 anaconda-activate.sh drwxr-xr-x 2 frey everyone 4 Apr 11 2022 bin : With the --pty flag added: [(it_nss:frey)@login00.darwin ~]$ salloc -p idle srun --pty /opt/shared/singularity/3.10.0/bin/singularity shell /opt/shared/singularity/prebuilt/postgresql/13.2.simg salloc: Granted job allocation 3953723 salloc: Waiting for resource configuration salloc: Nodes r1n00 are ready for job Singularity> On Feb 8, 2023, at 09:47 , Groner, Rob <rug...@psu.edu<mailto:rug...@psu.edu>> wrote: I tried that, and it says the nodes have been allocated, but it never comes to an apptainer prompt. I then tried doing them in separate steps. Doing salloc works, I get a prompt on the node that was allocated. I can then run "singularity shell <sif>" and get the apptainer prompt. If I prefix that command with "srun", then it just hangs and I never get the prompt. So that seems to be the sticking point. I'll have to do some experiments running singularity with srun. From: slurm-users <slurm-users-boun...@lists.schedmd.com<mailto:slurm-users-boun...@lists.schedmd.com>> on behalf of Jeffrey T Frey <f...@udel.edu> Sent: Tuesday, February 7, 2023 6:16 PM To: Slurm User Community List <slurm-users@lists.schedmd.com> Subject: Re: [slurm-users] slurm and singularity You don't often get email from f...@udel.edu. Learn why this is important The remaining issue then is how to put them into an allocation that is actually running a singularity container. I don't get how what I'm doing now is resulting in an allocation where I'm in a container on the submit node still! Try prefixing the singularity command with "srun" e.g. salloc <salloc-parameters> srun <srun-parameters> /usr/bin/singularity shell <path to sif>
