Hi Brian:
This works just as I expect for sbatch.
The example srun execution I showed was a non-array job, so the first half of
the "if []" statement holds. It is the second half, which deals with job
arrays, which has the period.
The value of TMP is correct, i.e. "/local/scratch/80472"
And the command, in the prolog script is correct, i.e. "/usr/bin/mkdir -p
${TMP}"
If I type that command during the interactive job, it does what I expect, i.e.
creates the directory $TMP = /local/scratch/80472
Regards,
Dave
________________________________
From: slurm-users <slurm-users-boun...@lists.schedmd.com> on behalf of Brian
Andrus <toomuc...@gmail.com>
Sent: Thursday, March 4, 2021 13:48
To: slurm-users@lists.schedmd.com <slurm-users@lists.schedmd.com>
Subject: Re: [slurm-users] prolog not passing env var to job
External.
I think it isn't running how you think or there is something not provided in
the description.
You have:
export TMP="/local/scratch/${SLURM_ARRAY_JOB_ID}.${SLURM_ARRAY_TASK_ID}"
Notice that period in there.
Then you have:
node001::~$ echo $TMP
/local/scratch/80472
There is no period.
In fact, SLURM_ARRAY_JOB_ID should be blank too if you are not running as an
array session.
However, to your desire for a job-specific tmp directory:
Check out the mktemp command. It should do just what you want. I use it for
interactive desktop sessions for users to create the temp directory that is
used for X sessions.
You just need to make sure the user has write access to the directory you are
creating the directory in (chmod 1777 for the parent directory is good)
Brian Andrus
On 3/4/2021 9:03 AM, Chin,David wrote:
Hi, Brian:
So, this is my SrunProlog script -- I want a job-specific tmp dir, which makes
for easy cleanup at end of job:
#!/bin/bash
if [[ -z ${SLURM_ARRAY_JOB_ID+x} ]]
then
export TMP="/local/scratch/${SLURM_JOB_ID}"
export TMPDIR="${TMP}"
export LOCAL_TMPDIR="${TMP}"
export BEEGFS_TMPDIR="/beegfs/scratch/${SLURM_JOB_ID}"
else
export TMP="/local/scratch/${SLURM_ARRAY_JOB_ID}.${SLURM_ARRAY_TASK_ID}"
export TMPDIR="${TMP}"
export LOCAL_TMPDIR="${TMP}"
export
BEEGFS_TMPDIR="/beegfs/scratch/${SLURM_ARRAY_JOB_ID}.${SLURM_ARRAY_TASK_ID}"
fi
echo DEBUG srun_set_tmp.sh
echo I am `whoami`
/usr/bin/mkdir -p ${TMP}
chmod 700 ${TMP}
/usr/bin/mkdir -p ${BEEGFS_TMPDIR}
chmod 700 ${BEEGFS_TMPDIR}
And this is my srun session:
picotte001::~$ whoami
dwc62
picotte001::~$ srun -p def --mem 1000 -n 4 -t 600 --pty /bin/bash
DEBUG srun_set_tmp.sh
I am dwc62
node001::~$ echo $TMP
/local/scratch/80472
node001::~$ ll !$
ll $TMP
/bin/ls: cannot access '/local/scratch/80472': No such file or directory
node001::~$ mkdir $TMP
node001::~$ ll -d !$
ll -d $TMP
drwxrwxr-x 2 dwc62 dwc62 6 Mar 4 11:52 /local/scratch/80472/
node001::~$ exit
So, the "echo" and "whoami" statements are executed by the prolog script, as
expected, but the mkdir commands are not?
Thanks,
Dave
--
David Chin, PhD (he/him) Sr. SysAdmin, URCF, Drexel
dw...@drexel.edu<mailto:dw...@drexel.edu> 215.571.4335 (o)
For URCF support: urcf-supp...@drexel.edu<mailto:urcf-supp...@drexel.edu>
https://proteusmaster.urcf.drexel.edu/urcfwiki
github:prehensilecode
________________________________
From: slurm-users
<slurm-users-boun...@lists.schedmd.com><mailto:slurm-users-boun...@lists.schedmd.com>
on behalf of Brian Andrus <toomuc...@gmail.com><mailto:toomuc...@gmail.com>
Sent: Thursday, March 4, 2021 10:12
To: slurm-users@lists.schedmd.com<mailto:slurm-users@lists.schedmd.com>
<slurm-users@lists.schedmd.com><mailto:slurm-users@lists.schedmd.com>
Subject: Re: [slurm-users] prolog not passing env var to job
External.
It seems to me, if you are using srun directly to get an interactive shell, you
can just run the script once you get your shell.
You can set the variables and then run srun. It automatically exports the
environment.
If you want to change a particular one (or more), use something like
--export=ALL,MYVAR=othervalue
do 'man srun' and look at the --export option
Brian Andrus
On 3/3/2021 9:28 PM, Chin,David wrote:
ahmet.mer...@uhem.itu.edu.tr<mailto:ahmet.mer...@uhem.itu.edu.tr> wrote:
> Prolog and TaskProlog are different parameters and scripts. You should
> use the TaskProlog script to set env. variables.
Can you tell me how to do this for srun? E.g. users request an interactive
shell:
srun -n 1 -t 600 --pty /bin/bash
but the shell on the compute node does not have the env variables set.
I use the same prolog script as TaskProlog, which sets it properly for jobs
submitted
with sbatch.
Thanks in advance,
Dave Chin
--
David Chin, PhD (he/him) Sr. SysAdmin, URCF, Drexel
dw...@drexel.edu<mailto:dw...@drexel.edu> 215.571.4335 (o)
For URCF support: urcf-supp...@drexel.edu<mailto:urcf-supp...@drexel.edu>
https://proteusmaster.urcf.drexel.edu/urcfwiki
github:prehensilecode
________________________________
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on behalf of mercan
<ahmet.mer...@uhem.itu.edu.tr><mailto:ahmet.mer...@uhem.itu.edu.tr>
Sent: Friday, February 12, 2021 16:27
To: Slurm User Community List
<slurm-users@lists.schedmd.com><mailto:slurm-users@lists.schedmd.com>; Herc
Silverstein
<herc.silverst...@schrodinger.com><mailto:herc.silverst...@schrodinger.com>;
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<slurm-us...@schedmd.com><mailto:slurm-us...@schedmd.com>
Subject: Re: [slurm-users] prolog not passing env var to job
External.
Hi;
Prolog and TaskProlog are different parameters and scripts. You should
use the TaskProlog script to set env. variables.
Regards;
Ahmet M.
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