[slurm-users] $TMPDIR does not honor "TmpFS"

[Jeffrey T Frey]

If you check the applicable code in src/slurmd/slurmstepd/task.c, TMPDIR is set to "/tmp" if it's not already set in the job environment and then TMPDIR is created if permissible.  It's your responsibility to set TMPDIR -- e.g. we have a plugin we wrote (autotmp) to set TMPDIR to per-job and per-step paths according to the job id.



> On Nov 21, 2018, at 10:33 , Michael Gutteridge <michael.gutteridge at gmail.com> wrote:
> 
> 
> I don't think that's a bug.  As far as I've ever known, TmpFS is only used to tell slurmd where to look for available space (reported as TmpDisk for the node).  The manpage only indicates that, not any additional functionality.  We set TMPDIR in a task prolog:
> 
> #!/bin/bash
> echo "export TMPDIR=/loc/scratch/${SLURM_JOB_ID}"
> echo "export SCRATCH_LOCAL=/loc/scratch/${SLURM_JOB_ID}"
> echo "export SCRATCH=/net/scratch/${SLURM_JOB_ID}"
> 
> - Michael
> 
> 
> On Wed, Nov 21, 2018 at 6:52 AM Shenglong Wang <sw77 at nyu.edu> wrote:
> We have TMPDIR setup inside prolog file. Hope users do not have absolute path /tmp inside their scripts.
> 
> #!/bin/bash
> 
> SLURM_BIN="/opt/slurm/bin"
> 
> SLURM_job_tmp=/state/partition1/job-${SLURM_JOB_ID}
> 
> mkdir -m 700 -p $SLURM_job_tmp
> chown $SLURM_JOB_USER $SLURM_job_tmp
> 
> echo "export SLURM_JOBTMP=$SLURM_job_tmp"
> echo "export SLURM_JOB_TMP=$SLURM_job_tmp"
> echo "export SLURM_JOB_TMPDIR=$SLURM_job_tmp"
> echo "export TMPDIR=$SLURM_job_tmp”
> 
> Best.
> Shenglong
> 
>> On Nov 21, 2018, at 9:44 AM, Roger Moye <rmoye at quantlab.com> wrote:
>> 
>> We are having the exact same problem with $TMPDIR.   I wonder if a bug has crept in?    I spoke to the SchedMD guys at SC18 last week and they were not aware of a bug but since more than one person is having this difficulty something must be wrong somewhere.
>>  
>> -Roger
>>  
>> From: slurm-users [mailto:slurm-users-bounces at lists.schedmd.com] On Behalf Of Douglas Duckworth
>> Sent: Wednesday, November 21, 2018 7:38 AM
>> To: slurm-users at lists.schedmd.com
>> Subject: [slurm-users] $TMPDIR does not honor "TmpFS"
>>  
>> Hi 
>>  
>> We are setting TmpFS=/scratchLocal in /etc/slurm/slurm.conf on nodes and controller.  However $TMPDIR value seems to be /tmp not /scratchLocal.  As a result users are writing to /tmp which we do not want.
>> 
>> We are not setting $TMPDIR anywhere else such as /etc/profile.d nor do users have it defined in their ~/.bashrc or ~/.bash_profile.  
>>  
>> We do not see any error messages anywhere which could indicate why the default value of /tmp overrides our value of of TmpFS.  
>>  
>> As I understand prolog scripts can change this value though, if that's the case, then what's the purpose of setting TmpFS in /etc/slurm/slurm.conf?
>>  
>> 
>> Thanks,
>> 
>> Douglas Duckworth, MSc, LFCS
>> HPC System Administrator
>> Scientific Computing Unit
>> Weill Cornell Medicine
>> 1300 York Avenue
>> New York, NY 10065
>> E: doug at med.cornell.edu
>> O: 212-746-6305
>> F: 212-746-8690
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>