Assuming the GUI produced script is as you indicated (I am not sure where you got the script you showed, but if it is not the actual script used by a job it might be worthwhile to examine the Command= file from scontrol show job to verify), then the only thing that should be different from a GUI submission and a manual submission is the submission environment. Does the manual submission work if you add --export=NONE to the sbatch command to prevent the exporting of environment variables? And maybe add a printenv to the script to see what environment is in both cases. Though I confess I am unable to think of any reasonable environmental setting that might cause the observed symptoms.
On Fri, Mar 22, 2019 at 11:23 AM Prentice Bisbal <pbis...@pppl.gov> wrote: > On 3/21/19 6:56 PM, Reuti wrote: > > Am 21.03.2019 um 23:43 schrieb Prentice Bisbal: > > > >> Slurm-users, > >> > >> My users here have developed a GUI application which serves as a GUI > interface to various physics codes they use. From this GUI, they can submit > jobs to Slurm. On Tuesday, we upgraded Slurm from 18.08.5-2 to > 18.08.6-2,and a user has reported a problem when submitting Slurm jobs > through this GUI app that do not occur when the same sbatch script is > submitted from sbatch on the command-line. > >> > >> […] > >> When I replaced the mpirun command with an equivalent srun command, > everything works as desired, so the user can get back to work and be > productive. > >> > >> While srun is a suitable workaround, and is arguably the correct way to > run an MPI job, I'd like to understand what is going on here. Any idea what > is going wrong, or additional steps I can take to get more debug > information? > > Was an alias to `mpirun` introduced? It may cover the real application > and even the `which mpirun` will return the correct value, but never be > executed. > > > > $ type mpirun > > $ alias mpirun > > > > may tell in the jobscript. > > > Unfortunately, the script is in tcsh, so the 'type' command doesn't work > since, it's a bash built-in function. I did use the 'alias' command to > see all the defined aliases, and mpirun and mpiexec are not aliased. Any > other ideas? > > Prentice > > > > > -- Tom Payerle DIT-ACIGS/Mid-Atlantic Crossroads paye...@umd.edu 5825 University Research Park (301) 405-6135 University of Maryland College Park, MD 20740-3831
