Dear virtualFlow community guys:
Nowdays, I ran into problems in VFVS. When I ran the programm ,the reports seemed normal, while when I checked with slurm command sacct ,which showed FAILED. The job.out read "Error was trapped Error in bash script one-step.sh Error on line 156 ". I check the code in one-step.sh, which locate in
"# Checking if all queues exited without error (“wait” waits for all of them, but always returns 0)
exit_code=0
for pid in ${pids[@]}; do
wait $pid || let “exit_code=1”
done
if [ “$exit_code” == “1” ]; then error_response_std $LINENO
fi
"
I have no idea what is wrong with this issue, can anyone tell me how to fix it?
the documents about this issue was loaded, and thanks a lot?
Hi, Oliv,
I changed the value of time by deleting “+%-N *10000” on line 183,194, 859 in one-queue.sh in the tools/templates folder. The job ran completed when checked by ./vf_report.sh command. While i have no idea how it works, you can try this. Also, I had anther problem as i discripted in the post. If you fixed the code, please tell me!
Thanks for the clarification.
I do get the same error in my out files:
* Trying to stop this queue and causing the jobline to fail...
srun: error: dancingfish: task 0: Exited with exit code 1
Error was trapped
Error in bash script /var/spool/slurm/slurmd/job00117/slurm_script
Error on line 298
I would not worry about it because your jobs run through, your ligands are docked, and this exit code 1 comes only at the end of one-steph.sh.
Hi, Oliv,
I was not perfect in VFVS code system, but I wanna find the problems with you.
first, I recommand you to check the slurm system when running jobs, with the command
“systemctl status slurmd.service” ,and “systemctl status slurmctld.service”.
If they work well, please send me the slurm_script, which can be found when the job is running, I will check if the traps are the one I had met.
