Hi,
I am trying to run virtualFlow in our lab workstation. When entered the command of ./vf_start_jobline.sh 1 5 templates/template1.slurm.sh submit 1, It showed error on line68(submit.sh:line 68: sbatch: command not found. Error in bash script submit.sh Error on line 68). Can you assist me?
Best,
Sen
Hello yasonson and welcome to the community!
As a first suggestion, you should turn verbosity_commands=standard to verbosity_commands=debug from your all.ctrl, repeat the run and analyze the resulting logs.
There is a very nice overview of the general approach one should take in case of encountering errors in our documentation:
https://docs.virtual-flow.org/documentation/-LdE8RH9UN4HKpckqkX3/troubleshooting#inspecting-log-files-and-workflow-files
Best,
Sorin
Hi Sorin,
Thank you for your reply. I have turned verbosity_commands=standard to verbosity_commands=debug from my all.ctrl, but it doesn’t work. It still shows error.
Best,
Sen
Hi yasonson,
The suggestion I made were not meant to fix the problem directly, but to allow you to evaluate the source of the problem (that is why I suggested consulting the logs after repeating the run).
Best,
Sorin
Hi Sorin,
I am trying to fix it but failed. Would you mind I give you a TeamViewer to assist me solve the problem. Thanks in advance .
Best,
Sen
Hi yasonson,
Did you fix this problem? I have the same issue.
Best,
Xianjie
Hi Xianjie,
Thanks for reaching out to me. Yes, I have run VirtualFlow on O2 cluster. You need to change partition=short of all.ctrl file.
Best,
Sen
Hi Xianjie,
I have the same issue. I tried to change partition = short of all.ctrl file but it did not work. Did you fix this problem?
Best,
RoseWoo
Hi Sorin,
I have the same issue. I found it that I need to change batchsystem=PBS. However, it still shows error. Is it any suggestion to fix this problem?
Thanks in advance.
Best,
RoseWoo
====================================================================
[baolu@blnode1 tools]$ ./vf_start_jobline.sh 1 5 templates/template1.pbs.sh submit 1
:: :: :: ::::. :::::: :: :: .::::. :: ::::: :: .::::. :: ::
:: :: :: :: :: :: :: :: :: :: :: :: :: :: :: :: :: ::
:::: :: :::. :: :: :: :::::: :: ::::: :: :: :: ::::::::
:: :: :: :: :: :::: :: :: :::: :: ::::: ‘::::’ :: ::
++ tr -d ‘[[:space:]]’
++ grep -m 1 ‘^batchsystem=’ …/workflow/control/all.ctrl
++ awk -F ‘[=#]’ ‘{print $2}’
batchsystem=PBS
echo ‘’
++ seq 1 5
for i in ‘$(seq ${start_jobline_no} ${end_jobline_no})’
cp templates/template1.pbs.sh …/workflow/job-files/main/1.job
sed -i ‘s/-1.1/-1.1/g’ …/workflow/job-files/main/1.job
cd helpers
. sync-jobfile.sh 1
++ ‘[’ 1 = -h ‘]’
++ [[ 1 -ne 1 ]]
++ trap ‘error_response_nonstd $LINENO’ ERR
++ jobline_no=1
++ controlfile=
+++ ls ‘…/…/workflow/control/-’
+++ true
++ ‘[’ -z ‘’ ‘]’
++ export controlfile=…/…/workflow/control/all.ctrl
++ controlfile=…/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^batchsystem=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ batchsystem=PBS
++ echo -e ‘Syncing the jobfile of jobline 1 with the controlfile file …/…/workflow/control/all.ctrl.’
Syncing the jobfile of jobline 1 with the controlfile file …/…/workflow/control/all.ctrl.
+++ grep -m 1 ‘^steps_per_job=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ steps_per_job_new=1
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
+++ grep -m 1 ’ -l nodes=’ …/…/workflow/job-files/main/1.job
++ job_line=’#PBS -l nodes=1:ppn=24’
++ steps_per_job_old=1:ppn=24
++ steps_per_job_old=1
++ sed -i s/nodes=1:/nodes=1:/g …/…/workflow/job-files/main/1.job
+++ grep -m 1 ‘^cpus_per_step=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ cpus_per_step_new=5
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
+++ grep -m 1 ’ -l nodes=’ …/…/workflow/job-files/main/1.job
++ job_line=’#PBS -l nodes=1:ppn=24’
++ cpus_per_step_old=24
++ sed -i s/ppn=24/ppn=5/g …/…/workflow/job-files/main/1.job
+++ cat …/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^timelimit=’
++ line=timelimit=05:00:00
+++ grep -m 1 ‘^timelimit=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ timelimit_new=05:00:00
++ ‘[’ PBS == SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
+++ grep -m 1 ‘^#PBS -l walltime=’ …/…/workflow/job-files/main/1.job
++ job_line=’#PBS -l walltime=00:12:00’
++ timelimit_old=00:12:00
++ sed -i s/00:12:00/05:00:00/g …/…/workflow/job-files/main/1.job
+++ cat …/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^partition=’
++ line=partition=shared
+++ grep -m 1 ‘^partition=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ partition_new=shared
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
++ sed -i ‘s/^#PBS -q .*/#PBS -q shared/g’ …/…/workflow/job-files/main/1.job
+++ cat …/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^job_letter=’
++ line=job_letter=t
+++ grep -m 1 ‘^job_letter=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ job_letter_new=t
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
++ sed -i ‘s/^#PBS -N [a-zA-Z]/#PBS -N t/g’ …/…/workflow/job-files/main/1.job
cd …
for i in ‘$(seq ${start_jobline_no} ${end_jobline_no})’
cp templates/template1.pbs.sh …/workflow/job-files/main/2.job
sed -i ‘s/-1.1/-2.1/g’ …/workflow/job-files/main/2.job
cd helpers
. sync-jobfile.sh 2
++ ‘[’ 2 = -h ‘]’
++ [[ 1 -ne 1 ]]
++ trap ‘error_response_nonstd $LINENO’ ERR
++ jobline_no=2
++ controlfile=
+++ ls ‘…/…/workflow/control/-’
+++ true
++ ‘[’ -z ‘’ ‘]’
++ export controlfile=…/…/workflow/control/all.ctrl
++ controlfile=…/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^batchsystem=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ batchsystem=PBS
++ echo -e ‘Syncing the jobfile of jobline 2 with the controlfile file …/…/workflow/control/all.ctrl.’
Syncing the jobfile of jobline 2 with the controlfile file …/…/workflow/control/all.ctrl.
+++ grep -m 1 ‘^steps_per_job=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ steps_per_job_new=1
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
+++ grep -m 1 ’ -l nodes=’ …/…/workflow/job-files/main/2.job
++ job_line=’#PBS -l nodes=1:ppn=24’
++ steps_per_job_old=1:ppn=24
++ steps_per_job_old=1
++ sed -i s/nodes=1:/nodes=1:/g …/…/workflow/job-files/main/2.job
+++ grep -m 1 ‘^cpus_per_step=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ cpus_per_step_new=5
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
+++ grep -m 1 ’ -l nodes=’ …/…/workflow/job-files/main/2.job
++ job_line=’#PBS -l nodes=1:ppn=24’
++ cpus_per_step_old=24
++ sed -i s/ppn=24/ppn=5/g …/…/workflow/job-files/main/2.job
+++ cat …/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^timelimit=’
++ line=timelimit=05:00:00
+++ grep -m 1 ‘^timelimit=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ timelimit_new=05:00:00
++ ‘[’ PBS == SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
+++ grep -m 1 ‘^#PBS -l walltime=’ …/…/workflow/job-files/main/2.job
++ job_line=’#PBS -l walltime=00:12:00’
++ timelimit_old=00:12:00
++ sed -i s/00:12:00/05:00:00/g …/…/workflow/job-files/main/2.job
+++ cat …/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^partition=’
++ line=partition=shared
+++ grep -m 1 ‘^partition=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ partition_new=shared
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
++ sed -i ‘s/^#PBS -q .*/#PBS -q shared/g’ …/…/workflow/job-files/main/2.job
+++ cat …/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^job_letter=’
++ line=job_letter=t
+++ grep -m 1 ‘^job_letter=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ job_letter_new=t
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
++ sed -i ‘s/^#PBS -N [a-zA-Z]/#PBS -N t/g’ …/…/workflow/job-files/main/2.job
cd …
for i in ‘$(seq ${start_jobline_no} ${end_jobline_no})’
cp templates/template1.pbs.sh …/workflow/job-files/main/3.job
sed -i ‘s/-1.1/-3.1/g’ …/workflow/job-files/main/3.job
cd helpers
. sync-jobfile.sh 3
++ ‘[’ 3 = -h ‘]’
++ [[ 1 -ne 1 ]]
++ trap ‘error_response_nonstd $LINENO’ ERR
++ jobline_no=3
++ controlfile=
+++ ls ‘…/…/workflow/control/-’
+++ true
++ ‘[’ -z ‘’ ‘]’
++ export controlfile=…/…/workflow/control/all.ctrl
++ controlfile=…/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^batchsystem=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ batchsystem=PBS
++ echo -e ‘Syncing the jobfile of jobline 3 with the controlfile file …/…/workflow/control/all.ctrl.’
Syncing the jobfile of jobline 3 with the controlfile file …/…/workflow/control/all.ctrl.
+++ grep -m 1 ‘^steps_per_job=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ steps_per_job_new=1
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
+++ grep -m 1 ’ -l nodes=’ …/…/workflow/job-files/main/3.job
++ job_line=’#PBS -l nodes=1:ppn=24’
++ steps_per_job_old=1:ppn=24
++ steps_per_job_old=1
++ sed -i s/nodes=1:/nodes=1:/g …/…/workflow/job-files/main/3.job
+++ grep -m 1 ‘^cpus_per_step=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ cpus_per_step_new=5
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
+++ grep -m 1 ’ -l nodes=’ …/…/workflow/job-files/main/3.job
++ job_line=’#PBS -l nodes=1:ppn=24’
++ cpus_per_step_old=24
++ sed -i s/ppn=24/ppn=5/g …/…/workflow/job-files/main/3.job
+++ cat …/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^timelimit=’
++ line=timelimit=05:00:00
+++ grep -m 1 ‘^timelimit=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ timelimit_new=05:00:00
++ ‘[’ PBS == SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
+++ grep -m 1 ‘^#PBS -l walltime=’ …/…/workflow/job-files/main/3.job
++ job_line=’#PBS -l walltime=00:12:00’
++ timelimit_old=00:12:00
++ sed -i s/00:12:00/05:00:00/g …/…/workflow/job-files/main/3.job
+++ cat …/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^partition=’
++ line=partition=shared
+++ grep -m 1 ‘^partition=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ partition_new=shared
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
++ sed -i ‘s/^#PBS -q .*/#PBS -q shared/g’ …/…/workflow/job-files/main/3.job
+++ cat …/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^job_letter=’
++ line=job_letter=t
+++ grep -m 1 ‘^job_letter=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ job_letter_new=t
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
++ sed -i ‘s/^#PBS -N [a-zA-Z]/#PBS -N t/g’ …/…/workflow/job-files/main/3.job
cd …
for i in ‘$(seq ${start_jobline_no} ${end_jobline_no})’
cp templates/template1.pbs.sh …/workflow/job-files/main/4.job
sed -i ‘s/-1.1/-4.1/g’ …/workflow/job-files/main/4.job
cd helpers
. sync-jobfile.sh 4
++ ‘[’ 4 = -h ‘]’
++ [[ 1 -ne 1 ]]
++ trap ‘error_response_nonstd $LINENO’ ERR
++ jobline_no=4
++ controlfile=
+++ ls ‘…/…/workflow/control/-’
+++ true
++ ‘[’ -z ‘’ ‘]’
++ export controlfile=…/…/workflow/control/all.ctrl
++ controlfile=…/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^batchsystem=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ batchsystem=PBS
++ echo -e ‘Syncing the jobfile of jobline 4 with the controlfile file …/…/workflow/control/all.ctrl.’
Syncing the jobfile of jobline 4 with the controlfile file …/…/workflow/control/all.ctrl.
+++ grep -m 1 ‘^steps_per_job=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ steps_per_job_new=1
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
+++ grep -m 1 ’ -l nodes=’ …/…/workflow/job-files/main/4.job
++ job_line=’#PBS -l nodes=1:ppn=24’
++ steps_per_job_old=1:ppn=24
++ steps_per_job_old=1
++ sed -i s/nodes=1:/nodes=1:/g …/…/workflow/job-files/main/4.job
+++ grep -m 1 ‘^cpus_per_step=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ cpus_per_step_new=5
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
+++ grep -m 1 ’ -l nodes=’ …/…/workflow/job-files/main/4.job
++ job_line=’#PBS -l nodes=1:ppn=24’
++ cpus_per_step_old=24
++ sed -i s/ppn=24/ppn=5/g …/…/workflow/job-files/main/4.job
+++ cat …/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^timelimit=’
++ line=timelimit=05:00:00
+++ grep -m 1 ‘^timelimit=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ timelimit_new=05:00:00
++ ‘[’ PBS == SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
+++ grep -m 1 ‘^#PBS -l walltime=’ …/…/workflow/job-files/main/4.job
++ job_line=’#PBS -l walltime=00:12:00’
++ timelimit_old=00:12:00
++ sed -i s/00:12:00/05:00:00/g …/…/workflow/job-files/main/4.job
+++ cat …/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^partition=’
++ line=partition=shared
+++ grep -m 1 ‘^partition=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ partition_new=shared
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
++ sed -i ‘s/^#PBS -q .*/#PBS -q shared/g’ …/…/workflow/job-files/main/4.job
+++ cat …/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^job_letter=’
++ line=job_letter=t
+++ grep -m 1 ‘^job_letter=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ job_letter_new=t
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
++ sed -i ‘s/^#PBS -N [a-zA-Z]/#PBS -N t/g’ …/…/workflow/job-files/main/4.job
cd …
for i in ‘$(seq ${start_jobline_no} ${end_jobline_no})’
cp templates/template1.pbs.sh …/workflow/job-files/main/5.job
sed -i ‘s/-1.1/-5.1/g’ …/workflow/job-files/main/5.job
cd helpers
. sync-jobfile.sh 5
++ ‘[’ 5 = -h ‘]’
++ [[ 1 -ne 1 ]]
++ trap ‘error_response_nonstd $LINENO’ ERR
++ jobline_no=5
++ controlfile=
+++ ls ‘…/…/workflow/control/-’
+++ true
++ ‘[’ -z ‘’ ‘]’
++ export controlfile=…/…/workflow/control/all.ctrl
++ controlfile=…/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^batchsystem=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ batchsystem=PBS
++ echo -e ‘Syncing the jobfile of jobline 5 with the controlfile file …/…/workflow/control/all.ctrl.’
Syncing the jobfile of jobline 5 with the controlfile file …/…/workflow/control/all.ctrl.
+++ grep -m 1 ‘^steps_per_job=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ steps_per_job_new=1
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
+++ grep -m 1 ’ -l nodes=’ …/…/workflow/job-files/main/5.job
++ job_line=’#PBS -l nodes=1:ppn=24’
++ steps_per_job_old=1:ppn=24
++ steps_per_job_old=1
++ sed -i s/nodes=1:/nodes=1:/g …/…/workflow/job-files/main/5.job
+++ grep -m 1 ‘^cpus_per_step=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ cpus_per_step_new=5
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
+++ grep -m 1 ’ -l nodes=’ …/…/workflow/job-files/main/5.job
++ job_line=’#PBS -l nodes=1:ppn=24’
++ cpus_per_step_old=24
++ sed -i s/ppn=24/ppn=5/g …/…/workflow/job-files/main/5.job
+++ cat …/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^timelimit=’
++ line=timelimit=05:00:00
+++ grep -m 1 ‘^timelimit=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ timelimit_new=05:00:00
++ ‘[’ PBS == SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
+++ grep -m 1 ‘^#PBS -l walltime=’ …/…/workflow/job-files/main/5.job
++ job_line=’#PBS -l walltime=00:12:00’
++ timelimit_old=00:12:00
++ sed -i s/00:12:00/05:00:00/g …/…/workflow/job-files/main/5.job
+++ cat …/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^partition=’
++ line=partition=shared
+++ grep -m 1 ‘^partition=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ partition_new=shared
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
++ sed -i ‘s/^#PBS -q .*/#PBS -q shared/g’ …/…/workflow/job-files/main/5.job
+++ cat …/…/workflow/control/all.ctrl
+++ grep -m 1 ‘^job_letter=’
++ line=job_letter=t
+++ grep -m 1 ‘^job_letter=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ job_letter_new=t
++ ‘[’ PBS = SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
++ sed -i ‘s/^#PBS -N [a-zA-Z]/#PBS -N t/g’ …/…/workflow/job-files/main/5.job
cd …
echo ‘’
[[ submit = \s\u\b\m\i\t ]]
cd helpers
++ seq 1 5
for i in ‘$(seq ${start_jobline_no} ${end_jobline_no})’
. submit.sh …/workflow/job-files/main/1.job
++ usage=’# Usage: . submit jobfile [quiet]’
++ ‘[’ …/workflow/job-files/main/1.job == -h ‘]’
++ [[ 1 -ne 1 ]]
++ trap ‘error_response_nonstd $LINENO’ ERR
+++ grep -m 1 ‘^batchsystem=’ …/…/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ batchsystem=PBS
++ jobfile=…/workflow/job-files/main/1.job
+++ echo …/workflow/job-files/main/1.job
+++ awk -F ‘[./]’ ‘{print $(NF-1)}’
++ jobline=1
++ cd …/
++ ‘[’ PBS == SLURM ‘]’
++ [[ PBS = \T\O\R\Q\U\E ]]
++ [[ PBS = \P\B\S ]]
++ msub …/workflow/job-files/main/1.job
submit.sh: line 70: msub: command not found
+++ error_response_nonstd 70
+++ echo ‘Error was trapped which is a nonstandard error.’
+++ tee -a /dev/stderr
Error was trapped which is a nonstandard error.
Error was trapped which is a nonstandard error.
+++ tee -a /dev/stderr
++++ basename submit.sh
+++ echo ‘Error in bash script submit.sh’
Error in bash script submit.sh
Error in bash script submit.sh
+++ echo ‘Error on line 70’
+++ tee -a /dev/stderr
Error on line 70
Error on line 70
+++ exit 1