Problem with slurm

[vishal.rossi]

Hi,
Does anybody here has an experience of submitting jobs with slurm scheduler.
My code is like this (an example) :
#########################################
#!/bin/bash -l
#SBatch -p default
#SBatch -N 1
#SBatch -n 1
#SBatch --mem-per-cpu=5gb
#SBatch --cpus-per-task=1
#SBatch -t 00:02:00

inp1=$inp
sid=$id
echo inp1:$inp1
echo sid:$sid

python /sw/conifer_v0.2.2/conifer.py rpkm --probes /sw/conifer_v0.2.2/sampledata/probes.txt --input $inp1 --output /conifer/control/rpkm/$sid.rpkm.txt
############################################

It's saved as script.sh.
I call the script from the terminal using :
sbatch script.sh inp AID2831_SID6849_21909_normal.Improved.bam id AID2831_SID6849_21909_normal

The code runs and then fails as it says that it couldn't find the input file.
even echo inp1:$inp1 shows that it's empty.
But when I hard code the inp and id in the code, I am able to run the script.


Does anyone knows where I am going wrong.

Thanks in advance.

Regards
Vishal

[dpryan]

N.B., this issue actually has nothing to do with slurm, you'd have the same issue just directly starting the script.

I'm not surprised that that's not working. Before getting to the actual issue, is there a reason you're invoking bash as a login shell in the shebang?

Anyway, the actual cause of your problem is that you don't initialize $inp and $id to anything. From how you invoke the script, I suspect that you believe that separating the arguments by a variable name in the script will take care of this. It won't. What you want is something like:

#!/bin/bash -l
#SBatch -p default
#SBatch -N 1
#SBatch -n 1
#SBatch --mem-per-cpu=5gb
#SBatch --cpus-per-task=1
#SBatch -t 00:02:00

inp1=$1
sid=$2

srun /sw/conifer_v0.2.2/conifer.py rpkm --probes /sw/conifer_v0.2.2/sampledata/probes.txt --input $inp1 --output /conifer/control/rpkm/$sid.rpkm.txt

And then invoke it like:

 sbatch script.sh AID2831_SID6849_21909_normal.Improved.bam AID2831_SID6849_21909_normal

I took the liberty of adding an srun into the script, which you'll probably need. BTW, your output path is probably wrong. At least if I were the sysadmin, there's no way I would allow a user to write anywhere on the system outside of ~ or /tmp (with the exception of a shared mount point on all of the nodes if that's not ~ (it's $WORK on our cluster, for example)).

[vishal.rossi]

Thanks

Hi Devon,

Thanks a lot for your help. The script runs perfectly well after your helpful suggestions.
when the cluster computer was on PBS/Torque, I was able to use
inp1=$inp
sid=$id

Didn't know that I have to use it in a different way on slurm.
By the way, I didn't use srun before my script but even then it's working well.

Regards
Vishal