Hi everyone!
I have been trying to run my simulation on BRAF server. However the script I am loading is not working. It shows the following error:
'Sbatch : error: This does not look like a batch script. The first
sbatch : error: line must start with #! followed by the path to an interpreter.
sbatch: error : for instance: #!/bin/sh
My script is as follows:
#! /bin/bash
#PBS -l node=1:ppn=12
#PBS -l walltime=120:00:00
#PBS -N conf_24
#PBS -q braf
#PBS -j oe
#PBS -V
#PBS -m n
#PBS -o stdout_file
#PBS -e stderr_file
cd $PBS_O_WORKDIR
export I_MPI_DEVICE=rdma
mpirun -np 16 /apps/gromacs/2020.3/mpich+gcc_10.2.0/gpu/gmx grompp_mpi -f step4.0_minimization.mdp -o conf24.tpr -c step3_input.pdb -r step3_input.gro
mpirun -np 16 /apps/gromacs/2020.3/mpich+gcc_10.2.0/gpu/gmx mdrun_mpi -v -deffnm conf24
Thanks and Regards
Dear Ravindra Singh Rawat
These links might be useful, have a look:
1. https://stackoverflow.com/questions/33488350/im-not-getting-an-error-message-in-my-qsub-error-log-even-though-im-running-in
2. https://wwwphy.princeton.edu//cluster/admin/tasks/pbs_error.html
3. https://docs.pace.gatech.edu/troubleshooting/ts_queue/
4. https://www.mathworks.com/matlabcentral/answers/98409-why-am-i-getting-a-qsub-directive-error-when-i-run-a-script-on-my-pbs-scheduler
5. http://www.definiteanswers.com/q/I-get-the-error-message-qsub-illegal-N-value-when-I-submit-a-PBS-job-What-does-this-mean-4d4a442cb5782
Kind Regards
Qamar Ul Islam
I'm not sure what it is about your script in particular that is throwing those errors, but the presence of "sbatch" indicates that the server is running Slurm (not PBS) as its job scheduling software. We recently made the transition from PBS to Slurm here at UMN, so maybe one of these references would be helpful:
https://www.msi.umn.edu/slurm/pbs-conversion
https://www.msi.umn.edu/content/job-submission-and-scheduling-slurm
Hi everyone
Thank you Krunalkumar Shah
, Matthew Joseph Michalska-Smith and Qamar Ul Islam for your kind suggestions. I have figured it out. The batch file that the server is running PBS so my script file should have"*.PBS" format instead of "*.sh". However I am now getting error that the directory for the "gmx_mpi" does not exist.- Badges
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