Not being able to run Gromacs on higher nodes

[Writam]

• I am running Gromacs software on Devcloud JupyterLab environment.
• I have downloaded Gromacs from https://ftp.gromacs.org/gromacs/gromacs-2021.3.tar.gz and installed using terminal following the installation guide  https://manual.gromacs.org/documentation/2021.3/install-guide/index.html

• tar xfz gromacs-2021.3.tar.gz
  cd gromacs-2021.3
  mkdir build
  cd build

  cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/u92385/GROMACS -S /home/u92385/GROMACS/gromacs-2021.3
  make
  make install

• I am creating the job file using command mpirun -np $n_cpus /home/u92385/Gromacs3/bin/gmx_mpi mdrun -ntomp 1 -v -deffnm em where em stands for em.tpr file I have uploaded as input file for Gromacs run commnad and submitting jobs through command !qsub -l nodes=3:ppn=2 hello-world-example where hello-world-example is theh job file written.
• It is running fine when nodes=2 in qsub command but Devcloud is restricting to use no of nodes >2. Whenever I am trying to run with nodes=3:ppn=2 in qsub command it returns an error like "qsub: submit error (Job exceeds queue resource limits MSG=job violates queue/server max resource limits)" .
• I want to run Gromacs on  higeher nodes.How to solve this issue and run Gromacs on nodes=3 and more?

[AthiraM_Intel]

Hi,

Thank you for posting in Intel Communities.

Could you please let us know whether you are using Intel DevCloud for oneAPI or Intel DevCloud for the Edge or DevCloud for FPGA ?

Thanks.

[Writam]

Hi,

Thanks for your response.

I am using Intel DevCloud for oneAPI.

Thanks,

[AthiraM_Intel]

Hi,

Thanks for the confirmation.

We are sorry you are experiencing issues using the DevCloud. We are working to optimize our queue policies to balance the needs of all users and currently we allow every user to run two jobs, one job running on two nodes simultaneously or two jobs each running on one node.

Hope this clarifies your query. If you need any further information, please let us know.

Thanks.

[AthiraM_Intel]

Hi,

We have not heard back from you. Could you please give us an update?

Thanks.

[Writam]

Hi,

I have understood that it has been restricted to use more than 2 nodes for job submission. It would be great if I get to know when I will be able to submit jobs in more than 2 nodes.

Thanks,

[AthiraM_Intel]

Hi,

We are checking on it internally, will let you know the updates soon.

Thanks.

[AthiraM_Intel]

Hi,

Sorry to inform you that, currently we allow every user to run two jobs, one job running on two nodes simultaneously or two jobs each running on one node. We are not planning to increase the limit as of now. We are sorry for the inconvenience.

If you have any further issue, please let us know.

Thanks

[AthiraM_Intel]

Hi,

Could you please give us an update? Is your query clarified?

Thanks.

[AthiraM_Intel]

Hi,

I have not heard back from you. This thread will no longer be monitored by Intel. If you need further assistance, please post a new question. 

Thanks.