Intel® DevCloud
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Not being able to run Gromacs on higher nodes

Writam
Beginner
1,188 Views
  • 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?
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9 Replies
AthiraM_Intel
Moderator
1,145 Views

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
Beginner
1,118 Views

Hi,

Thanks for your response.
I am using Intel DevCloud for oneAPI.
Thanks,
AthiraM_Intel
Moderator
1,071 Views

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
Moderator
1,013 Views

Hi,


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



Thanks.


Writam
Beginner
1,006 Views

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
Moderator
941 Views

Hi,


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



Thanks.


AthiraM_Intel
Moderator
870 Views

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
Moderator
771 Views

Hi,


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



Thanks.


AthiraM_Intel
Moderator
703 Views

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.


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