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Create and submit a job

Last Updated: Sep 03, 2021

This topic provides a quick start for creating a job in the Elastic High Performance Computing (E-HPC). In this topic, a job that simulates the motion of water molecules is created.

Prerequisites

A user is created. For more information, see Create a user.

Procedure

  1. Log on to the E-HPC console.

  2. In the top navigation bar, select a region.

  3. On the Cluster page, find gromacs-test, and click Job.

  4. In the Connect panel, specify a username, password, and port number for gromacs-test. Then, click Connect via SSH.

  5. Download and decompress the file of the example.

    Note

    This example is a simulation of water molecules. It is used to track the motion of water molecules in a specific space at a specified temperature.

    cd /home/gmx.test;
    wget https://public-ehpc-package.oss-cn-hangzhou.aliyuncs.com/water_GMX50_bare.tar.gz;
    tar xzvf water_GMX50_bare.tar.gz;
    chown -R gmx.test water-cut1.0_GMX50_bare;
    chgrp -R users water-cut1.0_GMX50_bare
  6. On the Cluster page of the E-HPC console, find gromacs-test, and click Connect.

  7. On the Job page, click Create Job.

  8. On the Create Job page, choose Create File > Template > pbs demo.

  9. Configure the job, as shown in the following figure. Then, click OK to submit the job.

    GROMACS job The following sample file shows how to configure a job file:

    Note

    In this example, a job is submitted by the user named gmx.test. This job is run on compute000, a compute node that contains eight vCPUs and one P100 GPU card. You can modify the cluster configurations based on the actual scenario.

    #!/bin/sh
    #PBS -j oe
    #PBS -l select=1:ncpus=8:mpiprocs=4
    #PBS -q workq
    
    export MODULEPATH=/opt/ehpcmodulefiles/   # The environment variables on which the module command depends.
    module load gromacs-gpu/2018.1
    module load openmpi/3.0.0
    module load cuda-toolkit/9.0
    export OMP_NUM_THREADS=1
    
    cd /home/gmx.test/water-cut1.0_GMX50_bare/0096
    /opt/gromacs-gpu/2018.1/bin/gmx_mpi grompp -f pme.mdp -c conf.gro -p topol.top -o topol_pme.tpr   # Preprocess the job file to generate a TPR input file.
    
    mpirun -np 4 /opt/gromacs-gpu/2018.1/bin/gmx_mpi mdrun -ntomp 1 -nsteps 100000 -pin on -s topol_pme.tpr   # In this case, -ntomp specifies the number of OpenMP threads associated with each process, and -nsteps specifies the number of iteration steps in the simulation.

Result

After you create and submit a job, you can view it on the Job page.

Click Details in the Actions column. In the Job Details panel, you can view the job details, including the job name, job ID, start time, the time when the job was last updated, and job running information.

Related operations

You can view the performance and result of the job. For more information, see View the performance and result of a job.