Create and submit a job - Elastic High Performance Computing

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

Log on to the E-HPC console.
In the top navigation bar, select a region.
On the Cluster page, find gromacs-test and click Connect.
In the Connect panel, specify a username, password, and port number for gromacs-test. Then, click Connect via SSH.

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

On the Cluster page of the E-HPC console, find gromacs-test and click Connect.
On the Job page, click the Submit Job tab.
On the Submit Job tab, set Job Template to pbs demo.

Configure the job and click Submit Job.

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.

Find the job and 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 at which the job is last updated, and job running information.

What to do next

View the performance and result of a job