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Working in The IITJ HPC System

This guide provides information on the IITJ HPC system software, including the operating system RHEL 6.9, job management system PBS with Torque, MPI libraries, Intel/GNU compilers, SSH login, Linux commands, job submission and monitoring, and OpenMP programming.

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Working in The IITJ HPC System

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  1. Working in The IITJ HPC System

  2. Software List Operating System RHEL 6.9 Job Management System Portable Batch System (pbs) PBS with torque Compilers, Languages Intel Fortran/C/C++ Compiler for Linux V11 GNU :Fortran/C/C++ Compiler 2

  3. Message Passing Interface (MPI) Libraries MVAPICH OPEN MPI 3

  4. Hostnames Master node (Use for Job Submit) hpc-login (192.168.1.33) Compute nodes node01 ........node42 4

  5. Basic login Remote login to the master node Terminal login using secure shell ssh –X username@192.168.1.33 Login From Windows Host PuTTY & Mobaxterm e.g. 5

  6. Login from Windows Host Using PuTTY to setup a secured connection: Host Name=192.168.1.33 6

  7. Linux commands Both master and compute nodes are installed with Linux Frequently used Linux command in HPC cluster 7

  8. Job Submission Procedure Prepare and compile a program, e.g. mpicc –o hello hello.c Prepare a job submission script, e.g. Qhello.pbs Submit the job using qsub. e.g. qsub Qhello.pbs Note the jobID. Monitor with qstat Examine the error and output file. e.g. hello.oJobID, hello.eJobID 8

  9. Compiling & Running MPI Programs • Using Openmpi • Setting path, at the command prompt, type: export PATH=/opt/openmpi/bin:$PATH • Compile using mpicc, mpiCC, mpif77 or mpif90, e.g. mpicc –o hello hello.c • Prepare hostfile (e.g. machines) number of compute nodes: hpc-login node01 node02 node03 • Run the program with a number of processor node: mpirun –np 4 –hostfile machines ./hello 9

  10. Prepare parallel job script, Qhello.pbs #!/bin/sh ### Job name #PBS -N hello #PBS -q large #PBS -l nodes=2:ppn=12 #PBS -l walltime=700:00:00 #PBS -e error #PBS -o output cd $PBS_O_WORKDIR mpirun –np 24 -machinefile $PBS_NODEFILE <Your executable PATH> <-any option> <Your input file name> <Your output file name> 10

  11. Job submission and monitoring • Submit the job qsub <your job submit file> • Note the jobID. e.g. 15238.NAME • Monitor by qstat. e.g qstat 15238 Job id Name User Time Use S Queue ------------------------- ---------------- --------------- -------- - ----- 15238.hpc-login hello test 0 R large

  12. Job monitoringShow the status of submitted jobs • qstat: • Delete jobID by qdel. e.g. qdel<JobID>

  13. OpenMP The OpenMP Application Program Interface (API) supports multi-platform shared-memory parallel programming in C/C++ and Fortran on all architectures, including Unix platforms and Windows NT platforms. Jointly defined by a group of major computer hardware and software vendors. OpenMP is a portable, scalable model that gives shared-memory parallel programmers a simple and flexible interface for developing parallel applications for platforms ranging from the desktop to the supercomputer. 13

  14. Sample openmp example #include <omp.h> #include <stdio.h> int main() { #pragma omp parallelprintf("Hello from thread %d, nthreads %d\n", omp_get_thread_num(),omp_get_num_threads()); } 14

  15. Good Practice in using IITJ HPC • Every user shall apply for his/her own computer user account to login to the master node of the HPC • The account must not be shared his/her account and password with the other users. • Every user must deliver jobs to the HPC cluster from the master node (hpc-login via the PBS (qsub) job queuing system. Automatically dispatching of job using scripts are not allowed. • Foreground jobs on the HPC cluster are restricted to program testing and the time duration should not exceed 1 minutes CPU time per job.

  16. Good Practice in using IITJ HPC • logout from the master node/compute nodes after use • delete unused files or compress temporary data • estimate the walltime for running jobs and acquire just enough walltime for running. • never run foreground job within the master node and the compute node • report abnormal behaviors.

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