1 / 51

Seminar for

Seminar for. New Cluster Users 18 May, 2010 High Performance Cluster Computing Centre (HPCCC) Faculty of Science Hong Kong Baptist University. Outline. Hardware configurations Recent Software Installed Basic Login and job submission procedure Parallel Program Examples

aliya
Download Presentation

Seminar for

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Seminar for New Cluster Users 18 May, 2010 High Performance Cluster Computing Centre (HPCCC) Faculty of Science Hong Kong Baptist University

  2. Outline Hardware configurations Recent Software Installed Basic Login and job submission procedure Parallel Program Examples Policy for usingsciblade.sci.hkbu.edu.hk Acknowledgement http://www.sci.hkbu.edu.hk/hpccc/sciblade 2

  3. Latest Cluster Hardware configurations

  4. Cluster Hardware This 256-node PC cluster (sciblade) consist of: Master node x 2 IO nodes x 3 (storage) Compute nodes x 256 Blade Chassis x 16 Management network Interconnect fabric 1U console & KVM switch Emerson Liebert Nxa 120k VA UPS 4

  5. Sciblade Cluster 256-node clusters supported by fund from RGC 5

  6. Hardware Configuration Master Node Dell PE1950, 2x Xeon E5450 3.0GHz (Quad Core) 16GB RAM, 73GB x 2 SAS drive IO nodes (Storage) Dell PE2950, 2x Xeon E5450 3.0GHz (Quad Core) 16GB RAM, 73GB x 2 SAS drive 3TB storage Dell PE MD3000 Compute nodes x 256 each Dell PE M600 blade server w/ Infiniband network 2x Xeon E5430 2.66GHz (Quad Core) 16GB RAM, 73GB SAS drive 6

  7. Hardware Configuration Blade Chassis x 16 Dell PE M1000e Each hosts 16 blade servers Management Network Dell PowerConnet 6248 (Gigabit Ethernet) x 6 Inerconnect fabric Qlogic SilverStorm 9120 switch Console and KVM switch Dell AS-180 KVM Dell 17FP Rack console Emerson Liebert Nxa 120kVA UPS 7

  8. Software List Operating System ROCKS 5.1 Cluster OS CentOS 5.3 kernel 2.6.18 Job Management System Portable Batch System MAUI scheduler Compilers, Languages Intel Fortran/C/C++ Compiler for Linux V11 GNU 4.1.2/4.4.0 Fortran/C/C++ Compiler 8

  9. Software List Message Passing Interface (MPI) Libraries MVAPICH 1.1 MVAPICH2 1.2 OPEN MPI 1.3.2 Mathematic libraries ATLAS 3.8.3 FFTW 2.1.5/3.2.1 SPRNG 2.0a(C/Fortran) /4.0(C++/Fortran) ScaLAPACK 1.8.0 9

  10. Software List • Molecular Dynamics & Quantum Chemistry • Gamess 2009R1 • Gaussian 03 • Gromacs 4.0.7 • LAMMPS • Namd 2.7b1 • Siesta 3.0b • Third-party Applications • MATLAB 2008b with pmatlab • TAU 2.18.2, VisIt 1.11.2 • Xmgrace 5.1.22 10

  11. Software List Queuing system Torque/PBS Maui scheduler Editors vi emacs 11

  12. Hostnames Master node External : sciblade.sci.hkbu.edu.hk Internal : frontend-0 IO nodes (storage) pvfs2-io-0-0, pvfs2-io-0-1, pvfs-io-0-2 Compute nodes compute-0-0.local, …, compute-0-255.local 12

  13. Basic Login and Job Submission Procedure

  14. Basic login Remote login to the master node Terminal login using secure shell ssh -l username sciblade.sci.hkbu.edu.hk Graphical login PuTTY & vncviewer e.g. [username@sciblade]$ vncserver New ‘sciblade.sci.hkbu.edu.hk:3 (username)' desktop is sciblade.sci.hkbu.edu.hk:3 It means that your session will run on display 3. 14

  15. Graphical login Using PuTTY to setup a secured connection: Host Name=sciblade.sci.hkbu.edu.hk 15

  16. Graphical login (con’t) ssh protocol version 16

  17. Graphical login (con’t) Port 5900 +display numbe (i.e. 3 in this case) 17

  18. Graphical login (con’t) Next, click Open, and login to sciblade Finally, run VNC Viewer on your PC, and enter "localhost:3" {3 is the display number} You should terminate your VNC session after you have finished your work. To terminate your VNC session running on sciblade, run the command [username@tdgrocks] $ vncserver –kill : 3 18

  19. Linux commands Both master and compute nodes are installed with Linux Frequently used Linux command in PC cluster http://www.sci.hkbu.edu.hk/hpccc/sciblade/faq_sciblade.php 19

  20. ROCKS specific commands ROCKS provides the following commands for users to run programs in all compute node. e.g. cluster-fork Run program in all compute nodes cluster-fork ps Check user process in each compute node cluster-kill Kill user process at one time tentakel Similar to cluster-fork but run faster 20

  21. Ganglia • Web based management and monitoring • http://sciblade.sci.hkbu.edu.hk/ganglia 21

  22. Job Submission Procedures

  23. 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 showq or qstat Examine the error and output file. e.g. hello.oJobID, hello.eJobID 23

  24. Sample Program: hello.c #include <stdio.h> #include “mpi.h” // MPI compiler header file void main(int argc, char **argv) { int nproc,myrank,ierr; ierr=MPI_Init(&argc,&argv); // MPI initialization // Get number of MPI processes MPI_Comm_size(MPI_COMM_WORLD,&nproc); // Get process id for this processor MPI_Comm_rank(MPI_COMM_WORLD,&myrank); printf (“Hello World!! I’m process %d of %d\n”,myrank,nproc); ierr=MPI_Finalize(); // Terminate all MPI processes } 24

  25. Compiling & Running MPI Programs • Using mvapich 1.1 • Setting path, at the command prompt, type: export PATH=/u1/local/mvapich1/bin:$PATH (uncomment this line in .bashrc) • Compile using mpicc, mpiCC, mpif77 or mpif90, e.g. mpicc –o hello hello.c • Prepare hostfile (e.g. machines) number of compute nodes: compute-0-0 compute-0-1 compute-0-2 compute-0-3 • Run the program with a number of processor node: mpirun –np 4 –machinefile machines ./hello 25

  26. Prepare parallel job script, Qhello.pbs #!/bin/sh ### Job name #PBS -N hello ### Declare job non-rerunable #PBS -r n #PBS -l nodes=20 #PBS -l walltime=00:08:00 # This job's working directory cd $PBS_O_WORKDIR echo Running on host `hostname` echo Time is `date` echo Directory is `pwd` echo This jobs runs on the following processors: echo `cat $PBS_NODEFILE` # Define number of processors NPROCS=`wc -l < $PBS_NODEFILE` echo This job has allocated $NPROCS nodes # Run the parallel MPI executable “hello" /u1/local/mvapich1/bin/mpirun -v -machinefile $PBS_NODEFILE -np $NPROCS ./hello 26

  27. Job submission and monitoring • Submit the job qsub Qhello.pbs • Note the jobID. e.g. 15238.sciblade2.sci.hkbu.edu.hk • Monitor by qstat. e.g qstat 15238 Job id Name User Time Use S Queue ------------------------- ---------------- --------------- -------- - ----- 15238.sciblade2 hello morris 0 R default

  28. Job monitoring • Show the status of submitted jobs showq 13896 dhhe Running 16 INFINITY Mon May 3 04:48:25 14402 dhhe Running 16 INFINITY Wed May 5 23:46:09 14403 dhhe Running 16 INFINITY Wed May 5 23:47:07 67 Active Jobs 2012 of 2024 Processors Active (99.41%) 253 of 253 Nodes Active (100.00%) IDLE JOBS---------------------- JOBNAME USERNAME STATE PROC WCLIMIT QUEUETIME 0 Idle Jobs BLOCKED JOBS---------------- JOBNAME USERNAME STATE PROC WCLIMIT QUEUETIME 14951 ggl Idle 32 4:00:00:00 Mon May 10 00:55:19 15011 justin Idle 32 7:00:00:00 Mon May 10 15:48:36 15098 hkbu09 Idle 50 33:08:00:00 Tue May 11 11:46:45 • Delete jobID by qdel. e.g. qdel 15238

  29. Assorted Program Examples

  30. Example codes • Updated example codes have been stored in /u1/local/share/examples/ • Copy all codes in one file /u1/local/share/examples.tar.gz • Unzip and Untar using tar xzvf examples.tar.gz

  31. Example 1: OpenMP /u1/local/share/examples/omp

  32. 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. 32

  33. OpenMP compiler choice gcc 4.40 or above compile with -fopenmp Intel 10.1 or above compile with –Qopenmp on Windows compile with –openmp on linux PGI compiler compile with –mp Absoft Pro Fortran compile with -openmp 33

  34. 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()); } 34

  35. serial-pi.c #include <stdio.h> static long num_steps = 10000000; double step; int main () { int i; double x, pi, sum = 0.0; step = 1.0/(double) num_steps; for (i=0;i< num_steps; i++){ x = (i+0.5)*step; sum = sum + 4.0/(1.0+x*x); } pi = step * sum; printf("Est Pi= %f\n",pi); } 35

  36. Openmp version of spmd-pi.c #include <omp.h> #include <stdio.h> static long num_steps = 10000000; double step; #define NUM_THREADS 8 int main () { int i, nthreads; double pi, sum[NUM_THREADS]; step = 1.0/(double) num_steps; omp_set_num_threads(NUM_THREADS); #pragma omp parallel { int i, id,nthrds; double x; id = omp_get_thread_num(); nthrds = omp_get_num_threads(); if (id == 0) nthreads = nthrds; for (i=id, sum[id]=0.0;i< num_steps; i=i+nthrds) { x = (i+0.5)*step; sum[id] += 4.0/(1.0+x*x); } } for(i=0, pi=0.0;i<nthreads;i++) pi += sum[i] * step; printf("Est Pi= %f using %d threads \n",pi,nthreads); } 36

  37. Submit parallel jobs into torque batch queue • Prepare a job script, say omp.pbs like the following #!/bin/sh ### Job name #PBS -N OMP-spmd ### Declare job non-rerunable #PBS -r n ### Mail to user ##PBS -m ae ### Queue name (small, medium, long, verylong) ### Number of nodes #PBS -l nodes=1:ppn=8 #PBS -l walltime=00:08:00 cd $PBS_O_WORKDIR export OMP_NUM_THREADS=8 ./omp_hello ./omp_test ./serial-pi ./omp-spmd-pi • Submit it using qsub qsub omp.pbs 37

  38. Example 2: Gaussian and Linda • Example directory: /u1/local/share/examples/g03/h2o • Gaussian .com file: h2o.com %nproclinda=4 %chk=water.chk # opt freq b3lyp/6-311+g(3df,2p) geom=connectivity test 0 1 O H 1 B1 H 1 B2 2 A1 B1 0.98000000 B2 0.98000000 A1 109.00000000 1 2 1.0 3 1.0 2 3

  39. Gaussian and Linda (Cont) • PBS scripts for running Gaussian 03: h2o.bat #!/bin/csh #PBS -l nodes=8:ppn=1 #PBS -r n #PBS -N h2o #PBS -e h2otest.err #PBS -o h2otest.log #PBS -m ae #PBS -q default #PBS -l walltime=168:00:00 # This job's working directory echo Working directory is $PBS_O_WORKDIR cd $PBS_O_WORKDIR setenv OMP_NUM_THREADS 4 setenv MKL_SERIAL no setenv GAUSS_LFLAGS "+v -nodefile ${PBS_NODEFILE}" g03l < h2o.com > h2o.log • Submit the pbs job by qsub qsub h2o.bat

  40. Example 3: Siesta 3.0b • Spanish Initiative for Electronic Simulations with Thousands of Atoms • perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. • Project website: http://www.icmab.es/siesta • Example directory: /u1/local/share/examples/siesta/h2o

  41. Siesta example input file h2o.fdf • Input file: Flexible data format (FDF), e.g. h2o.fdf SystemName Water molecule SystemLabel h2o NumberOfAtoms 3 NumberOfSpecies 2 %block ChemicalSpeciesLabel 1 8 O # Species index, atomic number, species label 2 1 H %endblock ChemicalSpeciesLabel AtomicCoordinatesFormat Ang %block AtomicCoordinatesAndAtomicSpecies 0.000 0.000 0.000 1 0.757 0.586 0.000 2 -0.757 0.586 0.000 2 %endblock AtomicCoordinatesAndAtomicSpecies

  42. Siesta sample pbs file h2o.pbs #!/bin/bash #PBS -N siesta-h2o #PBS -l nodes=8 #PBS -l walltime=6:00:00 #PBS -l pmem=512mb NCPU=`wc -l < $PBS_NODEFILE` cd $PBS_O_WORKDIR MPIPATH=/u1/local/mvapich2/bin ${MPIPATH}/mpirun_rsh -np ${NCPU} -hostfile ${PBS_NODEFILE} /u1/local/bin/siesta < h2o.fdf • Submit the above h2o.pbs using qsub • qsub h2o.pbs

  43. Example 4: pmatlab • Pmatlab developed by MIT Lincoln Laboratory • Installed with MATLAB 2008b • Example directory: /u1/local/share/examples/pmatlab • Startup.m : matlab startup file • RUN.m : control file for running in compute nodes • sample_app.m : main program • Qpmatlab.pbs : submit script

  44. Pmatlab : idea of distributed matrix • New data type: dmat • Overload functions: zeros, ones, rand, with an additional parameter Map • Map tell pmatlab how and where dmat must be distributed • Four components: • Grids, e.g [2 3], 2 x 3 grids • Distributions: • block – contiguous block of data • Cyclic – data are interleaved with processors • Block cyclic • Processor lists, e.g. [0:nCPUs]

  45. Pmatlab: examples of map grid

  46. 0 Example: Prime prime/prime.c prime/prime.f90 prime/primeParallel.c prime/Makefile prime/machines Compile by the command: make Run the serial program by ./primeC or ./primeF Run the parallel program by mpirun –np 4 –machinefile machines ./primeMPI Example: Ring ring/ring.c ring/Makefile ring/machines Compile program by the command: make Run the program in parallel by mpirun –np 4 –machinefile machines ./ring < in 3 1 2 Example: mcPi mcPi/mcPi.c mcPi/mc-Pi-mpi.c mcPi/Makefile mcPi/QmcPi.pbs Compile by the command:make Run the serial program by: ./mcPi ## Submit job to PBS queuing system by qsub QmcPi.pbs Example: Sorting sorting/qsort.c sorting/bubblesort.c sorting/script.sh sorting/qsort sorting/bubblesort Submit job to PBS queuing system by qsub script.sh 46

  47. Policy for using sciblade.sci.hkbu.edu.hk

  48. Policy • Every user shall apply for his/her own computer user account to login to the master node of the PC cluster, sciblade.sci.hkbu.edu.hk. • The account must not be shared his/her account and password with the other users. • Every user must deliver jobs to the PC cluster from the master node via the PBS job queuing system. Automatically dispatching of job using scripts or robots are not allowed. • Users are not allowed to login to the compute nodes. • Foreground jobs on the PC cluster are restricted to program testing and the time duration should not exceed 1 minutes CPU time per job.

  49. Policy (continue) • Any background jobs run on the master node or compute nodes are strictly prohibited and will be killed without prior notice. • The current restrictions of the job queuing system are as follows, • The maximum number of running jobs in the job queue is 8. • The maximum total number of CPU cores used in one time cannot exceed 512. • The restrictions in item 7 will be reviewed timely for the growing number of users and the computation need.

  50. Good Practice in using sciblade • logout from the master node 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 behaviours.

More Related