Kickstart tutorial on using sciblade cluster

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Kickstart tutorial on using sciblade cluster
for potential and new users 8 October,
2011 High Performance Cluster Computing Centre
(HPCCC) Faculty of Science Hong Kong Baptist
University
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Outline

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

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Latest Cluster Hardware configurations
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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

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Sciblade Cluster
256-node clusters supported by fund from RGC
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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

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Hardware Configuration

• Blade Chassis x 16
• Dell PE M1000e
• Each hosts 16 blade servers
• Management Network
• Dell PowerConnect 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

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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
• Intel Cluster Studio 2011
• GNU 4.1.2/4.4.0 Fortran/C/C Compiler

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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

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Software List

• Molecular Dynamics Quantum Chemistry
• Gamess 2009R1
• Gaussian 03, Gaussian 09
• 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

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Software List

• Queuing system
• Torque/PBS
• Maui scheduler
• Editors
• vi
• emacs

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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

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Basic Login and Job Submission Procedure
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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_at_sciblade vncserver
• New sciblade.sci.hkbu.edu.hk3 (username)'
  desktop is sciblade.sci.hkbu.edu.hk3
• It means that your session will run on display 3.

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Graphical login

• Using PuTTY to setup a secured connection Host
  Namesciblade.sci.hkbu.edu.hk

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Graphical login (cont)

• ssh protocol version

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Graphical login (cont)

• Port 5900 display numbe (i.e. 3 in this case)

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Graphical login (cont)

• Next, click Open, and login to sciblade
• Finally, run VNC Viewer on your PC, and enter
  "localhost3" 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_at_tdgrocks vncserver kill 3

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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_scib
  lade.php

cp cp f1 f2 dir1 copy file f1 and f2 into directory dir1
mv mv f1 dir1 move/rename file f1 into dir1
tar tar xzvf abc.tar.gz Uncompress and untar a tar.gz format file
tar tar czvf abc.tar.gz abc create archive file with gzip compression
cat cat f1 f2 type the content of file f1 and f2
diff diff f1 f2 compare text between two files
grep grep student search all files with the word student
history history 50 find the last 50 commands stored in the shell
kill kill -9 2036 terminate the process with pid 2036
man man tar displaying the manual page on-line
nohup nohup runmatlab a run matlab (a.m) without hang up after logout
ps ps -ef find out all process run in the systems
sort sort -r -n studno sort studno in reverse numerical order
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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

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Ganglia

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

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Job Submission Procedures
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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

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Sample Program hello.c
include ltstdio.hgt include mpi.h
// MPI compiler header file void
main(int argc, char argv) int nproc,myrank,i
err ierrMPI_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!! Im process d of
d\n,myrank,nproc) ierrMPI_Finalize()
// Terminate all MPI
processes
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Compiling Running MPI Programs

• Using mvapich 1.1
• Setting path, at the command prompt, type
• export PATH/u1/local/mvapich1/binPATH
• (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

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Prepare parallel job script, Qhello.pbs

• !/bin/sh
• Job name
• PBS -N hello
• Declare job non-rerunable
• PBS -r n
• PBS -l nodes20
• PBS -l walltime000800
• 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
• NPROCSwc -l lt 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

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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

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Job monitoring

• Show the status of submitted jobs
• showq

13896 dhhe Running 16
INFINITY Mon May 3 044825 14402
dhhe Running 16 INFINITY Wed May 5
234609 14403 dhhe Running
16 INFINITY Wed May 5 234707 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 4000000 Mon May 10 005519 15011
justin Idle 32
7000000 Mon May 10 154836 15098
hkbu09 Idle 50 33080000 Tue May
11 114645

• Delete jobID by qdel. e.g.
• qdel 15238

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Assorted Program Examples
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Example codes

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

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

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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

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Sample openmp example

• include ltomp.hgt
• include ltstdio.hgt
• int main()
• pragma omp parallelprintf("Hello from thread
  d, nthreads d\n", omp_get_thread_num(),
  omp_get_num_threads())

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serial-pi.c

• include ltstdio.hgt
• static long num_steps 10000000
• double step
• int main ()
• int i double x, pi, sum 0.0
• step 1.0/(double) num_steps
• for (i0ilt num_steps i)
• x (i0.5)step
• sum sum 4.0/(1.0xx)
• pi step sum
• printf("Est Pi f\n",pi)

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Openmp version of spmd-pi.c

• include ltomp.hgt
• include ltstdio.hgt
• static long num_steps 10000000
• double step
• define NUM_THREADS 8
• int main ()
• int i, nthreads double pi, sumNUM_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 (iid, sumid0.0ilt num_steps
  iinthrds)
• x (i0.5)step
• sumid 4.0/(1.0xx)

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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 nodes1ppn8
• PBS -l walltime000800
• cd PBS_O_WORKDIR
• export OMP_NUM_THREADS8
• ./omp_hello
• ./omp_test
• ./serial-pi
• ./omp-spmd-pi
• Submit it using qsub

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Example 2 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

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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

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Siesta sample pbs file h2o.pbs

• !/bin/bash
• PBS -N siesta-h2o
• PBS -l nodes8
• PBS -l walltime60000
• PBS -l pmem512mb
• NCPUwc -l lt PBS_NODEFILE
• cd PBS_O_WORKDIR
• MPIPATH/u1/local/mvapich2/bin
• MPIPATH/mpirun_rsh -np NCPU -hostfile
  PBS_NODEFILE /u1/local/bin/siesta lt h2o.fdf

• Submit the above h2o.pbs using qsub
• qsub h2o.pbs

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Example 3 pmatlab

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

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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. 0nCPUs

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Pmatlab examples of map grid
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Example Prime prime/prime.c prime/prime.f90 prim
e/primeParallel.c prime/Makefile prime/machines C
ompile 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/mach
ines Compile program by the command make Run
the program in parallel by mpirun np 4
machinefile machines ./ring lt in
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/bubbleso
rt.c sorting/script.sh sorting/qsort
sorting/bubblesort Submit job to PBS queuing
system by qsub script.sh
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Policy for using sciblade.sci.hkbu.edu.hk
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Policy

1. 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.
2. The account must not be shared his/her account
   and password with the other users.
3. 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.
4. Users are not allowed to login to the compute
   nodes.
5. Foreground jobs on the PC cluster are restricted
   to program testing and the time duration should
   not exceed 1 minutes CPU time per job.

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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.

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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.

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Acknowledgement

• When you make presentations or publish papers, we
  would appreciate it if you would kindly
  acknowledge the HPCCC by including
• "This research was conducted using the resources
  of the High Performance Cluster Computing Centre,
  Hong Kong Baptist University, which receives
  funding from Research Grant Council, University
  Grant Committee of the HKSAR and Hong Kong
  Baptist University."
• Use of Center resources constitutes an agreement
  to provide copies of any publication or news
  stories concerning research conducted using our
  systems and/or consulting services.
• Please send acknowledgement e-mail to
  hpccc_at_sci.hkbu.edu.hk. Thank you