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Kickstart tutorial
for Sciblade Cluster Users
19 Oct, 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
• Policy for using
sciblade.sci.hkbu.edu.hk
• Acknowledgement
http://www.sci.hkbu.edu.hk/hpccc/sciblade
2
Latest Cluster
Hardware configurations
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
Sciblade Cluster
256-node clusters supported by fund from RGC
5
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
Hardware Configuration
• Blade Chassis x 16
– Dell PE M1000e
– Each hosts 16 blade servers
• Management Network
– Dell PowerConnect 48 (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
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
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
Software List
• Molecular Dynamics & Quantum Chemistry
– Gamess 2009R1
– Gromacs 4.0.7
– LAMMPS
– Siesta 3.0b
– GPAW 0.7.2
• Third-party Applications
– MATLAB 2008b with pmatlab
– Lumerical FDTD
– TAU 2.18.2, Visit 1.11.2
– Xmgrace 5.1.22
10
Software List
• Queuing system
– Torque/PBS
– Maui scheduler
• Editors
– vi
– emacs
11
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
Basic Login and Job Submission
Procedure
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
Graphical login
• Using PuTTY to setup a secured
connection: Host Name=sciblade.sci.hkbu.edu.hk
15
Graphical login (con’t)
• ssh protocol version
16
Graphical login (con’t)
• Port 5900 +display number (i.e. 3 in this
case)
17
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
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
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
19
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
Ganglia
Web based management and monitoring
• http://sciblade.sci.hkbu.edu.hk/ganglia
21
Job Submission Procedures
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 returned.
• Monitor with showq or qstat
• Examine the error and output file. e.g.
hello.oJobID, hello.eJobID
23
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
Compiling & Running MPI Programs
• Using mvapich 1.1
1. Setting path, at the command prompt, type:
export PATH=/u1/local/mvapich1/bin:$PATH
(uncomment this line in .bashrc)
2. Compile using mpicc, mpiCC, mpif77 or mpif90, e.g.
mpicc –o hello hello.c
3. Prepare hostfile (e.g. machines) number of compute
nodes:
compute-0-0
compute-0-1
compute-0-2
compute-0-3
4. Run the program with a number of processor node:
mpirun –np 4 –machinefile machines ./hello
25
Prepare parallel job script, Qhello.pbs
#!/bin/sh
### Job name
#PBS -N hello
### Declare job non-rerunable
#PBS -r n
#PBS -l nodes=10:ppn=2
#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
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
27
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 28
Assorted Program Examples
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
30
Example: Ring 0 Example: Prime
prime/prime.c
ring/ring.c 3 1 prime/prime.f90
ring/Makefile prime/primeParallel.c
2 prime/Makefile
ring/machines prime/machines
Compile program by the command: Compile by the command: make
make Run the serial program by
./primeC or ./primeF
Run the program in parallel by Run the parallel program by
mpirun –np 4 –machinefile mpirun –np 4 –machinefile
machines ./ring < in machines ./primeMPI
Example: Sorting Example: mcPi
mcPi/mcPi.c
sorting/qsort.c mcPi/mc-Pi-mpi.c
sorting/bubblesort.c mcPi/Makefile
sorting/script.sh mcPi/QmcPi.pbs
sorting/qsort
sorting/bubblesort Compile by the command: make
Run the serial program by: ./mcPi ##
Submit job to PBS queuing system by Submit job to PBS queuing system by
qsub script.sh qsub QmcPi.pbs
31
Example 1: OpenMP
/u1/local/share/examples/omp
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.
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
34
Sample openmp example
#include <omp.h>
#include <stdio.h>
int main() {
#pragma omp parallel
printf("Hello from thread %d, nthreads %d\n",
omp_get_thread_num(),
omp_get_num_threads());
}
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);
}
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);
}
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
38
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
39
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
40
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
41
Example 3: 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
42
Pmatlab : idea of distributed matrix
• New data type: dmat
• Overload functions: zeros, ones, rand, with an
additional parameter Map
• Map tells pmatlab how and where dmat must
be distributed with three 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]
43
Pmatlab: examples of map grid
44
RUN.m
% RUN.m is a generic script for running pMatlab scripts.
% Define number of processors to use
Ncpus = 4;
% Name of the script you want to run
mFile = 'sample_app';
% Define cpus.
% Empty implies run on host.
% cpus = {};
% Get path to PBS node file on ITC Linux cluster
pbs_path=getenv('PBS_NODEFILE');
% Specify machine names to run remotely.
cpus = textread(pbs_path,'%s')';
% Specify which machines to run on
% cpus = {'compute-0-0', 'compute-0-1', 'compute-0-2', 'compute-0-3'};
% Abort left over jobs
MPI_Abort;
pause(2.0);
% Delete left over MPI directory
MatMPI_Delete_all;
pause(2.0);
% Define global variables
global pMATLAB;
% Run the script.
['Running: ' mFile ' on ' num2str(Ncpus) ' cpus']
eval(MPI_Run(mFile, Ncpus, cpus));
45
sample_app.m
N = 2^10; % NxN Matrix size. % Finalize the pMATLAB program
M = 8; disp('SUCCESS');
format long; if (PARALLEL)
% Turn parallelism on or off. pMatlab_Finalize;
PARALLEL = 1; % Can be 1 or 0. OK to change. end
% Create Maps.
mapX = 1; mapY = 1;
if (PARALLEL)
% Initialize pMatlab.
pMatlab_Init;
Ncpus = pMATLAB.comm_size;
my_rank = pMATLAB.my_rank;
% Break up channels.
mapX = map([1 Ncpus], {}, 0:Ncpus-1);
mapY = map([1 Ncpus], {}, 0:Ncpus-1);
end
% Allocate data structures.
X1 = rand(N,M,mapX);
X2 = rand(N,M,mapX);
Y = zeros(N,M,mapY);
Z = zeros(1,M,mapY);
x1local=local(X1);
x2local=local(X2);
R=x1local .* x1local + x2local .* x2local;
R= R<=1;
sumR=sum(R);
Z = put_local(Z,sumR);
A = agg(Z);
epi= sum(A)/M/N * 4.0
46
Qpmatlab.pbs
#!/bin/sh
### Job name
#PBS -N pmatlab
### Declare job non-rerunable
#PBS -r n
### Output files
###PBS -e pmatlab.err
###PBS -o pmatlab.log
### Mail to user
#PBS -m ae
### Queue name (small, medium, long, verylong)
### Number of nodes (node property ev67 wanted)
#PBS -l nodes=4
#PBS -l walltime=00:20:00
# This job's working directory
###echo Working directory is $PBS_O_WORKDIR
cd $PBS_O_WORKDIR
/u1/local/bin/matlab -nodisplay -r RUN
47
Example: Ring 0 Example: Prime
prime/prime.c
ring/ring.c 3 1 prime/prime.f90
ring/Makefile prime/primeParallel.c
2 prime/Makefile
ring/machines prime/machines
Compile program by the command: Compile by the command: make
make Run the serial program by
./primeC or ./primeF
Run the program in parallel by Run the parallel program by
mpirun –np 4 –machinefile mpirun –np 4 –machinefile
machines ./ring < in machines ./primeMPI
Example: Sorting Example: mcPi
mcPi/mcPi.c
sorting/qsort.c mcPi/mc-Pi-mpi.c
sorting/bubblesort.c mcPi/Makefile
sorting/script.sh mcPi/QmcPi.pbs
sorting/qsort
sorting/bubblesort Compile by the command: make
Run the serial program by: ./mcPi ##
Submit job to PBS queuing system by Submit job to PBS queuing system by
qsub script.sh qsub QmcPi.pbs
48
Policy for using
sciblade.sci.hkbu.edu.hk
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.
50
Policy (continue)
6. Any background jobs run on the master node or
compute nodes are strictly prohibited and will be
killed without prior notice.
7. 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.
8. The restrictions in item 7 will be reviewed timely for
the growing number of users and the computation
need.
51
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.
52
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@sci.hkbu.edu.hk. Thank you
53
Thank you!
Questions?
