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1. Introduction

Gowonda is a 792 core HPC cluster and consists of a mixture of SGI Altix XE and SGI® Rackable™ C2114-4TY14 servers. It is managed by the eResearch Services unit in Information Services. Gowonda was made possible by a grant from the Queensland Cyber Infrastructure Foundation (QCIF) and funding from the University Electronic Infrastructure Capital Fund.

Gowonda will be used to run computations that require large amount of computing resources. All Griffith University researchers and researchers from QCIF affiliated institutions will be able to get access to Gowonda. Similarly Griffith researchers can call upon additional resources from QCIF affiliated institutions if required. Gowonda is a major increase in capability for Griffith University and its partners.
It formally came into operation on Aug 1st 2011.

There is no plan to charge for legitimate research usage of gowonda. However, we will need to meet expectations of the stakeholders. Consequently, we will need to be able to account for all usage on the cluster to satisfy our stakeholders. Information is provided below about how you can assist in this.

This document is loosely modeled after “A Beginner's Guide to the Barrine Linux HPC Cluster” written by Dr. David Green (HPC manager, UQ) , ICE Cluster User Guide written by Bryan Hughes and Wiki pages of the City University of New York (CUNY) HPC Center (see reference for further details).

2. Gowonda Overview

2.1 Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Node Type

Total Number of Cores

Total Amount of Memory (GB)

Compute Nodes

Cores Per node

Mem per Node (GB)

Memory per Core

Processor Type

Small Memory Nodes

48

48

4

(n001-n004)

12

12

1

Intel(R) Xeon(R) CPU X5650 @ 2.67GHz

Medium Memory Nodes

108

216

9

(n005-n009,n010-n012,n019)

12

24

2

Intel(R) Xeon(R) CPU X5650 @ 2.67GHz

Large Memory Nodes

72

288

6

(n013-n018)

12

48

4

Intel(R) Xeon(R) CPU X5650 @ 2.67GHz

Extra Large Memory Nodes with GPU (see table below for more details about GPU)

48

384

4

(n020-n023)

12

96

8

Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
NVIDIA Tesla C2050

Extra Large Memory Nodes (no GPU)

96

768

8

(n031-n038)

12

96

8

Intel(R) Xeon(R) CPU X5650 @ 2.67GHz

Special Nodes (no GPU)

64

128

16

(n039-n042)

16

32

2

Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz

Special Large Memory Nodes (no GPU)

64

1024

8

(n044-n047)

16

256

16

Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz

Special Large Memory Nodes (no GPU)

192

1536

24

(aspen01-aspen12)

16

128

8

Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz

Please note that each of the Extra Large nodes (n020,n021, n022 and n023) have 2 nvidia tesla C-2050 GPU cards.

Node Type

Programming Model

Total Number of CUDA Cores

Total Amount of Memory (GB)

Compute Nodes

CUDA Cores Per node

CUDA cards per node

Mem per Node (GB)

Memory per Core

Processor Type

Extra Large Memory Nodes with GPU

GPU

4X2X448

384

4

(n020-n023)

2X448

2

96

8

Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
NVIDIA Tesla C2050

Special Administrative Nodes (Not used for computing purposes)

Node Type

Node Name

Total Number of Cores

Total Amount of Memory (GB)

Mem per Node (GB)

Memory per Core

Processor Type

File Servers

n024,n025

24

96G

48GB

4GB

Intel(R) Xeon(R) CPU X5650 @ 2.67GHz

Test Node

testhpc

12

24G

24GB

2GB

Intel(R) Xeon(R) CPU X5650 @ 2.67GHz

login Node

gowonda

12

48G

48GB

4GB

Intel(R) Xeon(R) CPU X5650 @ 2.67GHz

Admin Node

n030 (admin)

12

24G

24GB

2GB

Intel(R) Xeon(R) CPU X5650 @ 2.67GHz

More information about the Intel(R) Xeon(R) CPU X5650 processor can be obtained here.

In addition to the above, there is a special windows HPC node.

Node type

Total Number of Cores

Total Amount of Memory (GB)

Compute Nodes

Cores Per node

Mem per Node (GB)

Memory per Core

Processor Type

OS

Windows 2008 Large Memory Node

12

48

1

n029

12

48

4

Intel(R) Xeon(R) CPU X5650 @ 2.67GHz

Windows 2008 R2 with windows HPC pack

Instructions for using the Windows HPC is given in a separate user guide

2.2 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

The operating system on gowonda is RedHat Enterprise Linux (RHEL) 6.1 updated with SGI foundation-2.4 suite and accelerate-1.2 support package. The queuing system used is PBS Pro 11 . The exception is the Windows HPC node which runs Windows 2008 R2 with Windows HPC pack and Windows HPCS job scheduler. Gowonda has the following compilers and parallel library software. Much more detail on each can be found below.

  • GNU C, C++ and Fortran compilers;
  • Portland Group, Inc. optimizing C, C++, and Fortran compilers (currently awaiting to be installed);
  • The Intel Cluster Studio including the Intel C, C++ and Fortran compilers, Math and Kernel Library;
  • Intel MPI , SGI's proprietary MPT and OpenMPI
  • Oracle Solaris Studio Compiler (formerly called Sun Studio Compiler)

The following third party applications are currently installed or will be installed shortly. The Gowonda HPC Center staff will be happy to work with any user interested in installing additional applications, subject to meeting that application's license requirements.

Software

Version

Usage

Status

AutoDOCK

4.2.3

Module load autodock423 autodockvina112

Installed

Bioperl



TBI (To be Installed)

Blast



Installed

CUDA

4.0

module load cuda/4.0

Installed)

Gaussian03


module load gaussian/g03

Installed

Gaussian09


module load gaussian/g09

Installed

Gromacs



Installed

gromos

1.0.0

module load gromos/1.0.0

Installed

MATLAB

2009b,2011a

module load matlab/2009b,module load matlab/2011a 

Installed

MrBayes



TBI (To be Installed)

NAMD


module load NAMD/NAMD28b1

Installed

numpy

1.5.1

module load python/2.7.1

Installed

PyCogent

-

module load python/2.7.1

Installed

qiime



To be Installed

R


module load R/2.13.0

Installed

SciPy

0.9.0

module load python/2.7.1

Installed

VASP

-

-

TBI

The following graphics, IO, and scientific libraries are also supported.

Software

Version

Usage

Status

Atlas

3.9.39

 module load ATLAS/3.9.39

Installed

FFTW

3.2.2.,3.3a

  module load fftw/3.3-alpha-intel 

Installed

GSL-

1.09,1.15

 module load  module load gsl/gsl-1.15 

Installed

LAPACK-

3.3.0

-

-

NETCDF-

3.6.2,3.6.3,4.0,4.1.1,4.1.2

 e.g. module load NetCDF/4.1.2

Installed

3 Support

3.1 Hours of Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ..

The fourth Thursday mornings in the month from 8:00AM to 12PM are normally reserved (but not always used) for scheduled maintenance. Please plan accordingly. Unplanned maintenance to remedy system related problems may be scheduled as needed. Reasonable attempts will be made to inform users running on those systems when these needs arise.

3.2 User Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Users are encouraged to read this Wiki carefully. In particular, the sections on compiling and running parallel programs, and the section on the PBS Pro batch queuing system will give you the essential knowledge needed to use the gowonda cluster.

Gowonda cluster staff along with outside vendors also offer some courses to the Griffith HPC community in parallel programming techniques, HPC computing architecture, and the essentials of using our systems. Please follow our mailings on the subject and feel free to inquire about such courses. We can schedule training visits and classes at the various Griffith campuses. Please let us know if such are training visit is of interest.

Users with further questions or requiring immediate assistance in use of the systems should submit a ticket here


Support staff may be contacted via:
Griffith Library and IT help 3735 5555 or X55555
email support: Submit form 
You can log cases on service desk (category: eResearch services.HPC)

eResearch Services, Griffith University
Phone: +61 - 7 - 373 56649 (GMT +10 Hours)
Email:  Submit a Question to the HPC Support Team
Web: eresearch.griffith.edu.au

3.3 Service Alerts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Any major disruptions/events will be communicated through emails. These emails will be logged on the following web pages as well.

Major Service Alerts
https://conf-ers.griffith.edu.au/display/GHCD/Service+Alerts

Minor Service Alerts
https://conf-ers.griffith.edu.au/display/GHCD/Service+Alerts

Mail outs
https://conf-ers.griffith.edu.au/display/GHCD/Service+Alerts

3.4 Data storage, retention/deletion, and back-ups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Home Directories

Each user account, upon creation, is provided a home directory (/export/home/staffNumber) with a default 100 GB storage ceiling on each system. A user may request an increase in the size of their home directory if there is a special need. The HPC staff will endeavor to satisfy reasonable requests, but storage is not unlimited. Please regularly remove unwanted files and directories to minimize this burden.

Currently user home directories are not backed up. It is your responsibility to backup your data in /export/home/<snumber> and /scratch to an external source"

In addition to the home directory, users have access to a /scratch directory. A soft link to this scratch directory is also provided in the home directory. Files on system temporary and scratch directories are not backed up. All files older than 15 days will be deleted from the /scratch/<snumber> directory.

4 Access

4.1 Request an account on gowonda

Please fill out this form:
https://conf-ers.griffith.edu.au/display/GHCD/Griffith+HPC+Account+Request+Form
A staff from the gowonda HPC cluster team will contact you to provide you with login details.

4.2 Login . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ..

To log in to the cluster, ssh to

gc-prd-hpclogin1.rcs.griffith.edu.au

You will need to be connected to the Griffith network (either at Griffith or through vpn from home).

Please check VPN installation instruction here:

https://intranet.secure.griffith.edu.au/computing/remote-access/accessing-resources/virtual-private-network

ssh on windows platform . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . ..

To use X11 port forwarding, Install Xming X Server for Windows first.
See instructions here

If X11 forwading is not needed (true for most cases), do not install it.

To install a ssh client e.g. putty, please follow this instruction

ssh on Linux platform and mac platform . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . ..

ssh -Y gc-prd-hpclogin1.rcs.griffith.edu.au

Once you are on the system, have a look around. Your home directory is stored in:
/exports/home/<SNumber>

where you have 100GB of allocated space.

Work space is available at:

/scratch/<snumber>

which is a "scratch" area for short lived data. All data older than 15 days is deleted from this folder.
You should not read or write directly into your home directory with submitted jobs - they should always use the "/scratch/<snumber>" filesystem

4.3 File Transfers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Please check these instructions for transferring files between your desktop and gowonda cluster

https://conf-ers.griffith.edu.au/display/GHCD/Transferring+files+between+your+desktop+and+gowonda+cluster

The other method is to mount your gowonda home drive as follows

Mounting gowonda on Windows clients

Use win-sshfs to mount gowonda on windows:

http://code.google.com/p/win-sshfs/

First download the win-sshfs and install it on your windows machine.
After the installation, start the win-sshfs manager:

Start - All Programs - win-sshfs --> sshfs manager

Click on the Add button and fill in the details:

After saving the connection, click the mount button. It just becomes a drive on your desktop and can be used to transfer files back and forth from gowonda and local desktop.

Mounting gowonda on linux based clients:

The sshfs application is a FUSE program which will mount filesystems from SFTP servers.

FUSE (Filesystem in Userspace) is an interface which allows user programs, such as sshfs, to export a virtual filesystem to the Linux kernel. In this way, such filesystems can be attached to the Linux file hierarchy. This is particularly useful if you want to use Linux commands, scripts or programs to access your files on the remote server.

If you have access to FUSE on your Linux workstation or laptop, you can use sshfs to mount any of our gateway fileservers.

To install fuse-sshfs

sudo apt-get install sshfs    (Ubuntu)
yum install fuse-sshfs     (Fedora)

On CentOS or RHEL, FUSE and fuse-sshfs are available from the RPMforge repository. Go to https://rpmrepo.org/RPMforge/Using to see how to add RPMforge as a yum repository and then install sshfs as above.

On Fedora and RHEL or CentOS, the user must belong to group fuse in order to mount remote filesystems with the sshfs command.

To add yourself to group fuse, edit file /etc/group (as the root user, or with sudo). Find the line:

fuse:x:474:

and add your username to the end, separated by a comma from other usernames, if present. (The group number may differ).

First, you need to create a local directory as the mount point for the remote filesystem. Then give the sshfs command to mount your files from the fileserver. The format of the command is:

mkdir ~/f   (vreate local directory mount point)

sshfs user@host: mountpoint

e.g:

sshfs s12345@server.griffith.edu.au:  ~/f


Sshfs will prompt you for your password. Use you standard University password. You will then see your remote web site files in directory /myprojectsite.

ls ~/f
cgi-bin  E.G.User  index.htm  TestScriptSchoolsComscZ.pdf


To unmount (disconnect) the fileserver, use the fusermount -u command:

fusermount -u ~/f

5 Software Modules

Gowonda uses the Modules package to allow users to quickly load various environments. The command
module can be used to load and unload these environments.

module list    <=== This will list all the currently load environments

No Modulefiles Currently Loaded.
module avail   <=== This will list all the available environments on gowonda

------------------------------------------------------------------------------------------------------ /usr/share/Modules/modulefiles -------------------------------------------------------------------------------------------------------
MPInside/3.1       compiler/gcc-4.4.4 module-cvs         modules            mpiplace/1.01      null               perfcatcher        sgi-upc/1.04       use.own
chkfeature         dot                module-info        mpi/intel-4.0      mpt/2.04           perfboost          scotch/5.1.11      sgi-upc-devel/1.04

------------------------------------------------------------------------------------------------------------- /etc/modulefiles --------------------------------------------------------------------------------------------------------------
openmpi-x86_64

------------------------------------------------------------------------------------------------------------ /sw/com/modulefiles ------------------------------------------------------------------------------------------------------------
ATLAS/3.8.3                      NetCDF/4.1.2                     fftw/3.3-alpha-intel             intel-cc-10/10.1.018             intel-itac/8.0.0.011(default)    intel-tools-11/11.2.137          netCDF/4.0
ATLAS/3.9.39                     R/2.13.0                         gaussian/g03                     intel-cc-11/11.1.072             intel-itac/8.0.1.009             matlab/2009b                     netCDF/4.1.1
NAMD/NAMD28b1                    autodock/autodock423             gaussian/g09                     intel-cmkl-11/11.1.072(default)  intel-mpi/3.2.2.006(default)     matlab/2011a                     netCDF/4.1.2
NetCDF/3.6.2-shared              autodock/autodockvina112         gromos/1.0.0(default)            intel-cmkl-11/11.2.137           intel-mpi/4.0.0.027              mpt/2.00                         nose/1.0.0
NetCDF/3.6.3                     cuda/4.0                         gromos/1.0.0++                   intel-fc-10/10.1.018             intel-mpi/4.0.1.007              mpt/2.02                         python/2.7.1(default)
NetCDF/4.0                       fftw/3.2.2-gnu                   gsl/gsl-1.09                     intel-fc-11/11.1.072(default)    intel-ptu/3.2.001                netCDF/3.6.2-shared              python/3.1.4
NetCDF/4.1.1                     fftw/3.2.2-intel                 gsl/gsl-1.15                     intel-fc-11/12.0.2.137           intel-tools-11/11.1.072(default) netCDF/3.6.3

module load matlab/2009b
 module list
Currently Loaded Modulefiles:
  1) matlab/2009b

module swap matlab/2009b matlab/2011a
 module list
Currently Loaded Modulefiles:
  1) matlab/2011a

module unload  matlab/2011a
 module list
No Modulefiles Currently Loaded.

module load intel-fc-11/12.0.2.137
module load intel-mpi/4.0.1.007
module load mpi/intel-4.0

OR: module load  intel-fc-11/12.0.2.137 intel-mpi/4.0.1.007 mpi/intel-4.0
==
 module list
Currently Loaded Modulefiles:
  1) intel-fc-11/12.0.2.137   2) intel-mpi/4.0.1.007      3) mpi/intel-4.0

module unload intel-fc-11/12.0.2.137  intel-mpi/4.0.1.007 mpi/intel-4.0

 module list
No Modulefiles Currently Loaded.

To use specific software (e.g: matlab, intel compilers, etc), its environment must be loaded first. You will also need to load them in the PBS script (more about it can be seen later in this manual). There are also software specific documentation available here.

5.1 cuda/4.0. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

 module load cuda/4.0
[root@n002 ~]# module list
Currently Loaded Modulefiles:
  1) cuda/4.0

The cuda libraries and binaries are loaded with this. The GPUs are installed only on n020,n021,n022 and n023.
More information can be found here.

https://conf-ers.griffith.edu.au/display/GHCD/cuda

5.2 intel-mpi/4.0.0.027 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

This module provides access to Intel MPI commands. This is the recommended means of running MPI programs on Gowonda. Once this module has been loaded, commands such as mpicc will default to the Intel version. There is a SGI proprietary mpi called mpt that can also be used on Gowonda.

More information about mpi on gowonda can be found here.
https://conf-ers.griffith.edu.au/display/GHCD/mpi

5.3 intel-cc-11/11.1.072, intel-cmkl-11/11.2.137, intel-fc-11/12.0.2.137 . . . . . . . . . . . . . . . . . . . . . . . . .

These modules provide access to the Intel C and Fortran compilers, respectively. Once this module is loaded
the Intel C compiler can be accessed by running icc. Once this module is loaded the Intel Fortran compiler
can be accessed by running ifort. If a program is compiled with the Intel compilers then the respective
-libs program should be loaded in the running environment.

6 Program Compilation

6.1 Serial Program Compilation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

The Intel Compiler Suite

Intel's Cluster Studio (ICS) compilers, debuggers, profilers, and libraries are available on Gowonda.

module load intel-cc-11/11.1.072
icc  -V

Compiling a C program:

icc  -O3 -unroll mycode.c

The line above invokes Intel's C compiler (also used by Intel mpicc). It requests level 3 optimization and that loops be unrolled for performance. To find out more about 'icc', type 'man icc'.

Similarly for Intel Fortran and C++.

Compiling a Fortran program:

ifort -O3 -unroll mycode.f90

Compiling a C++ program:

icpc -O3 -unroll mycode.C
The Portland Group Compiler Suite

This is currently not installed on gowonda but is expected to be made available in the near future

The GNU Compiler Suite

The GNU compilers, debuggers, profilers, and libraries are available on Gowonda

To check for the default version installed:

gcc  -v

Compiling a C program:

gcc  -O3 -funroll-loops mycode.c

The line above invokes GNU's C compiler (also used by GNU mpicc). It requests level 3 optimization and that loops be unrolled for performance. To find out more about 'gcc', type man gcc.

Similarly for Fortran and C++.

Compiling a Fortran program:

gfortran -O3 -funroll-loops mycode.f90

Compiling a C++ program (uses gcc):

gcc -O3 -funroll-loops mycode.C

6.2 OpenMP and OpenMP SMP-Parallel Program Compilation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

All the compute nodes on Gowonda include at least 2 sockets and multiple cores. These multicore SMP compute nodes offer the Gowonda user community the option of creating parallel programs using the OpenMP Symmetric Multi-Processing (SMP) parallel programming model. SMP parallel programming with the OpenMP model (and other SMP models) has been around for a long time because early parallel HPC systems were built only with shared memories.

In the SMP model, multiple processors work within a single program image and the same memory space. This eliminates the need to copy data from one program (process) image to another (required by MPI) and simplifies the parallel run-time environment significantly. As such, writing parallel programs to the OpenMP standard is generally easier and requires fewer lines of code. However, the size of the problem that can be addressed using OpenMP is limited by the amount of memory on a single compute node, and the parallel performance improvement to be gained is limited by the number of processors (cores) within the node that can address that same memory space. At present in Gowonda, OpenMP applications can run with a maximum of 12 cores (24 if hyperthreading is used).

Here, a simple OpenMP parallel version of the standard C "Hello, World!" program is set to run on 8 cores:

#include <omp.h>
#include <stdio.h>
#include <stdlib.h>

#define NPROCS 8

int main (int argc, char *argv[]) {

   int nthreads, num_threads=NPROCS, tid;

  /* Set the number of threads */
  omp_set_num_threads(num_threads);

  /* Fork a team of threads giving them their own copies of variables */
#pragma omp parallel private(nthreads, tid)
  {

  /* Each thread obtains its thread number */
  tid = omp_get_thread_num();

  /* Each thread executes this print */
  printf("Hello World from thread = %d\n", tid);

  /* Only the master thread does this */
  if (tid == 0)
     {
      nthreads = omp_get_num_threads();
      printf("Total number of threads = %d\n", nthreads);
     }

   }  /* All threads join master thread and disband */

}

An excellent and comprehensive tutorial on OpenMP with examples can be found at the Lawrence Berkeley National Lab web site: https://computing.llnl.gov/tutorials/openMP

Compiling This OpenMP Program Using the Intel Compiler Suite

The intel C compiler requires the '-openmp' option, as follows:

 icc  -o hello_world.exe -openmp hello_world.c 

When run this program produces the following output:

 ./hello_world.exe
Hello World from thread = 0
Hello World from thread = 6
Hello World from thread = 3
Hello World from thread = 5
Hello World from thread = 1
Hello World from thread = 2
Total number of threads = 8
Hello World from thread = 4
Hello World from thread = 7

OpenMP is supported in both Intel's Fortran and C++ compilers as well.

Compiling This OpenMP Program Using the GNU Compiler Suite
The GNU C compiler requires the '-fopenmp' option, as follows:

 gcc  -o hello_world.exe -fopenmp hello_world.c

The program produces the same output, although the order of the print statements cannot be predicted and will not be the same over repeated runs. OpenMP is supported in both GNU's Fortran and C++ compilers as well.

6.3 MPI and MPI Parallel Program Compilation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

The Message Passing Interface (MPI) is a hardware-independent parallel programming and communications library callable from C, C++, or Fortran. Quoting from the MPI standard:

MPI is a message-passing application programmer interface (API), together with protocol and semantic specifications for how its features must behave in any implementation.

MPI has become the de facto standard approach for parallel programming in HPC. MPI is a collection of well-defined library calls (an Applications Program Interface, or API) for transferring data (packaged as messages) between completely independent processes within independent address spaces. These processes could be running within a single physical node or across distributed nodes connected by an interconnect such as GigaBit Ethernet or InfiniBand. MPI communication is generally two-sided with both the sender and receiver of the data actively participating in the communication events. Both point-to-point and collective communication is supported. MPI's goals are high performance, scalability, and portability. MPI remains the dominant parallel programming model used in high-performance computing today.

The original MPI-1 release was not designed with any special features to support traditional shared memory or distributed-shared memory parallel architectures, and MPI-2 provides only limited distributed, shared-memory support with some one-sided, remote direct memory access routines (RDMA). Nonetheless, MPI programs are regularly run on shared memory computers because the model is parallel architecture paradigm neutral. Writing parallel programs using the MPI model (as opposed to shared-memory models such as OpenMPI) requires the careful partitioning of program data among the communicating processes to reduce the number of communication events that can sap the performance of parallel applications when they are run at larger scale (with more processors).

There are several versions of MPI, including proprietary versions from Intel and SGI. We request the Gowonda users to use by default Intel MPI.

Parallel implementations of the "Hello world!" program in C and Fortran are presented here to give the reader a feel for the look of MPI code

hello_mpi

cat hello_mpi.c

/*The Parallel Hello World Program*/
#include <stdio.h>
#include <mpi.h>

main(int argc, char **argv)
{
   int node;

   MPI_Init(&argc,&argv);
   MPI_Comm_rank(MPI_COMM_WORLD, &node);

   printf("Hello World from Node %d\n",node);

   MPI_Finalize();
}

To compile this:

module load intel-fc-11/12.0.2.137
module load  intel-mpi/4.0.1.007
module load mpi/intel-4.0

mpicc -o hello_mpi hello_mpi.c -lmpi

Sample PBS script
cat pbs.run7

#!/bin/bash -l
#PBS -m abe
### Mail to user
#PBS -M <yourEmail>@griffith.edu.au
### Job name
#PBS -N mpi
#PBS -l walltime=60:00:00
## Please note the walltime above . This value * must * be set so that if the
## MPI program runs in an infinite loop , or something similar , it will be
## killed after the given wall time .
### Number of nodes:Number of CPUs:Number of threads per node
#PBS -l select=2:ncpus=12:mpiprocs=7
## The number of nodes is given by the select =<NUM > above
NODES=2
##$PBS_NODEFILE is a node-list file created with select and mpiprocs options by PBS
### The number of MPI processes available is mpiprocs * nodes
NPROCS=14
# This job's working directory
echo "Working directory is $PBS_O_WORKDIR"
cd $PBS_O_WORKDIR
source $HOME/.bashrc
module load intel-fc-11/12.0.2.137
module load  intel-mpi/4.0.1.007
module load mpi/intel-4.0
echo "Starting job"
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`
##mpirun  -machinefile   $PBS_NODEFILE  /export/home/s2594054/pbs/mpi/p1.out
mpirun -f $PBS_NODEFILE -n "$NODES" -r ssh -n "$NPROCS"    /export/home/s2594054/pbs/mpi/2/hello_mpi
echo "Done with job"


qsub  pbs.run7
2659.pbsserver

qstat
2659.pbsserver    mpi              s2594054          00:00:00 R workq

cat  mpi.o2659
Working directory is /export/home/SNUMBER/pbs/mpi/2
Starting job
Running on host n010
Time is Wed Jul 27 08:37:14 EST 2011
Directory is /export/home/SNUMBER/pbs/mpi/2
n010 n010 n010 n010 n010 n010 n010 n020 n020 n020 n020 n020 n020 n020
Hello World from Node 0
Hello World from Node 2
Hello World from Node 4
Hello World from Node 6
Hello World from Node 3
Hello World from Node 1
Hello World from Node 5
Hello World from Node 9
Hello World from Node 11
Hello World from Node 7
Hello World from Node 13
Hello World from Node 8
Hello World from Node 10
Hello World from Node 12
Done with job

qsub -I pbs.run7
cd $PBS_O_WORKDIR
module load intel-fc-11/12.0.2.137
module load  intel-mpi/4.0.1.007
module load mpi/intel-4.0

mpirun -f $PBS_NODEFILE -n 2 -r ssh -n 14    /export/home/SNUMBER/pbs/mpi/2/hello_mpi
Hello World from Node 0
Hello World from Node 2
Hello World from Node 1
Hello World from Node 4
Hello World from Node 6
Hello World from Node 3
Hello World from Node 8
Hello World from Node 5
Hello World from Node 13
Hello World from Node 7
Hello World from Node 12
Hello World from Node 10
Hello World from Node 11
Hello World from Node 9

OR

 mpirun -r ssh -f $PBS_NODEFILE --totalnum=$NPROCS --verbose -l -machinefile $PBS_NODEFILE -np $(wc -l  $PBS_NODEFILE | gawk '{print $1}')  /export/home/s2594054/pbs/mpi/2/hello_mpi
running mpdallexit on n016
LAUNCHED mpd on n016  via
RUNNING: mpd on n016
LAUNCHED mpd on n020  via  n016
RUNNING: mpd on n020
3: Hello World from Node 3
2: Hello World from Node 2
0: Hello World from Node 0
6: Hello World from Node 6
4: Hello World from Node 4
1: Hello World from Node 1
5: Hello World from Node 5
7: Hello World from Node 7
11: Hello World from Node 11
12: Hello World from Node 12
10: Hello World from Node 10
13: Hello World from Node 13
8: Hello World from Node 8
9: Hello World from Node 9

The following could work as well

mpirun -r ssh -f $PBS_NODEFILE --totalnum=$NPROCS --verbose -l -machinefile $PBS_NODEFILE -np 8 /export/home/SNUMBER/pbs/mpi/p1.out

mpirun -r ssh -f $PBS_NODEFILE --totalnum=$NPROCS --verbose -l -machinefile $PBS_NODEFILE -np $(wc -l  $PBS_NODEFILE | gawk '{print $1}') /export/home/SNUMBER/pbs/mpi/p1.out

--totalnum specifies the total number of mpds to start
    -np number - number of processes
      -n <n> or -np <n>            # number of processes to start

mpirun -f $PBS_NODEFILE -n  $(cat  $PBS_NODEFILE | gawk '{print $1}'|sort|uniq|wc -l) -r ssh -n  $(wc -l  $PBS_NODEFILE | gawk '{print $1}') /export/home/SNUMBER/pbs/mpi/p1.out

To check if mpd is working well:

mpdcheck -f $PBS_NODEFILE -v


Another version of MPI that will be supported is OpenMPI. OpenMPI (completely different from and not to be confused with OpenMP) is a project combining technologies and resources from several previous MPI projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) with the stated aim of building the best freely available MPI library. OpenMPI represents the merger between three well-known MPI implementations:

  • FT-MPI from the University of Tennessee
  • LA-MPI from Los Alamos National Laboratory
  • LAM/MPI from Indiana University

with contributions from the PACX-MPI team at the University of Stuttgart. These four institutions comprise the founding members of the OpenMPI development team.

These MPI implementations were selected because OpenMPI developers thought that each excelled in one or more areas. The stated driving motivation behind OpenMPI is to bring the best ideas and technologies from the individual projects and create one world-class open source MPI implementation that excels in all areas. The OpenMPI project names several top-level goals:

  • Create a free, open source software, peer-reviewed, production-quality complete MPI-2 implementation.
  • Provide extremely high, competitive performance (low latency or high bandwidth).
  • Directly involve the high-performance computing community with external development and feedback (vendors, 3rd party researchers, users, etc.).
  • Provide a stable platform for 3rd party research and commercial development.
  • Help prevent the "forking problem" common to other MPI projects.
  • Support a wide variety of high-performance computing platforms and environments.

OpenMPI may be used to run jobs compiled with the Intel, PGI, or GNU compilers. Two simple MPI programs, one written in C and another in Fortran are shown below as examples. A good online tutorial on MPI can be found at LLNL here . A tutorial on parallel programming in general here

Example hello.c

#include <stdio.h>
#include <mpi.h>

int main (argc, argv)
int argc;
char *argv[];
{
 int rank, size;

 MPI_Init (&argc, &argv);    /* starts MPI */
 /* get current process id */
 MPI_Comm_rank (MPI_COMM_WORLD, &rank);
 /* get number of processes */
 MPI_Comm_size (MPI_COMM_WORLD, &size);
 printf( "Hello world from process %d of %d\n", rank, size );
 MPI_Finalize();
 return 0;
}

Example hello.f90

program hello
include 'mpif.h'
integer rank, size, ierror, tag, status(MPI_STATUS_SIZE)

call MPI_INIT(ierror)
call MPI_COMM_SIZE(MPI_COMM_WORLD, size, ierror)
call MPI_COMM_RANK(MPI_COMM_WORLD, rank, ierror)
print*, 'node', rank, ': Hello world'
call MPI_FINALIZE(ierror)
end

6.4 GPU Parallel Programming with Intel Compilers and NVIDIA's CUDA Fortran Programming Model . . . . . . . . . . . . . . . . . .

7 Requesting Resources

 Warning
Do not run jobs on the login node "gc-prd-hpclogin1.rcs.griffith.edu.au" Please use it for compilation and small debugging runs only. 

Resources are requested through qsub.
A required option for all resource requests is walltime. By default all jobs have default walltime of 0 minutes. You can specify a walltime for your job with a -l option to qsub in the form of -l walltime=1:00 for one minute, or -l walltime=1:00:00 for one hour. There is currently no upper limit for walltime, the system is in place to help the scheduler.

7.1 Submit Jobs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .


qsub <pbscriptFile>


A pbs simple script file is as follows:

#!/bin/sh
#PBS -m abe
#PBS -M emailID@griffith.edu.au
#PBS -N Simple_Test
#PBS -q workq
#####PBS -W group_list=gaussian
#PBS -l walltime=00:15:00
#PBS -l select=1:ncpus=1:mpiprocs=1
###source $HOME/.bashrc
echo "Hello"
echo "Starting job"
module load  matlab/2011a
module list
sleep 228
echo "test Done"
echo "Done with job"

7.2 Monitor Jobs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

qstat -1an

7.3 Delete Jobs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

qdel <jobID>

7.4 Check the current status of the cluster  .. . . . . . . . . . . . . . . . . . . . . . . . .

pbsnodes

pbsjobs

pbsqueues

To view the current cluster status, you use the elinks text browser on the login node to view the status like below:

pbsnodes   (elinks http://localhost:3000/nodes)

pbsjobs (elinks http://localhost:3000/jobs)

pbsqueues (elinks http://localhost:3000/queues)

(You can press "Q" to quit from the below text-based browsers

8 Examples

8.1 Intel MPI and Compiler with Interactive Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

qsub -I -l walltime=00:15:00 -l select=2:ncpus=2:mpiprocs=2

This puts you in an interactive mode with two chunks of 2 mpiprocs assigned (Total of 4 cores)

8.2 Intel MPI and Compiler with Batch Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

9 Windows HPC node User Guide

Please see the following link for Windows HPC user guide. 

http://confluence.rcs.griffith.edu.au:8080/display/GHPC/Windows+HPC+User+Guide

Update: This facility has been removed and is no longer available on gowonda

10 Acknowledgements

We encourage you to acknowledge significant support you have received from the Griffith University eResearch Services Team in your publications.

The following text is suggested as a starting point. (Please feel free to augment or modify as you see fit, in particular naming individuals who have been of assistance. If you wish to cite particular references please contact the relevant individuals):

"We gratefully acknowledge the support of the Griffith University eResearch Services Team and the use of the High Performance Computing Cluster "Gowonda" to complete this research."

If you need to give hardware specifics for readers to reproduce results, it is:

  • Intel Xeon CPU X5650 processor@2.67GHz
  • QDR 4 x InfiniBand Interconnect

For more technical information, please check here

Please advise us of this acknowledgment by emailing us at eresearch-services@griffith.edu.au for our record keeping.

Reference

1. Green, David. A Beginner's Guide to the Barrine Linux HPC Cluster. http://www.qcif.edu.au/Facilities

2. Hughes, Bryan. “TCC's ICE Cluster User Guide”. http://infohost.nmt.edu/~khan/ice-user.pdf.

3. HPC Facility , CUNY. http://wiki.csi.cuny.edu/cunyhpc/index.php/Main_Page

4. Monash University e-Research Centre http://www.monash.edu.au/eresearch/about/services.html

5. CPU information : http://www.cpu-world.com/CPUs/Xeon/Intel-Xeon%20X5650%20-%20AT80614004320AD%20(BX80614X5650).html

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