File name: USING CHPC SUN FUSION

File realease date: 29 January 2013

File version: 6.00

Author: Technical Team

Email: helpdesk@chpc.ac.za

Website: www.chpc.ac.za

Contact: 021 658 2740/58/60

Compilers and libraries that CHPC suppport are available from the following folders:

• compilers: /opt/gridware/compilers
• libraries: /opt/gridware/libraries

You can also use Intel compilers by adding the following modules:

or sunstudio and gnu

Applications like gaussian and amber have their own modules.

XXX Also see the last section XXX XXX Every compiler, library and app should have a module XXX

Here is an example on how to use an amber at CHPC :

module list
module avail
module add intel
module add amber

Note that CHPC only support applications that are installed in /opt/gridware/applications

We discourage users from installing any applications on their home directories. Users can install their own applications in /opt/gridware/users/ which will also not be supported by CHPC.

USING A TERMINAL (linux or mac )

ssh username@sun.chpc.ac.za 

USING PUTTY (windows)

- Open Putty.exe - Select Category: Session - Under Host Name or IP address enter sun.chpc.ac.za (from anywhere in the internet) - Port: 22 - Connection Type: SSH - Saved Session: e.g. CHPC-SUN - Close window on exit: Only on clean exit - Click Open - login as: your username - Password: your password

48x Sun Blade X6250 (2 x Intel Xeon quad core 3.0 Ghz/16GB RAM) Compute blade (48 nodes) running OSCAR 64 bit (amd64 aka x86_64)

144 x Sun Blade X6275 (2 x Intel Xeon quad core 2.93 Ghz/12GB RAM) Compute blades (288 nodes) running CentOS (Redhat derived) 5.8 64 bit (amd64 aka x86_64)

48 x Sun Blade X6275 (4 x Intel(R) Xeon(R) CPU X5670 @ 2.93GHz) , 24GB RAM Compute blades (96 nodes) running Centos 5.8 x86_64 bit (amd64 aka x86_64)

60 x Sun Blade X6275 (8 x Intel(R) Xeon(R) CPU X5670 @ 2.93GHz) , 36GB RAM Compute blades (240 nodes) running Centos 5.8 x86_64 bit (amd64 aka x86_64)

M9000-64 SPARC64 VII: Up to 64 CPUs (512 Cores) with each CMU having 128GB RAM running SOLARIS 10 (sparc64)

1x Sun Fire X4600 Visualization Node with nVidia QuadroPlex running RHEL 5.1 (amd64 aka x86_64)

Note that more information on how to use Moab and Moab flags you can visit http://www.clusterresources.com/

test.job example:

XXX explain that user needs to create a plain text file for the job script XXX

#!bin/bash
#MSUB -l nodes=1:ppn=12
#MSUB -l walltime=2:00:00
#MSUB -l feature=dell|westmere
#MSUB -m be
#MSUB -V
#MSUB -o /lustre/SCRATCH2/users/username/file.out
#MSUB -e /lustre/SCRATCH2/users/username/file.err
#MSUB -d /lustre/SCRATCH2/users/username/
#MSUB -mb
 

##### Running commands

nproc=`cat $PBS_NODEFILE | wc -l`
mpirun -np $ncproc -machinefile $PBS_NODEFILE <executable> <innput>

submit test:

msub test.job

You can view your job using the following :

checkjob -v -v jobid

CHPC offer 450TB shared temporary lustre storage for users to store their output files. This is a temporary storage, users are advised to remove their data after each successful run. Data will be purged when the storage approaches 80%. Read CHPC Storage Policy: http://www.chpc.ac.za/use-policy

The home directory /export/home/ is backed up daily. Only files that need to be backed up should be stored here. Only max 5GB data per user should be stored in this directory. Applications installed on this directories will not be supported.

If there are any request for storage please send it to helpdesk@chpc.ac.za

XXX WHAT ARE THE MODULE NAMES FOR THESE???

XXX WHERE IS BLAS, ATLAS, LAPACK ???