System Specifications
|
Number of Processors |
64 |
|
Processor Type |
Itanium 2 |
|
Processor Speed |
1.5 GHz |
|
Main Memory |
128 GB |
|
Operating System |
SUSE LINUX® Enterprise Server for SGI® Altix® Systems kernel: 2.6.5-7.252-sn2 |
BACH's Software
|
Software |
Version |
Build |
Package ID |
Status |
Manuals |
|---|---|---|---|---|---|
|
Intel® c/c++ (icc) |
9.0 |
20051201 |
l_cc_c_9.0.030 |
installed |
|
|
Intel® Fortran (ifort) |
9.0 |
20051201 |
l_fc_c_9.0.031 |
installed |
|
|
Intel® Debugger (idb) |
9.0-16 |
20051202 |
N/A |
installed |
|
|
Intel® VtuneTM Performance Analyzer |
3.0 |
N/A |
N/A |
installed |
|
|
Intel® Integrated Performance Primitives |
4.1 |
N/A |
l_ipp_ia32_itanium_p_4.1.010 |
installed |
|
|
Intel® Math Kernel Library |
7.2 |
N/A |
l_mkl_p_7.2.007 |
installed |
|
|
PBS Pro |
N/A |
N/A |
N/A |
installed |
|
|
Total View (totalview) |
7.1.1 |
N/A |
N/A |
installed |
PBS Queuing System
We are running Altair's PBSPro queuing system. Some of the common commands are:
|
Command |
Description |
|---|---|
|
qsub |
To submit a batch job |
|
qstat |
To see all jobs and their status |
|
qdel |
To kill a job |
|
qalter |
To modify options on a submitted, pending job |
For more information in these commands, please use man <command> or look in the User Guide.
To submit a job use the qsub command. The user should submit their job using a script file. A PBSPro job file allows for specification of options at the beginning of the file prefaced by the #PBS delimiter and then followed by PBS commands.
For example, to run the MPI executable "myMPI" on 16 processors for 5 hours using 3GB of memory, you could use the following script file:
------------------------------------------------------------------------------------------------
#!/bin/csh
#PBS
-N myjob
#PBS -l ncpus=16,mem=3000000kb#PBS
-l walltime=5:00:00
#PBS
-q normal
cd ${your_work_directory}
<other
commands> mpirun
-np 16 ./myMPI
<other
commands>
-------------------------------------------------------------------------------------------------
For example, to run an OpenMP executable "myOpenMP" on 16 processors for 5 hours, you could use the following script file:
------------------------------------------------------------------------------------------------
#!/bin/csh
#PBS
-N myjob
#PBS -l ncpus=16,mem=3000000kb#PBS
-l walltime=5:00:00
#PBS
-q normal
cd ${your_work_directory}
<other
commands>
setenv KMP_STACKSIZE 1g
setenv OMP_DYNAMIC FALSE
setenv KMP_LIBRARY turnaround
setenv OMP_NUM_THREADS 16
./myOpenMP
<other commands>
-------------------------------------------------------------------------------------------------
For example, to run a job using Totalview, you could use the following script file:
------------------------------------------------------------------------------------------------
#!/bin/csh
#PBS
-N myjob
#PBS -l ncpus=4#PBS
-l walltime=1:00:00
#PBS
-q normal
cd ${your_work_directory}
<other
commands>
# to
debug a parallel program such as
# mpirun -np ./myMPI
# use
totalview
# you must have connected to bach with ssh and
X-windows tunneling.
# xhost + bach.scs.gmu.edu; ssh -X -l
username bach.scs.gmu.edu.
COMMAND=mpirun
ARGUMENTS="-np 16 ./myMPI"
totalview $COMMAND -a
$ARGUMENTS
<other commands>
-------------------------------------------------------------------------------------------------
Then to submit any of these jobs and have PBSPro read and correctly interpret the directives, run the command:
%qsub
myscript
You can include just about anything you would include from a terminal session (setting environment variables, changing directories, moving files) and the commands will be executed in order.
Last updated 03/13/06 11:00 am