This is an old revision of the document!
To submit jobs to run on CHPC systems, you must write a shell script that will run your job, and then use
msub to put it on the queue. msub needs information, like which cluster to run your code on, and where to put any errors or output from the job. This extra information can be put within the script, disguised from the shell as special comments, or put on the command line when submitting the job.
The Sun system is divided into partitions where each partition represents a separate physical system:
dellfor the new Dell Intel Westmere cluster
westmerefor the Sun Intel Westmere cluster
harpertownfor the Intel Harpertown cluster
nehalemfor the Intel Nahalem cluster
sparcfor the Sparc M9000 SMP
vizfor the AMD Opteron visualization node
testfor the test (pre- and post-processing) nodes (also Intel Nehalem chipsets)
Users can specify different cluster partitions by adding a
-l feature flag in their job submission script or when running the
msub command. For example
msub -l feature=nehalem
You are able to choose more than one partition, provided, of course, your code can execute on the requested hardware. The syntax looks like:
msub -l feature=nehalem|harpertown
to use both
The new Westmere clusters are now open to be used and we hope that this will reduce the waiting time and the number of queuing jobs. The new Westmere clusters have their own partitions called “
westmere” for the Sun Westmere cluster and “
dell” for the Dell Westmere cluster.
NB: The new Dell cluster runs a different O/S from the Sun clusters. Please see the special instructions in the Dell section of this user guide.
Please note that each node of Westmere has 12 cores, so please change the processes per node value from
ppn=12 only when you run on the
To run on one of the Westmere clusters specify the
dell partition as follows:
For example, in your script
#MSUB -l feature=westmere #MSUB -l nodes=1:ppn=12
Or on the command line
msub -l feature=westmere -l nodes=1:ppn=12 <scriptname>
See the Dell section of this user guide for information on using the new Dell Westmere cluster.
The Moab scheduler has several different queues on the Sun systems for different sized and priority jobs:
NOTE: Users need to log a call at http://www.chpc.ac.za/apply-additional/ two weeks in advance if they need to use the special or priority queues.
Note that it is not necessary for users to specify queues since moab will automatically choose the correct queue for you from the information supplied in your job script e.g. using “msub -l nodes=1: ppn=8 and msub -l walltime”
Edit the file with, for example,
#/bin/sh #MSUB -l nodes=1:ppn=8 #MSUB -l feature=nehalem|harpertown #MSUB -l walltime=3:00:00 #MSUB -m be #MSUB -V #MSUB -o /export/home/username/scratch/stdout #MSUB -e /export/home/username/scratch/stderr #MSUB -d /export/home/username/scratch #MSUB -mb ##### Running commands exe=/opt/gridware/usersexecutable nproc=`cat $PBS_NODEFILE | wc -l` mpirun -np $nproc -machinefile $PBS_NODEFILE $exe > users.out
To submit this job (the
mpi.job file) use the
By default the job will be submitted to small queue since it only requests 8 processors.
NB: Your job MUST be located on the scratch partition, otherwise it will fail to run.
You have to specify
-I flag when submitting your job, i.e.
There will be a delay while the scheduler allocates and logs you into a free compute node. You can target a specific free node:
msub -I -l nodes=cnode-9-23
Users can use the same script and just change the walltime to 10 minutes or less and then change
#MSUB -l feature=nehalem|harpertown
#MSUB -l feature=test
in the job script.
Note that GPU cluster has 5 compute nodes and each node has 16 processors and 4 GPUs. In addition the head node (login node) has one each of C2070 and C1060 GPU cards.
vi mpi.job as before.
###These lines are for Moab #MSUB -l nodes=2:ppn=16:gpus=4 #MSUB -l feature=c2070 #MSUB -l walltime=168:00:00 #MSUB -m be #MSUB -V #MSUB -o /GPU/home/username/stdout #MSUB -e /GPU/home/username/stderr #MSUB -d /GPU/home/username #MSUB -mb ##### Running commands echo "original machine file is:" echo "++++++++++" cat $PBS_NODEFILE echo "++++++++++" cat $PBS_NODEFILE|sed -e 's/.*/&-ib/'>$PBS_STEP_OUT.hostfile echo "modified machine file is:" echo "++++++++++" cat $PBS_STEP_OUT.hostfile exe=location of the executable nproc=`cat $PBS_NODEFILE | wc -l` cd /GPU/home/username/testjob/ mpirun $nproc $exe > /GPU/home/username/testjob/OUTPUT
msub mpi.job at the Linux command line to submit your job.
In this example we have requested four C2070 GPUs and 32 processors
The BlueGene has been decommissioned and is no longer available.
Users can only use 32, 64, 128, 256 or 512 processors (
mpi.job file contains:
###These lines are for Moab #MSUB -l ppn=128 #MSUB -l walltime=168:00:00 #MSUB -m be #MSUB -V #MSUB -o /CHPC/work/username/testjob/out #MSUB -e /CHPC/work/username/testjob/err #MSUB -d /CHPC/work/username/testjob/ #MSUB -mb ##### Running commands /bgsys/drivers/ppcfloor/bin/mpirun -np 128 \ -mode VN -exe LOCATIONOFTHEEXECUTABLE
As before, use
msub mpi.job to submit the job.
Create a test job using a text editor: the job script file is a shell script file and should be a plain Ascii text file with Unix style line end characters. The easiest way to create the file is to use one of the standard Linux text editors, for example, vi or vim:
to create a file called
test.job. Note that you do not have to use the extension
.job for your file but it is a very useful convention that allows you to easily distinguish job script files from other script files (which end in
.sh by convention).
Include the following in your script, for more info check http://www.clusterresources.com
To get the definitions, and details of other flags, of the MSUB statements run the command
man msub online version.
###These lines are for Moab #MSUB -l nodes=4:ppn=8 #MSUB -l walltime=2:00:00 #MSUB -m be #MSUB -o /export/home/nmonama/scratch/test/dlpoly.3.07.out #MSUB -e /export/home/nmonama/scratch/test/dlpoly.3.07.err #MSUB -d /export/home/nmonama/scratch/test #MSUB -mb #MSUB -M firstname.lastname@example.org ##### Running commands NP=`cat $PBS_NODEFILE | wc –l` mpirun –np $NP –machinefile $PBS_NODEFILE DLPOLY_3.07.SPARC.Y
Details of each line of the job script:
SCRIPT Description/Ntes #MSUB -a Declares the time after which the job is eligible for execution. Syntax: (brackets delimit optional items with the default being current date/time): #MSUB -A account Defines the account associated with the job. #MSUB -e Defines the file name to be used for stderr. #MSUB -d path Specifies the directory in which the job should begin executing. #MSUB -h Put a user hold on the job at submission time. #MSUB -j oe Combine stdout and stderr into the same output file #MSUB -l string Defines the resources that are required by the job #MSUB -m options Defines the set of conditions (a=abort,b=begin,e=end) when the server will send a mail message about the job to the user #MSUB -N name Gives a user specified name to the job #MSUB -o filename Defines the file name to be used for stdout. #MSUB -p priority Assigns a user priority value to a job #MSUB -q queue Run the job in the specified queue (short.q,long.q,graphics.q,serial.q and interactive.q) #MSUB -r y Automatically rerun the job is there is a system failure #MSUB -S path Specifies the shell which interprets the job script. The default is your login shell. #MSUB -v list Specifically adds a list (comma separated) of environment variables that are exported to the job #MSUB -V Declares that all environment variables in the msub environment are exported to the batch job. #MSUB -W This option has been deprecated and should be ignored.
To submit the test job script use the following on the Linux command line:
NB: Your job should always write its output to scratch. It will be faster if it reads its input from there as well.
There are various controls of Moab and Loadleveler that can help you to manage your job:
Some of Moab controls are as follows:
|msub||Scheduler job submission|
|showq||Show queued jobs|
|showres||Show existing reservations|
|showstart||Show estimate of when job can or will start|
|checkjob||Provide report for specified job|