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--- guide:moab [2011/04/07 16:22]
smabakane
+++ guide:moab [2021/12/09 16:42] (current)
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-The following CHPC HPC systems (e1350, Blue Gene/P and Sun Microsytems) use schedulers and resources managers to schedule and run jobs in the systems. Below is the detail information:
+======A Guide to the Moab Job Scheduler at the CHPC======
-  e1350 cluster - Moab (Scheduler) and Torque (Resource manager).
+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.
-  Blue Gene/P - Loadleveler (Resource manager).
-  Sun Microsystems - Moab (Scheduler) and Torque (Resource manager).
-Herewith an example script of Moab in e1350 cluster:
+====SUN HYBRID SYSTEM====
-  #!/bin/sh
+===PARTITIONS===
-  #MSUB -l nodes=8:ppn=8
-  #MSUB -l walltime=100:00:00
-  #MSUB -m be
-  #MSUB -V
-  #MSUB -o /CHPC/work/username/test/test.out
-  #MSUB -e /CHPC/work/username/test/test.err
-  #MSUB -d /CHPC/work/username/test
-  #MSUB -r y
-  #MSUB -M email.address
-  #print the time and date
+The Sun system is divided into //partitions// where each partition represents a separate physical system:
-  date
-  cd /CHPC/work/username/test
+  - ''dell'' for the new **Dell** Intel Westmere cluster
-  nproc=`wc $PBS_NODEFILE| awk '{print $1}'`
+  - ''westmere'' for the Sun Intel Westmere cluster
-  /CHPC/usr/local/mpiexec-0.83/bin/mpiexec -n $nproc ./EXECUTABLENAME
+  - ''harpertown'' for the Intel Harpertown cluster
+  - ''nehalem'' for the Intel Nahalem cluster
+  - ''sparc'' for the Sparc M9000 SMP
+  - ''viz'' for the AMD Opteron visualization node
+  - ''test'' for 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 ''nehalem'' and ''harpertown'' clusters.
+===Sun and Dell Westmere Clusters===
+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 **//[[guide:dell|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=8'' to ''ppn=12'' **only** when you run on the ''westmere'' or ''del'' partition.
+To run on one of the Westmere clusters specify the ''westmere'' or ''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 **//[[guide:dell|Dell]]//** section of this user guide for information on using the new Dell Westmere cluster.
+===QUEUES===
+The Moab scheduler has several different queues on the Sun systems for different sized and priority jobs:
+  - small (min processors=1 , max processors = 8 , max walltime = 336 hours)
+  - par32 (min processors=9 , max processors = 32 , max walltime = 336 hours)
+  - par64 ( min processors=33 ,max processors = 64 , max walltime = 336 hours)
+  - big ( min processors=65,max processors = 128 , max walltime = 336 hours)
+  - test (min processors=1 , max processors = 8 , max walltime = 10 minutes)
+  - interactive (max processors = 2 )
+  - special ( min processors=129 , max processors = 512 , max walltime = 336hours )
+  - priority ( min processors=129 , max processors = 768 , max walltime = 336hours )
+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"
+===Job script example:===
+===MPI job===
+Edit the file with, for example,  ''vi mpi.job''
+<file bash mpi.job>
+#/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
+</file>
+To submit this job (the ''mpi.job'' file) use the ''msub'' command:
+  msub mpi.job
+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.
+===Interactive job===
+You have to specify ''-I'' flag when submitting your job, i.e.
+  msub -I
+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
+===Test jobs===
+Users can use the same script and just change the walltime to 10 minutes or less and then change
+  #MSUB -l feature=nehalem|harpertown
+to
+  #MSUB -l feature=test
+in the job script.
+====GPU CLUSTER====
+===PARTITIONS===
+  - //C2070// (8 of these Nvidia //Fermi// GPU cards are available on two nodes)
+  - //C1060// (12 of these Nvidia //Tesla// GPU cards are available on three nodes)
+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.
+===Job script example:===
+===MPI job over infiniband===
+Edit with ''vi mpi.job'' as before.
+<file bash mpi.job>
+###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
+</file>
+Type ''msub mpi.job'' at the Linux command line to submit your job.
+In this example we have requested four C2070 GPUs and 32 processors
+====(Obsolete) BlueGene/P CLUSTER====
+The BlueGene has been decommissioned and is no longer available.
+Users can only use 32, 64, 128, 256 or 512 processors (''ppn'').
+===Job script example:===
+===MPI job===
+The ''mpi.job'' file contains:
+<file bash mpi.job>
+###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
+</file>
+As before, use ''msub mpi.job'' to submit the job.
+======Moab Summary======
+====SUBMITTING A JOB USING MOAB====
+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:
+  vi test.job
+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'' [[http://www.adaptivecomputing.com/resources/docs/mwm/commands/msub.php|online version]].
+<file bash job.msub>
+###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 nmonama@csir.co.za
+##### Running commands
+NP=`cat $PBS_NODEFILE | wc –l`
+mpirun –np $NP –machinefile $PBS_NODEFILE DLPOLY_3.07.SPARC.Y
+</file>
+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:
+  msub test.job
+**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:
+| Command | Description |
+^ msub | Scheduler job submission |
+^ showq | Show queued jobs |
+^ canceljob | Cancel job |
+^ showres | Show existing reservations |
+^ showstart | Show estimate of when job can or will start |
+^ checkjob | Provide report for specified job |
-Below is an example script of Moab in Blue Gene/P:
-  #@ job_type = bluegene
-  #@ bg_size = 64
-  #@ class = BGP
-  #@ input = /dev/null
-  #@ output = dlpoly.$(jobid).out
-  #@ error = dlpoly.$(jobid).err
-  #@ wall_clock_limit = 12:00:00
-  #@ resources = ConsumableCpus(1)
-  #@ node_usage = shared
-  #@ cluster_list = BGP
-  #@ notification = complete
-  #@ queue
-  /bgsys/drivers/ppcfloor/bin/mpirun -np 32 -mode VN -cwd /CHPC/work/username/test -exe EXECUTABLENAME

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