1. IT MANAGEMENT OF FME, 21 ST JULY 2010

2.  THE HPC FACILITY  USING PUTTY AND WINSCP TO ACCESS THE SERVER  SENDING FILES TO THE SERVER  RUNNING JOBS  MONITORING JOBS  COPY RESULTS BACK FROM THE SERVER

3.  Sunfire  8 CPUs x 6 Nodes - Quad-Core AMD Opteron(tm) Processor 2376 HE (2.3 GHz)  Interconnected using Infiniband and Ethernet  Each Node has 8 GB of memory  Storage capacity - 100 GB at the moment

4.  Using Torque - torque-server-2.3.6-1cri.slc4 and torque-mom-2.3.6-1cri.slc4  Scheduler - maui-server-3.2.6p21- snap.1224706197.2.slc4  Current MPI does not utilise Infiniband. This soon will be fixed.

5.  THE HPC FACILITY  USING PUTTY AND WINSCP TO ACCESS THE SERVER  SENDING FILES TO THE SERVER  RUNNING JOBS  MONITORING JOBS  COPY RESULTS BACK FROM THE SERVER

6.  Using putty.exe  http://fkm.utm.my/ftp/pub/Windows/putty/putty.exe  Using winscp.exe  http://fkm.utm.my/ftp/pub/Windows/winscp/winscp.exe

7.  Server : fkm.utm.my  Port : 2323 It will connect to ce.utmgrid.utm.my via MyREN

9. press YES

11. Click NEW

13. 1.click YES 2.click Continue 3.enter Your Password

15.  THE HPC FACILITY  USING PUTTY AND WINSCP TO ACCESS THE SERVER  SENDING FILES TO THE SERVER  RUNNING JOBS  MONITORING JOBS  COPY RESULTS BACK FROM THE SERVER

16. 1.Search files to be transferred at the left panel. 2.Create a new directory on the right panel. 3.Select files on the left panel. 4.Copy from left to right.

17.  THE HPC FACILITY  USING PUTTY AND WINSCP TO ACCESS THE SERVER  SENDING FILES TO THE SERVER  RUNNING JOBS  MONITORING JOBS  COPY RESULTS BACK FROM THE SERVER

18.  We need to configure the necessary files before we could run our model.  There are several files needed to be prepared before we could run the job.  Using putty.exe....

19.  Type ‘pico model_journal’  Enter file/read-case your_input_file.cas solve/init/initialize-flow solve/iterate 400 file/binary-files n file/confirm-overwrite n file/write-data your_output_file.dat exit y  Press Control–O to save  Press Enter  Press Control-X to exit

20.  prepare the pbs-script, type ‘pico pbs-script’  Enter the following #!/bin/sh #PBS -q utm #PBS -N istas.model3d #PBS -l nodes=1:ppn=8 #PBS -M istaz@mail.fkm.utm.my #PBS -m abe nCPU=8 version=3d journal=model_journal cd $PBS_O_WORKDIR /opt/exp_soft/share/istas/ansys_inc/v121/fluent/bin/fluent $version -t$nCPU -g -i $journal - mpi=openmpi -cnf=$PBS_NODEFILE  Press Ctrl-O to save  Press Enter  Press Ctrl-X to exit

21.  Finally we want to submit the job,  just type ‘qsub pbs-script’  type ‘qstat’ to see the status of your job.  an email will be sent to you to let you know the job has started.  another email will be sent to let you know the job has ended.  You could open WINSCP again to copy the output back to your PC.

22.  Prepare a pbs-script, type ‘pico pbs-script’ #!/bin/bash #PBS -q utm #PBS -l nodes=1:ppn=8 #PBS -l walltime=1000:00:00 #PBS -N myjobname.date.runNumberX # Go to the directory from which you submitted the job cd $PBS_O_WORKDIR cpus=$(wc -l $PBS_NODEFILE | awk '{print $1}') mp_host_list="[" for n in $(sort -u $PBS_NODEFILE) do mp_host_list="${mp_host_list}['$n',$(grep -c $n $PBS_NODEFILE)]," done mp_host_list=$(echo ${mp_host_list} | sed -e "s/,$/]/") echo "mp_host_list=${mp_host_list}" > abaqus_v6.env echo "abaquslm_license_file=\"27000@ce.utmgrid.utm.my\"" >> abaqus_v6.env echo "mp_rsh_command = 'ssh -x -n -l %U %H %C'" >> abaqus_v6.env # Run the job /opt/exp_soft/share/apps/Abaqus/Commands/abaqus analysis mp_mode=MPI cpus=$cpus job=MYJOBNAME interactive

23.  to run the job, type ‘qsub pbs-script’  to view the status, type ‘qstat’ Job id Name User Time Use S Queue ------------------------- ---------------- --------------- -------- - ----- 12374.ce STDIN euasia016 0 Q euasia 12375.ce STDIN euasia006 0 Q euasia 12376.ce STDIN euasia001 0 Q euasia 12379.ce STDIN euasia001 0 Q euasia 12388.ce...14072010.1327 istaz 00:00:26 R utm

24.  qsub: Once a PBS job script is created, it is submitted to PBS via the qsub command. In its simplest form, qsub takes a single parameter, the name of the script file that you wish to submit.  qstat: The qstat command will allow you to view the contents of the PBS queue.  node1:~/test> qstat Job id Name User Time Use S Queue ---------------- ---------------- ---------------- -------- - ----- 147.node1 testjob psmith 0 R default

25.  qdel: The qdel command takes a single argument, a job number. You can use qdel to abort execution of your job: qdel 147 would cancel execution of the job shown in the qstat example above.  qalter: The qalter command is helpful for altering the parameters of a job after it's submitted. qalter takes two arguments: the PBS directive that you wish to change (like -l), and the job number that you want to change. For example, if you forgot to set the walltime that your job requires, you can change it after it's been submitted:  node1:~> qalter -l walltime=4:00:00 147

26.  pbsnodes: The pbsnodes command, while a useful PBS administration command, can also be informative to the PBS user. pbsnodes -a will list all PBS nodes, their attributes, and job status. This is a useful way to get a list of valid machine properties for use in a #PBS -l directive. node1:~> pbsnodes -a node2 state = free np = 2 properties = gigabit,pcn,m2048,dual,p1800,athlon ntype = cluster