it management of fme, 21 st july 2010. the hpc facility using putty and winscp to access the...
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FLUENT AND ABAQUS COURSE FOR HPC
IT MANAGEMENT OF FME, 21ST JULY 2010
TABLE OF CONTENTS
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
HPC @ CICT
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
QUEUE SYSTEM
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.
TABLE OF CONTENTS
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
ACCESSING THE SYSTEM
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
LOGIN INTO THE SYSTEM VIA PUTTY AND WINSCP
Server : fkm.utm.my Port : 2323
It will connect to ce.utmgrid.utm.my via MyREN
VIA PUTTY
VIA PUTTY
press YES
VIA PUTTY
VIA WINSCP
Click NEW
VIA WINSCP
VIA WINSCP
1. click YES2. click Continue3. enter Your Password
VIA WINSCP
TABLE OF CONTENTS
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
SENDING FILES TO THE SERVER
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.
TABLE OF CONTENTS
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
CONFIGURATION
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 ....
FLUENT
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
FLUENT
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 [email protected]#PBS -m abenCPU=8version=3djournal=model_journalcd $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
FLUENT
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.
ABAQUS
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 jobcd $PBS_O_WORKDIR
cpus=$(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 $PBS_NODEFILE)],"donemp_host_list=$(echo ${mp_host_list} | sed -e "s/,$/]/")echo "mp_host_list=${mp_host_list}" > abaqus_v6.envecho "abaquslm_license_file=\"[email protected]\"" >> abaqus_v6.envecho "mp_rsh_command = 'ssh -x -n -l %U %H %C'" >> abaqus_v6.env
# Run the job/opt/exp_soft/share/apps/Abaqus/Commands/abaqus analysis mp_mode=MPI cpus=$cpus job=MYJOBNAME interactive
ABAQUS
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 euasia12375.ce STDIN euasia006 0 Q euasia12376.ce STDIN euasia001 0 Q euasia12379.ce STDIN euasia001 0 Q euasia12388.ce ...14072010.1327 istaz 00:00:26 R utm
USEFUL PBS COMMANDS
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
CONT...
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
CONT...
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