[Wien] question about how to continue calculation on a supercomputer with unix system
Dong Su
Dong.Su at asu.edu
Thu Dec 6 20:17:24 CET 2007
Dear Peter and Wien2k community:
I tried to run wien2k on a supercomputer in our institute.(The information of the computer can be found at:
http://hpc.asu.edu/hpcusersupport.php#running ) I installed it on the headnode and it was working fine.
For doing parallel calculation I have to use a "Job Scripts" as following:
#!/bin/bash
#PBS -l nodes=8
#PBS -q devel
#PBS -j oe
#PBS -o Example.output
#PBS -l walltime=12:00:00
cd $PBS_O_WORKDIR
mpiexec /home/user/mpiprogram
meanings:
* #!/bin/bash the shell to run the script under.
* #PBS -l nodes=8 sets how many processors to run on
* #PBS -q devel sets the queue to run in
* #PBS -j oe Combine stdout and stderr into the same file
* #PBS -o Example.output redirects the output from your job to Example.output
* #PBS -l walltime=12:00:00 sets your walltime estimate to 12 hours. The time takes the form Days:Hours:Minutes:Seconds
* cd $PBS_O_WORKDIR makes sure the job run from the directory where it was submitted from.
* mpiexec ... or .../yourprogram is the program to run. If you need to use something, put the use command before this line.
There is a limitation on the walltime: around 40 hours. After running 40 hours, the job will be killed automatically.
If I want to calculate a complex structure which needs a long time.
My question is may I continue to run the work after the job was killed? (like VASP which returns the results during calculation )
I may underestimate the walltime I need for the calculation. I may continue my calculation based on the result I already have when the job was killed.
Another question is the memory limitations for these four queues are 1GB/processor by default. In this case ,how many k_points can I use? Does the k-points limitation change with the number of nodes(let us say: any difference bewteen 8 nodes and 32 nodes)?
Thank you very much!
Dong SU,Ph.D
Dept. Of Physics, Arizona State University
P.O. Box 871504
Tempe, Arizona 85287-1504
Phone: 480-965-6327
Fax: 480-965-7954
E-mail: dong.su at asu.edu
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