[Wien] wien2k installation: XSEDE
Gavin Abo
gsabo at crimson.ua.edu
Tue Nov 5 04:24:48 CET 2019
Comments:
Edison does look retired [1].
Based on the usage of hostname in Bushra's job file (below), it looks
like that is configured for a shared memory super computer.
However, if the super computer is not a shared memory (single node)
system but a distributed memory (multiple node) system [2], the use of
hostname is potentially problematic.
That is because on a distributed memory system the head node typical is
not a compute node [3].
One bad thing that can happen is that head node calculations can break
the cluster login, for example [4]:
/Do NOT use the login nodes for work. If everyone does this, the login
nodes will crash keeping 700+ HPC users from being able to login to the
cluster.//
/
It depends on local policy, but most clusters I have seen have a policy
that the system administrators can permanently take away a user's access
to the cluster if a calculation is executed on the head node, for
example [5]:
/CHTC staff reserve the right to kill any long-running or problematic
processes on the head nodes and/or disable user accounts that violate
this policy, and users may not be notified of account deactivation./
Instead of hostname, the job file usually needs to get a node list that
it gets from the queuing system's job scheduler. That could be a script
like gen.machines [6] or Machines2W [7]. Or it could be environment
variable, which name depends on the queuing system, for example the
PBS_NODEFILE variable for PBS [8,9].
[1]
https://www.nersc.gov/news-publications/nersc-news/nersc-center-news/2019/edison-supercomputer-to-retire-after-five-years-of-service/
[2]
https://www.researchgate.net/figure/Shared-vs-Distributed-memory_fig3_323108484
[3] https://zhanglab.ccmb.med.umich.edu/docs/node9.html
[4] https://hpc.oit.uci.edu/running-jobs
[5] http://chtc.cs.wisc.edu/HPCuseguide.shtml
[6] https://docs.nersc.gov/applications/wien2k/
[7] SRC_mpiutil: http://susi.theochem.tuwien.ac.at/reg_user/unsupported/
[8] Script for "pbs":
http://susi.theochem.tuwien.ac.at/reg_user/faq/pbs.html
[9]
http://docs.adaptivecomputing.com/torque/4-0-2/Content/topics/commands/qsub.htm
On 11/4/2019 6:37 AM, Dr. K. C. Bhamu wrote:
> Dear Bushra,
>
> I hope you are using the same cluster you are using before (NERSC:
> cori/edison).
> From your job file it seems that you want to submit job on edison (28
> cores).
> Please make sure that edison is still working. My available
> information says that edison has retired now. Please confirm from the
> system admin.
> I would suggest you to submit job on cori. A job file is there on
> web-page of NERSC.
>
> Anyway, please send the details as Prof. Peter has requested so that
> he can help you.
>
>
> Regards
> Bhamu
>
> On Mon, Nov 4, 2019 at 1:14 PM Peter Blaha
> <pblaha at theochem.tuwien.ac.at <mailto:pblaha at theochem.tuwien.ac.at>>
> wrote:
>
> What means: " does not work" ??
>
> We need details.
>
> On 11/3/19 10:48 PM, BUSHRA SABIR wrote:
> > Hi experts,
> > I am working on super computer with WIEN2K/19.1 and using the
> following
> > job file, but this job file is not working for parallel run of
> LAPW1.
> > Need help to improve this job file.
> > #!/bin/bash
> > #SBATCH -N 1
> > #SBATCH -p RM
> > #SBATCH --ntasks-per-node 28
> > #SBATCH -t 2:0:00
> > # echo commands to stdout
> > # set -x
> > module load mpi
> > module load intel
> > export SCRATCH="./"
> >
> > #rm .machines
> > #write .machines file
> > echo '#' .machines
> > # example for an MPI parallel lapw0
> > #echo 'lapw0:'`hostname`' :'$nproc >> .machines
> > # k-point and mpi parallel lapw1/2
> >
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> > echo '1:'`hostname`':1' >> .machines
> >
> > echo 'granularity:1' >>.machines
> > echo 'extrafine:1' >>.machines
> > export SCRATCH=./
> > runsp_lapw -p -ec 0.000001 -cc 0.0001 -i 40 -fc 1.0
> >
> >
> > Bushra
> >
> >
> >
> ------------------------------------------------------------------------
> >
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>
> --
>
> P.Blaha
> --------------------------------------------------------------------------
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> Email: blaha at theochem.tuwien.ac.at
> <mailto:blaha at theochem.tuwien.ac.at> WIEN2k: http://www.wien2k.at
> WWW: http://www.imc.tuwien.ac.at/TC_Blaha
> --------------------------------------------------------------------------
>
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