[Wien] wien2k installation: XSEDE
Gavin Abo
gsabo at crimson.ua.edu
Tue Nov 5 04:41:28 CET 2019
Of note, if the XSEDE in your subject line uses slurm as in the
documentation here:
https://portal.xsede.org/documentation-overview#compenv-jobs
You likely need the SLURM_JOB_NODELIST variable as given in your slurm
documentation. For example, the slurm documentation (currently Version
19.05) here:
https://slurm.schedmd.com/srun.html#lbAH
On 11/4/2019 8:24 PM, Gavin Abo wrote:
>
> 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
>> >
>> >
>> >
>> ------------------------------------------------------------------------
>> >
>> > _______________________________________________
>> > Wien mailing list
>> > Wien at zeus.theochem.tuwien.ac.at
>> <mailto:Wien at zeus.theochem.tuwien.ac.at>
>> > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>> > SEARCH the MAILING-LIST at:
>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>> >
>>
>> --
>>
>> 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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