April 2019 - claix18-slurm-pilot - lists.rwth-aachen.de

Cancel registration
by Mayara Bortolotti Rossini 26 Apr '19

26 Apr '19

Dear, I would like to cancel my registration on the "claix18-slurm-pilot" Thanks Best Regards, Mayara

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MATLAB
by Georg Schultes 25 Apr '19

25 Apr '19

Dear All, I tried to run MATLAB using a script, but it delivered an error. Can anyone tell me if MATLAB is already preinstalled? If it is preinstalled, what are the commands to load the corresponding modules? Thanks for your help and best regards, Georg

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Re: #BSUB -P abcd4321
by Martin C. Schwarzer 25 Apr '19

25 Apr '19

Dear Subrata, dear all, The error message is from slurm itself. For whatever reason, it doesn't find the the slurm configuration file. Which frontend (login) are you using? For example on the login nodes you should be able to locate the file, with all read flags set: > login18-1:~$ echo $HOSTNAME > login18-1.hpc.itc.rwth-aachen.de > login18-1:~$ locate slurm.conf > /etc/clustershell/groups.conf.d/slurm.conf.example > /etc/slurm/slurm.conf > /usr/share/doc/slurm-18.08.5-2/html/slurm.conf.html > /usr/share/man/man5/slurm.conf.5.gz > login18-1:~$ ls -lah /etc/slurm/slurm.conf > -r--r--r-- 1 root root 7.3K Apr 18 11:08 /etc/slurm/slurm.conf On a different frontend, i.e. the copy server, you cannot: > copy:~$ echo $HOSTNAME > copy.hpc.itc.rwth-aachen.de > copy:~$ locate slurm.conf > /etc/clustershell/groups.conf.d/slurm.conf.example > /usr/share/doc/slurm-18.08.5-2/html/slurm.conf.html > /usr/share/man/man5/slurm.conf.5.gz > copy:~$ ls -lah /etc/slurm/slurm.conf > ls: cannot access /etc/slurm/slurm.conf: No such file or directory Why sbatch is available on the node is a different question then: > copy:~$ command -v sbatch > /usr/bin/sbatch On the old frontends the configuration file obviously doesn't exist either, but sbatch still exists. > cluster:~$ echo $HOSTNAME > cluster.rz.RWTH-Aachen.DE > cluster:~$ locate slurm.conf > /etc/clustershell/groups.conf.d/slurm.conf.example > /usr/share/doc/slurm-18.08.5-2/html/slurm.conf.html > /usr/share/man/man5/slurm.conf.5.gz > cluster:~$ command -v sbatch > /usr/bin/sbatch So make sure you login to one of the login nodes. Best, Martin Dr. Martin C. Schwarzer RWTH Aachen University (Leitner Group, Hölscher Subgroup) Worringerweg 2; 52074 Aachen; Germany http://orcid.org/0000-0001-8435-9624 E-mails sent by me are always PGP/MIME signed. If you are unable to open attachments because of this, you might be using an outdated e-mail client. In this case, please contact me and I will send you the message with PGP/inline instead. On 2019-04-25 10:04, Subrata Pramanik wrote: > Dear All, > > I am using Gromacs with following script: > > #!/usr/bin/env zsh > > #SBATCH -p c18m > #SBATCH --account=jara0187 > #SBATCH -J Subrata1 > #SBATCH -o GROMACSJOB.o%J > #SBATCH -e GROMACSJOB.e%J > #SBATCH --mail-user=s.pramanik(a)biotec.rwth-aachen.de > <mailto:s.pramanik@biotec.rwth-aachen.de> > #SBATCH --mail-type=BEGIN > #SBATCH --mail-type=end > #SBATCH -n 24 > #SBATCH --mem-per-cpu=5000 > #SBATCH -t 24:00:00 > > ###### end of Slurm directives ###### > > ###### start of shell commands ###### > > ### load the necessary module files > module load CHEMISTRY > module load gromacs/5.1.2 > > #path for job file > > cd $HOME/run1-test > > > # Start the MPI-parallel mdrun directly ... > > $SLURM_NTASKS gmx_mpi mdrun -deffnm md_0_1 -cpi md_0_1.cpt -append > > I am getting this error: > sbatch: error: s_p_parse_file: unable to status file > /etc/slurm/slurm.conf: No such file or directory, retrying in 1sec up to > 60sec > sbatch: error: ClusterName needs to be specified > sbatch: fatal: Unable to process configuration file > > If anybody has any suggestions, please let me know. > > Thanks in advance. > > Best regards, > Subrata > > > > > > > > > > On Thu, Apr 25, 2019 at 9:57 AM Julien Guénolé > <guenole(a)imm.rwth-aachen.de <mailto:guenole@imm.rwth-aachen.de>> wrote: > > Thanks to answer to the list: it can always be helpful to others... > > If you get an error with these, > > #SBATCH -p c18m > #SBATCH --account=jara0187 > > I don't know what to suggest more. > > Best wishes, > Julien > > On 25/04/2019 09:20, Subrata Pramanik wrote: >> Dear Julien, >> >> Thank you for your suggestion. >> >> In the LSF, I had this way: >> >> ##BSUB -P rwth0031 >> #BSUB -P jara0187 >> >> In the SLURM, I changed in these ways: >> >> #SBATCH -p c18m >> #SBATCH --account=jara0187 >> >> OR >> >> #SBATCH -p rwth0031 >> #SBATCH --account=jara0187 >> >> In both cases, I am getting the same error: >> sbatch: error: s_p_parse_file: unable to status file >> /etc/slurm/slurm.conf: No such file or directory, retrying in 1sec >> up to 60sec >> sbatch: error: ClusterName needs to be specified >> sbatch: fatal: Unable to process configuration file >> >> I am herewith sending the script file. If possible, please have a >> look and suggest me. >> >> Thanks in advance. >> >> Best regards, >> Subrata. >> >> >> On Wed, Apr 24, 2019 at 5:36 PM Julien Guénolé >> <guenole(a)imm.rwth-aachen.de <mailto:guenole@imm.rwth-aachen.de>> >> wrote: >> >> As indicated by the error message, did you try to specify the >> ClusterName? For example: >> >> #SBATCH -p c18m >> >> if there is still an error, a copy of the batch file could be >> useful! >> >> Best wishes, >> Julien >> >> >> On 24/04/2019 17:27, Subrata Pramanik wrote: >>> Hi all, >>> >>> >>> I am trying to submit a job to Gromacs using cluster. >>> >>> With LSF, it was working well. >>> >>> I am getting the follwong error: >>> >>> sbatch: error: s_p_parse_file: unable to status file >>> /etc/slurm/slurm.conf: No such file or directory, retrying in >>> 1sec up to 60sec >>> sbatch: error: ClusterName needs to be specified >>> sbatch: fatal: Unable to process configuration file >>> >>> Please suggest me to solve this problem. >>> >>> Thanks in advance. >>> >>> Best regards, >>> Subrata. >>> >>> >>> On Tue, Mar 12, 2019 at 8:20 PM Philipp Rüßmann >>> <p.ruessmann(a)fz-juelich.de >>> <mailto:p.ruessmann@fz-juelich.de>> wrote: >>> >>> Dear Marek, >>> >>> the command is #SBATCH --account=abcd1234. >>> >>> Cheers, >>> Philipp >>> >>> >>> Am 12.03.19 um 20:01 schrieb simon(a)isf.rwth-aachen.de >>> <mailto:simon@isf.rwth-aachen.de>: >>> > Hi all, >>> > >>> > Is there an equivalent of the #BSUB -p command in SLURM >>> as well? >>> > >>> > Best Wishes, >>> > Marek >>> > _______________________________________________ >>> > claix18-slurm-pilot mailing list -- >>> claix18-slurm-pilot(a)lists.rwth-aachen.de >>> <mailto:claix18-slurm-pilot@lists.rwth-aachen.de> >>> > To unsubscribe send an email to >>> claix18-slurm-pilot-leave(a)lists.rwth-aachen.de >>> <mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de> >>> >>> >>> -- >>> Dr. rer. nat. Philipp Rüßmann >>> Peter Grünberg Institut (PGI-1) and Institute for >>> Advanced Simulation (IAS-1) >>> Forschungszentrum Jülich GmbH, D-52425 Jülich >>> Tel.: +49 2461 61-5523 >>> E-Mail: p.ruessmann(a)fz-juelich.de >>> <mailto:p.ruessmann@fz-juelich.de> >>> >>> >>> >>> ------------------------------------------------------------------------------------------------ >>> ------------------------------------------------------------------------------------------------ >>> Forschungszentrum Juelich GmbH >>> 52425 Juelich >>> Sitz der Gesellschaft: Juelich >>> Eingetragen im Handelsregister des Amtsgerichts Dueren >>> Nr. HR B 3498 >>> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen >>> Huthmacher >>> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt >>> (Vorsitzender), >>> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. >>> Harald Bolt, >>> Prof. Dr. Sebastian M. Schmidt >>> ------------------------------------------------------------------------------------------------ >>> ------------------------------------------------------------------------------------------------ >>> _______________________________________________ >>> claix18-slurm-pilot mailing list -- >>> claix18-slurm-pilot(a)lists.rwth-aachen.de >>> <mailto:claix18-slurm-pilot@lists.rwth-aachen.de> >>> To unsubscribe send an email to >>> claix18-slurm-pilot-leave(a)lists.rwth-aachen.de >>> <mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de> >>> >>> >>> >>> -- >>> Yours Sincerely, >>> >>> Subrata Pramanik >>> >>> _______________________________________________ >>> claix18-slurm-pilot mailing list -- claix18-slurm-pilot(a)lists.rwth-aachen.de <mailto:claix18-slurm-pilot@lists.rwth-aachen.de> >>> To unsubscribe send an email to claix18-slurm-pilot-leave(a)lists.rwth-aachen.de <mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de> >> >> -- >> ************************************************** >> Dr. Julien GUÉNOLÉ >> Research Group Head >> ---------------------- >> Institute of Physical Metallurgy and Metal Physics >> RWTH Aachen University >> Kopernikusstrasse 14 >> 52074 Aachen, GERMANY >> ---------------------- Room 202 >> Phone [office] +49 241 80 26866 >> Email guenole(a)imm.rwth-aachen.de <mailto:guenole@imm.rwth-aachen.de> >> Web http://www.julien-guenole.fr >> Twitter @nanouayeur >> ************************************************** >> >> _______________________________________________ >> claix18-slurm-pilot mailing list -- >> claix18-slurm-pilot(a)lists.rwth-aachen.de >> <mailto:claix18-slurm-pilot@lists.rwth-aachen.de> >> To unsubscribe send an email to >> claix18-slurm-pilot-leave(a)lists.rwth-aachen.de >> <mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de> >> >> >> >> -- >> Yours Sincerely, >> >> Subrata Pramanik > > -- > ************************************************** > Dr. Julien GUÉNOLÉ > Research Group Head > ---------------------- > Institute of Physical Metallurgy and Metal Physics > RWTH Aachen University > Kopernikusstrasse 14 > 52074 Aachen, GERMANY > ---------------------- Room 202 > Phone [office] +49 241 80 26866 > Email guenole(a)imm.rwth-aachen.de <mailto:guenole@imm.rwth-aachen.de> > Web http://www.julien-guenole.fr > Twitter @nanouayeur > ************************************************** > > _______________________________________________ > claix18-slurm-pilot mailing list -- > claix18-slurm-pilot(a)lists.rwth-aachen.de > <mailto:claix18-slurm-pilot@lists.rwth-aachen.de> > To unsubscribe send an email to > claix18-slurm-pilot-leave(a)lists.rwth-aachen.de > <mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de> > > > > -- > Yours Sincerely, > > Subrata Pramanik > > _______________________________________________ > claix18-slurm-pilot mailing list -- claix18-slurm-pilot(a)lists.rwth-aachen.de > To unsubscribe send an email to claix18-slurm-pilot-leave(a)lists.rwth-aachen.de >

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Re: #BSUB -P abcd4321
by Julien Guénolé 25 Apr '19

25 Apr '19

Thanks to answer to the list: it can always be helpful to others... If you get an error with these, #SBATCH -p c18m #SBATCH --account=jara0187 I don't know what to suggest more. Best wishes, Julien On 25/04/2019 09:20, Subrata Pramanik wrote: > Dear Julien, > > Thank you for your suggestion. > > In the LSF, I had this way: > > ##BSUB -P rwth0031 > #BSUB -P jara0187 > > In the SLURM, I changed in these ways: > > #SBATCH -p c18m > #SBATCH --account=jara0187 > > OR > > #SBATCH -p rwth0031 > #SBATCH --account=jara0187 > > In both cases, I am getting the same error: > sbatch: error: s_p_parse_file: unable to status file > /etc/slurm/slurm.conf: No such file or directory, retrying in 1sec up > to 60sec > sbatch: error: ClusterName needs to be specified > sbatch: fatal: Unable to process configuration file > > I am herewith sending the script file. If possible, please have a look > and suggest me. > > Thanks in advance. > > Best regards, > Subrata. > > > On Wed, Apr 24, 2019 at 5:36 PM Julien Guénolé > <guenole(a)imm.rwth-aachen.de <mailto:guenole@imm.rwth-aachen.de>> wrote: > > As indicated by the error message, did you try to specify the > ClusterName? For example: > > #SBATCH -p c18m > > if there is still an error, a copy of the batch file could be useful! > > Best wishes, > Julien > > > On 24/04/2019 17:27, Subrata Pramanik wrote: >> Hi all, >> >> >> I am trying to submit a job to Gromacs using cluster. >> >> With LSF, it was working well. >> >> I am getting the follwong error: >> >> sbatch: error: s_p_parse_file: unable to status file >> /etc/slurm/slurm.conf: No such file or directory, retrying in >> 1sec up to 60sec >> sbatch: error: ClusterName needs to be specified >> sbatch: fatal: Unable to process configuration file >> >> Please suggest me to solve this problem. >> >> Thanks in advance. >> >> Best regards, >> Subrata. >> >> >> On Tue, Mar 12, 2019 at 8:20 PM Philipp Rüßmann >> <p.ruessmann(a)fz-juelich.de <mailto:p.ruessmann@fz-juelich.de>> wrote: >> >> Dear Marek, >> >> the command is #SBATCH --account=abcd1234. >> >> Cheers, >> Philipp >> >> >> Am 12.03.19 um 20:01 schrieb simon(a)isf.rwth-aachen.de >> <mailto:simon@isf.rwth-aachen.de>: >> > Hi all, >> > >> > Is there an equivalent of the #BSUB -p command in SLURM as >> well? >> > >> > Best Wishes, >> > Marek >> > _______________________________________________ >> > claix18-slurm-pilot mailing list -- >> claix18-slurm-pilot(a)lists.rwth-aachen.de >> <mailto:claix18-slurm-pilot@lists.rwth-aachen.de> >> > To unsubscribe send an email to >> claix18-slurm-pilot-leave(a)lists.rwth-aachen.de >> <mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de> >> >> >> -- >> Dr. rer. nat. Philipp Rüßmann >> Peter Grünberg Institut (PGI-1) and Institute for Advanced >> Simulation (IAS-1) >> Forschungszentrum Jülich GmbH, D-52425 Jülich >> Tel.: +49 2461 61-5523 >> E-Mail: p.ruessmann(a)fz-juelich.de >> <mailto:p.ruessmann@fz-juelich.de> >> >> >> >> ------------------------------------------------------------------------------------------------ >> ------------------------------------------------------------------------------------------------ >> Forschungszentrum Juelich GmbH >> 52425 Juelich >> Sitz der Gesellschaft: Juelich >> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR >> B 3498 >> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher >> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt >> (Vorsitzender), >> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald >> Bolt, >> Prof. Dr. Sebastian M. Schmidt >> ------------------------------------------------------------------------------------------------ >> ------------------------------------------------------------------------------------------------ >> _______________________________________________ >> claix18-slurm-pilot mailing list -- >> claix18-slurm-pilot(a)lists.rwth-aachen.de >> <mailto:claix18-slurm-pilot@lists.rwth-aachen.de> >> To unsubscribe send an email to >> claix18-slurm-pilot-leave(a)lists.rwth-aachen.de >> <mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de> >> >> >> >> -- >> Yours Sincerely, >> >> Subrata Pramanik >> >> _______________________________________________ >> claix18-slurm-pilot mailing list -- claix18-slurm-pilot(a)lists.rwth-aachen.de <mailto:claix18-slurm-pilot@lists.rwth-aachen.de> >> To unsubscribe send an email to claix18-slurm-pilot-leave(a)lists.rwth-aachen.de <mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de> > > -- > ************************************************** > Dr. Julien GUÉNOLÉ > Research Group Head > ---------------------- > Institute of Physical Metallurgy and Metal Physics > RWTH Aachen University > Kopernikusstrasse 14 > 52074 Aachen, GERMANY > ---------------------- Room 202 > Phone [office] +49 241 80 26866 > Email guenole(a)imm.rwth-aachen.de <mailto:guenole@imm.rwth-aachen.de> > Web http://www.julien-guenole.fr > Twitter @nanouayeur > ************************************************** > > _______________________________________________ > claix18-slurm-pilot mailing list -- > claix18-slurm-pilot(a)lists.rwth-aachen.de > <mailto:claix18-slurm-pilot@lists.rwth-aachen.de> > To unsubscribe send an email to > claix18-slurm-pilot-leave(a)lists.rwth-aachen.de > <mailto:claix18-slurm-pilot-leave@lists.rwth-aachen.de> > > > > -- > Yours Sincerely, > > Subrata Pramanik -- ************************************************** Dr. Julien GUÉNOLÉ Research Group Head ---------------------- Institute of Physical Metallurgy and Metal Physics RWTH Aachen University Kopernikusstrasse 14 52074 Aachen, GERMANY ---------------------- Room 202 Phone [office] +49 241 80 26866 Email guenole(a)imm.rwth-aachen.de Web http://www.julien-guenole.fr Twitter @nanouayeur **************************************************

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#BSUB -P abcd4321
by simon＠isf.rwth-aachen.de 24 Apr '19

24 Apr '19

Hi all, Is there an equivalent of the #BSUB -p command in SLURM as well? Best Wishes, Marek

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HPCWORK files unavailable
by Wickel, Noah Frederic 23 Apr '19

23 Apr '19

Dear Admins and CLAIX-18 users, as of today I found, from both login18-1 and login18-2 nodes, the /hpcwork/ directory to be completely empty. That is, i don't see my own folder nor any other users folders. The terminal tells me that $HPCWORK is not a directory. Is this a temporary incident, or did I miss an important announcement? Has anyone else encountered this? Best, Noah

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$CFXHOSTS: unable to find master host
by simon＠isf.rwth-aachen.de 18 Apr '19

18 Apr '19

Dear all, i attach my jobsubmission file with the error: :::::::::::::: slurm_ansys.sh :::::::::::::: #!/usr/local_rwth/bin/zsh ### Job name #SBATCH -J CFX_OpenMPI ### File / path where output will be written, the %J is the job id #SBATCH -o CFX_OpenMPI.%J ### Request the time you need for execution in minutes ### The format for the parameter is: [hour:]minute, ### that means for 80 minutes you could also use this: 1:20 #SBATCH -t 24:00:00 ### Request virtual memory you need for your job in MB #SBATCH --mem-per-cpu 2G #SBATCH --nodes=1 ### Request the number of compute slots you want to use #SBATCH --cpus-per-task=8 ### Enable Verbose Output #SBATCH -V #SBATCH --mail-type=end #SBATCH --mail-user=sim(a)isf.rwth-aachen.de #SBATCH --account=rwth0398 ### Change to the work directory cd $WORK/Droplet CFX/ more slurm_ansys.sh ### Purge default MPI and Compiler to use the CFX MPI implementation module purge ### load modules and execute module load TECHNICS module load ansys ### start non-interactive batch job cfx5solve -def droplets_scaled2_sim.def -par-dist "$CFXHOSTS" -start-method "Intel MPI Distributed Parallel" -ccl R.ccl ### (OK) Unloading intelmpi 2018.4.274 (!!) neither LSF nor SLURM environment present, environment broken? (OK) Unloading Intel Suite 19.0.1.144 (WW) ATTENTION!!! Unloading this module can result in inoperable software!!! (OK) Loading TECHNICS environment (!!) Please notice: Using ansys requires payment. (!!) If in doubt, please contact your institute's IT-administrator or servicedesk(a)itc.rwth-aachen.de. (!!) Run the workbench GUI using runwb2 (OK) Loading ansys 19.3 Warning! The parallel start method specified in the input file: IBM MPI Local Parallel, is not a default parallel start method for this platform and has therefore been preserved. A different start method may be specified using the -start-method option. An error has occurred in cfx5solve: Unable to find the master host ncm0067.hpc.itc.rwthaachen.de (ncm0067.hpc.itc.rwth-aachen.de) in the host list: at least one partition must be assigned to the master host. I dont understand why im receiving this error. Did somehthing change in $CFXHOSTS?? Best Regards, Marek

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/hpcwork unstable
by Johannes Sauer 12 Apr '19

12 Apr '19

Dear all, I keep having problems with (input) files on /hpcwork. I'm submitting my jobs on login18-2.hpc.itc.rwth-aachen.de Sometimes its not possible to ls a directory which has files linked to hpcwork, the system just hangs. I also had jobs not starting or failing between different steps due to files that could not be found. Is this an issue with hpcwork, should I move my files to work or my home directory? Best Johannes -- M.Sc. Johannes Sauer Researcher Institut fuer Nachrichtentechnik RWTH Aachen University Melatener Str. 23 52074 Aachen Tel +49 241 80-27678 Fax +49 241 80-22196 sauer(a)ient.rwth-aachen.de http://www.ient.rwth-aachen.de

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Problem with GUI on login18-x-1, login18-x-2
by simon＠isf.rwth-aachen.de 11 Apr '19

11 Apr '19

Dear all, I have noticed a problem with my GUI applications (Ansys CFX, cfx5pre, etc). Following protocol i wanted to use these applications via the "GUI"-dialogue nodes login18-x-1, login18-x-2. The application started but the part of the GUI which displays the 3D mesh, the 3D geometry or the 3D domain set up could not be displayed (it gave a glitch, showing only the fixed screen "behind" the GUI, when the GUI was loaded). I am not very much bothered by this, since it works perfectly fine on login18-1, but i feel like im "abusing" the system, so i wanted to report this issue. I case more information is required, because for the isse to show an actual case needs to be loaded in Ansys CFX, i can attach screenshots the next time. Best Regards, Marek Simon

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unable to use project-based compute cluster
by Zhijian Li 09 Apr '19

09 Apr '19

Dear all, I applied a project, called rwth0233, and would like to use it on the new system. When I set -A=rwth0233, and submit the jobs, I got below error information: >> sbatch: error: [E] Given account rwth0233 not found in config. >> sbatch: error: Batch job submission failed: Unspecified error Previously, I could use it on Bull Cluster by setting -P rwth0233. So how can I use this computation resource now? or the project-based quota has not been transferred to the new system. Thanks, Zhijian *______________________________* Zhijian Li Institute for Computational Genomics RWTH Aachen University Pauwelsstrasse 19 52074 Aachen, Germany

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