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

Abaqus problem with host list
by Krishna Murthy, Karthik Ravi 07 Oct '19

07 Oct '19

Dear All, In the past (LSF) it was possible to submit parallel jobs on several cores for ABAQUS. However, now with SLURM i encounter the problem stated below: Abaqus Error: The number of cpus used is more than the total number of processors specified by the host list. mp_host_list: [['ncm0081.hpc.itc.rwth-aachen.de', 1]]. Abaqus/Analysis exited with error(s). I suspect it is due to a fautly setting of the enviromental variable $R_WLM_ABAQUSHOSTLIST, as the job submission script, found on the RWTH documentation website states: cat << EOF > $abaqus_v6.env #verbose = 3 #ask_delete = OFF mp_file_system = (SHARED, LOCAL) mp_host_list = $R_WLM_ABAQUSHOSTLIST EOF It seems like currently there is only one host in that list, which i suspect to be insufficient when running on, let say 16 cores. Best Regards, Karthik

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Abaqus problem with host list
by ravi.krishna＠rwth-aachen.de 28 Aug '19

28 Aug '19

Dear All, In the past (LSF) it was possible to submit parallel jobs on several cores for ABAQUS. However, now with SLURM i encounter the problem stated below: Abaqus Error: The number of cpus used is more than the total number of processors specified by the host list. mp_host_list: [['ncm0081.hpc.itc.rwth-aachen.de', 1]]. Abaqus/Analysis exited with error(s). I suspect it is due to a fautly setting of the enviromental variable $R_WLM_ABAQUSHOSTLIST, as the job submission script, found on the RWTH documentation website states: cat << EOF > $abaqus_v6.env #verbose = 3 #ask_delete = OFF mp_file_system = (SHARED, LOCAL) mp_host_list = $R_WLM_ABAQUSHOSTLIST EOF It seems like currently there is only one host in that list, which i suspect to be insufficient when running on, let say 16 cores. Best Regards, Karthik

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Interactive working with graphic support
by Janssen, Johannes 04 Jul '19

04 Jul '19

Hi all, I need to use a CLAIX node for an interactive job, but my attempt to submit a job, ssh to the allocated node and work on it was not successful since I need graphic support (this is only provided with full x11-forwarding, right?). Is there a better way than working on a mostly free login node (login 1/2/3/4/x-1/x-2) in the hope that the (RAM consuming) process is not killed? Best regards Johannes -- Johannes Janssen, M.Sc. Institute of Jet Propulsion and Turbomachinery RWTH Aachen University Templergraben 55 52062 Aachen Germany Tel: +49 241 80 95508 Fax: +49 241 80 92229 E-mail: Janssen(a)ist.rwth-aachen.de<mailto:Janssen@ist.rwth-aachen.de> www: http://www.ist.rwth-aachen.de<http://www.ist.rwth-aachen.de/>

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Jobs are cancelled
by Zhijian Li 26 Jun '19

26 Jun '19

Dear all, Is it just me or is there anyone whose jobs are cancelled constantly? Since yesterday, I found that my jobs submitted to c18g are always cancelled by command: *squeue -u $USER -p c18g | tail -n +2 | awk '{print $1}' | xargs scancel* I am pretty sure that I didn't run it to kill the jobs. Anyone has similar situation or idea about it? Thanks and best, Zhijian *______________________________* Zhijian Li Institute for Computational Genomics RWTH Aachen University Pauwelsstrasse 19 52074 Aachen, Germany

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Segmentation fault
by Esposito, Stefania 18 Jun '19

18 Jun '19

Dear all, I have a recurrent problem with some simulations. After the simulation starts, when the software (Converge CFD) is reading the input files, I get the following message: [cid:image002.jpg@01D525BB.1EC114E0] In this case, I required 16 cores for the simulation. I asked the software support and they say that it is a cluster issue. When I get this error, some additional files in the simulation folder are created: [cid:image003.png@01D525BB.1EC114E0] I already tried to change the number of cores when I submit the simulation, but I get anyways the same error. Do you know what is the problem and how can I solve it? Thank you and best regards, Stefania M.Sc. Stefania Esposito Wissenschaftliche Mitarbeiterin / Research Associate Gasoline Powertrains Lehrstuhl für Verbrennungskraftmaschinen VKA Institute for Combustion Engines VKA RWTH Aachen University Forckenbeckstr. 4 52074 Aachen, Germany Phone: +49 241 80 24233 E-Mail: esposito_st(a)vka.rwth-aachen.de<mailto:esposito_st@vka.rwth-aachen.de> Internet: www.vka.rwth-aachen.de<http://www.vka.rwth-aachen.de/>

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Jobs occasionally failing
by Johannes Sauer 27 May '19

27 May '19

Hi all, some of my jobs are failing. It happens very rarely and with no apparent reason. Log says it got SIGKILL, although sacct just says COMPLETED. I had a job this week with this problem and it ran without issue after restarting it. This is particularly annoying since my jobs usually take > 1 day. I'm not exceeding my requested runtime or memory limits. I had just another one like it. I restarted it and believe it will run through without issue. I attached what sacct reported. It failed on ncm0217. Anyone had issues like this? 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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Single node jobs and wall time limit
by Mathias Schumacher 26 May '19

26 May '19

Dears all, I have a rather simple question (and maybe this has already been asked too many times here). Is it still the case on both the CLAIX-2018 and CLAIX-2016 machines managed via SLURM that a single node calculation can be run with 120 h max. wall time instead of the standard 24 h wall time? Submitting such a job gives JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 2245709 c16m dgrid_Ag ms368752 PD 0:00 1 (AssocMaxWallDurationPerJobLimit) when I set, e.g., #SBATCH --time 48:00:00 in the corresponding job script. Many thanks in advance, Mathias Schumacher

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Long Queue
by simon＠isf.rwth-aachen.de 23 May '19

23 May '19

Hi everybody, It seems like in the past two weeks something happened and now the queue is extremely long. I submitted a job yesterday afternoon and only today at 2pm ist started (and immediately exited as it wasnt debugged yet, but this is not the issue). Before that it usually started within moments (<5min). It seems like an enormous ammount of jobs is being started at once. Is this purposefully? Is there any chance to restrict that (like # of jobs per user)? Or is it just, that my project has such a low priority? Best Regards, Marek

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Compiling C/C++ into a 32bit binary
by Svejda, Jan 23 May '19

23 May '19

Dear all, I need to compile C/C++ sources into a 32bit binary, though 32bit libraries are unavailable on the cluster. I have searched the available modules, none of them seem to be dedicated to 32bit. These are the compilation errors I get upon compilation: /rwthfs/rz/SW/gcc/CENTOS-7.3/7.3.0/bin/../libexec/gcc/x86_64-pc-linux-gnu/7.3.0/cc1plus: error while loading shared libraries: libmpfr.so.6: cannot open shared object file: No such file or directory make[2]: *** [CMakeFiles/cwvalidator.dir/cwvalidator.cpp.o] Error 1 make[2]: *** Waiting for unfinished jobs.... /rwthfs/rz/SW/gcc/CENTOS-7.3/7.3.0/bin/../libexec/gcc/x86_64-pc-linux-gnu/7.3.0/cc1: error while loading shared libraries: libmpfr.so.6: cannot open shared object file: No such file or directory make[2]: *** [CMakeFiles/cwvalidator.dir/picoc/platform.c.o] Error 1 make[1]: *** [CMakeFiles/cwvalidator.dir/all] Error 2 make: *** [all] Error 2 Would it be possible to add also 32-bit libraries onto the cluster system? I am using the GCC 7+ compiler, so it would be enough to install these libraries: gcc-multilib, g++-multilib. I am looking forward to hearing from you. Yours faithfully, Jan Svejda

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No space left on device
by simon＠isf.rwth-aachen.de 23 May '19

23 May '19

Dear all, After my simulations were finally started from the queue, they exited almost immediately with simmilar errors: #1------------------------------------------------------------------------------------------------------- +--------------------------------------------------------------------+ | An error has occurred in cfx5solve: | | | | Cannot create working file def (linking from | | /rwthfs/rz/cluster/work/ms958471/Ansys_Lichtbogencluster/IIW2019/- | | 2019-05-20_Cathode_Mok_EM_Gauss2000W_withDrop_1.5mm.def): | | | | No space left on device | +--------------------------------------------------------------------+ This run of the ANSYS CFX Solver has finished. #2--------------------------------------------------------------------------------------------------------- +--------------------------------------------------------------------+ | ERROR #001100279 has occurred in subroutine ErrAction. | | Message: | | copy_dataset: write data block failed: No space left on device | | | | | | | | | | | +--------------------------------------------------------------------+ #3--------------------------------------------------------------------- +--------------------------------------------------------------------+ | An error has occurred in cfx5solve: | | | | Error reported by IO module: recreate_indextable: warning: file | | was not closed correctly, data may be inconsistent | +--------------------------------------------------------------------+ +--------------------------------------------------------------------+ | An error has occurred in cfx5solve: | | | | Error reported by IO module: write_index: fwrite failed writing | | format: Bad file descriptor | +--------------------------------------------------------------------+ +--------------------------------------------------------------------+ | An error has occurred in cfx5solve: | | | | Error reported by IO module: iif_flush: write_index failed | +--------------------------------------------------------------------+ +--------------------------------------------------------------------+ | An error has occurred in cfx5solve: | | | | Error reported by IO module: cfxwriteString: (fputs failed) | | syserr:: Bad file descriptor | +--------------------------------------------------------------------+ These are problems on top of the extra long queue that have happend today for the first time. 2 or 3 weeks ago, these simulations would run flawlessly. I suspect that something strange is happening. Best Regards, Marek

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