February 2019 - claix18-slurm-pilot

Submission rejections when using ntasks-per-node
by Sven Hansen 15 Feb '19

15 Feb '19

Dear users, thanks to several reports we have discovered a problem when trying to submit multi-node jobs that request more than 24 tasks per node. In general a resource request looking like this should work perfectly fine: (...) #SBATCH --nodes=5 #SBATCH --ntasks-per-node=48 (...) Theoretically this would allow you to make full use of 5 nodes. Currently, however, sbatch rejects such job scripts claiming that there were no hosts suitable for dispatchment. Despite this, the following request (...) #SBATCH --ntasks=240 (...) works as intended while being semantically equal in this scenario. We are not sure exactly what is causing this problem but do suspect a bug in slurm, possibly in conjunction with the Skylake-SP CPUs. If you are affected, we recommend to use --ntasks only for the time being. We will change the documentation accordingly so that you can build your job scripts upon correct templates. The problem has been relayed to the developers, we will have to wait for their assessment. Please excuse any inconvenience. Best, Sven -- Sven Hansen IT Center Abteilung: Systeme und Betrieb RWTH Aachen University Seffenter Weg 23 52074 Aachen (Germany) Tel.: + 49 241 80-29114 s.hansen(a)itc.rwth-aachen.de www.itc.rwth-aachen.de

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Re: Multi-Node ANSYS simulations
by Gier, Thomas 12 Feb '19

12 Feb '19

Hello Marcus, unfortunately I get essentially the same problem. srun spawns #cores instances of the CFX solver, every one of which tries to access all cores. Since they still try to communicate with the other node over ssh the result is the same error as below. Regards, Thomas Von: Marcus Wagner [mailto:wagner@itc.rwth-aachen.de] Gesendet: Dienstag, 12. Februar 2019 15:21 An: claix18-slurm-pilot(a)lists.rwth-aachen.de Betreff: [claix18-slurm-pilot] Re: Multi-Node ANSYS simulations Dear Thomas, could you please test the following: srun cfx5solve -batch -parallel -partition $SLURM_NTASKS -def job.def -par-dist "$CFXHOSTS" -start-method "Intel MPI Distributed Parallel". Best Marcus On 2/12/19 11:10 AM, Gier, Thomas wrote: Hello, I'm having issues running ANSYS CFX calculations across multiple nodes. Single-node simulations run fine, but multi-node configurations crash because ssh connections are being denied: " +--------------------------------------------------------------------+ | An error has occurred in cfx5solve: | | | | Remote connection to ncm0791.hpc.itc.rwthaachen.de | | (ncm0791.hpc.itc.rwth-aachen.de) could not be started, or exited | | with return code 255. It gave the following output: | | | | Permission denied (publickey,gssapi-keyex,gssapi-with-mic,pass- | | word,hostbased). | | | | Check that you have typed the hostname correctly, and that you | | have an account "tg084461" on the specified host with access | | permission from this host. You can use the following command to | | check the connection to a UNIX machine: | | | | ssh ncm0791.hpc.itc.rwth-aachen.de uname | +--------------------------------------------------------------------+" Am I missing something in my submission script, or is this a cluster config issue? Regards, Thomas Gier _______________________________________________ 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> -- Marcus Wagner, Dipl.-Inf. IT Center Abteilung: Systeme und Betrieb RWTH Aachen University Seffenter Weg 23 52074 Aachen Tel: +49 241 80-24383 Fax: +49 241 80-624383 wagner(a)itc.rwth-aachen.de<mailto:wagner@itc.rwth-aachen.de> www.itc.rwth-aachen.de<http://www.itc.rwth-aachen.de>

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Multi-Node ANSYS simulations
by Gier, Thomas 12 Feb '19

12 Feb '19

Hello, I'm having issues running ANSYS CFX calculations across multiple nodes. Single-node simulations run fine, but multi-node configurations crash because ssh connections are being denied: " +--------------------------------------------------------------------+ | An error has occurred in cfx5solve: | | | | Remote connection to ncm0791.hpc.itc.rwthaachen.de | | (ncm0791.hpc.itc.rwth-aachen.de) could not be started, or exited | | with return code 255. It gave the following output: | | | | Permission denied (publickey,gssapi-keyex,gssapi-with-mic,pass- | | word,hostbased). | | | | Check that you have typed the hostname correctly, and that you | | have an account "tg084461" on the specified host with access | | permission from this host. You can use the following command to | | check the connection to a UNIX machine: | | | | ssh ncm0791.hpc.itc.rwth-aachen.de uname | +--------------------------------------------------------------------+" Am I missing something in my submission script, or is this a cluster config issue? Regards, Thomas Gier

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General questions and problems with 256 node jobs
by Sebastian Achilles 05 Feb '19

05 Feb '19

Hi, a few questions/points form my side: - Claix 18 is using Intel OPA. What network topology is used? I guess it is a Fat tree. Is it blocking or non-blocking? Is it 1:2 blocking as on Claix 16? - Have you configured topology-aware resource allocation within the SLURM scheduler, in other words does the scheduler knows the topology and tries to minimize the hop-count? - I assume TurboBoost is enabled by default? Is it possible (or will it be possible in the future) to include an option to switch TurboBoost off? E.g. on JURECA it is possible to disable TurboBoost with `#SBATCH --disable-turbomode` for measurements. Otherwise it is possible to set frequencies with likwid? - I tried to run jobs with 256 nodes. I am getting an MPI error (cf. job 92414): nrm008.hpc.itc.rwth-aachen.de.233340PSM2 no hfi units are active (err=23) [245] MPI startup(): tmi fabric is not available and fallback fabric is not enabled Any ideas where this is coming from? Should I manually adjust I_MPI_FABRICS? I don't want to set the fallback fabric, since this would be TCP and would significantly impact performance. Affected jobs are not canceled but are running into the time limit. Theses errors are only occurring on the nrm nodes, not on the ncm nodes. Could there be a problem with the nrm nodes? Currently I am using the partition c18m, which contains both nodes types. How can I only select ncm nodes? - Historic jobs can not be viewed with scontrol or sstat. sacct on the other hand works. For example: $ scontrol show job 90949 slurm_load_jobs error: Invalid job id specified $ sstat --format=AveCPU,AvePages,AveRSS,AveVMSize,JobID -j 90945 AveCPU AvePages AveRSS AveVMSize JobID ---------- ---------- ---------- ---------- ------------ sstat: error: couldn't get steps for job 90945 - Some of my jobs don't appear in the queue and are not scheduled, even if sbatch returns `Submitted batch job 92365` - You are using a hand-build module system. One issue with this approach is that dependencies are not dissolved properly. For example loading the module python does something unexpected. A short example: $ module load intel; ldd main.x | grep mkl intel/19.0 already loaded, doing nothing [ WARNING ] libmkl_intel_lp64.so => /opt/intel/Compiler/19.0/1.144/rwthlnk/mkl/lib/intel64_lin/libmkl_intel_lp64.so (0x00002ac58b9ee000) libmkl_core.so => /opt/intel/Compiler/19.0/1.144/rwthlnk/mkl/lib/intel64_lin/libmkl_core.so (0x00002ac58c53c000) libmkl_intel_thread.so => /opt/intel/Compiler/19.0/1.144/rwthlnk/mkl/lib/intel64_lin/libmkl_intel_thread.so (0x00002ac5906c8000) $ module load python; ldd main.x | grep mkl Loading python 2.7.12 [ OK ] The SciPy Stack available: http://www.scipy.org/stackspec.html Build with GCC compilers. libmkl_intel_lp64.so => /usr/local_rwth/sw/python/2.7.12/x86_64/extra/lib/libmkl_intel_lp64.so (0x00002abea70ad000) libmkl_core.so => /usr/local_rwth/sw/python/2.7.12/x86_64/extra/lib/libmkl_core.so (0x00002abea7bcb000) libmkl_intel_thread.so => /usr/local_rwth/sw/python/2.7.12/x86_64/extra/lib/libmkl_intel_thread.so (0x00002abea96ba000) Using mkl_get_version_string() shows that the python mkl is version 2017.0.0 instead of the expected 2019.0.1 version that should be loaded. A different approach to a hand-build module system would be using easybuild to create the module system. This would avoid such issues. The blue print paper can be found here: http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=7830454 JSC has published there easybuild configuration on github: https://github.com/easybuilders/JSC The config files from HPC-UGent are also publicly available. Best, Sebastian

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Network Performance
by Sebastian Achilles 05 Feb '19

05 Feb '19

Hi all, I have looked into the Network Performance on CLAIX18. I have measured latency and bandwidth for intra and inter node communication. I have used the Intel IMB PingPong Benchmark complied with the modules intel/19.0 and intelmpi/2019. To get a sufficient statistic I have submitted 64 jobs with 1 node using 2 tasks and 64 jobs with 2 nodes using 1 task each, respectively. The scheduler has started the jobs on different sets of nodes. I have attached the results, showing the configuration and the average, min and max of the measurement. Let's first look at the inter node communication: I have measured an average latency of 2.12 usec. In the best case I measured 1 usec and in the maximum is 7.1 usec. The bandwidth is on average 6488 Mbytes/sec. The maximum is 11995 Mbytes/sec and minimum is 2483 Mbytes/sec. The latency for intra node communication looks okay, however the bandwidth shows variation. On average theses results don't correspond with the advertised values from Intel. Either I have done something wrong or I haven't understood the topology or there is a problem with the machine. Have you run such a benchmark as well? Can you observe something similar? @Marcus: To get a better understanding of the machine, could you please share a bit more information on the network topology: - How many levels does the tree have? - On which level is the tree pruned? - Could you send me the connectivity file / connection map, e.g. a list of cables connecting the nodes, edge and core switches? I would like to add the hop count information into my result. (I have a script for computing the hop count from a connection map. Depending on the format I just need to adjust the reading routine) Cheers, Sebastian

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Clang & C++14
by Philipp Berger 05 Feb '19

05 Feb '19

Dear list, apparently the Clang installation is build against the headers of the default GCC 4.8.5, which limits its understanding of C++ to C++11. Would it be possible to at least target the headers of GCC5? That would at least support C++14. Of course, with GCC8.2.0 being available as well, C++17 should also be possible ;) Kind regards, Philipp -- Philipp Berger https://moves.rwth-aachen.de/people/berger/ Software Modeling and Verification Group RWTH Aachen University Phone +49/241/80-21206 Ahornstraße 55, 52056 Aachen, Germany

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Maintenance and additionally requeued jobs
by Marcus Wagner 05 Feb '19

05 Feb '19

Dear all, i made a mistake yesterday and misinterpreted the TIME column of 'squeue'. For PENDING jobs, it shows the requested time, for RUNNING jobs, it shows the time since jobstart. So the following jobs will hit the maintenance mark of 9 o'clock. So I also had to requeue them: 111600,116276,116231,116287,119637,119647,118940,119631 Best Marcus -- Marcus Wagner, Dipl.-Inf. IT Center Abteilung: Systeme und Betrieb RWTH Aachen University Seffenter Weg 23 52074 Aachen Tel: +49 241 80-24383 Fax: +49 241 80-624383 wagner(a)itc.rwth-aachen.de www.itc.rwth-aachen.de

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Maintenance
by Marcus Wagner 04 Feb '19

04 Feb '19

Dear all, we will have to do another maintenance. It will begin tomorrow at 9:00 o'clock. Sorry for the short period, in which we could inform you. Longer running jobs hda to be requeued. That are the following JobIDs: 117826, 116379 Best Marcus -- Marcus Wagner, Dipl.-Inf. IT Center Abteilung: Systeme und Betrieb RWTH Aachen University Seffenter Weg 23 52074 Aachen Tel: +49 241 80-24383 Fax: +49 241 80-624383 wagner(a)itc.rwth-aachen.de www.itc.rwth-aachen.de

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