Hi, You can upload a log file to a file-sharing service and share the link :-)
Mark On Fri, Feb 16, 2018 at 8:22 PM Osmany Guirola Cruz < osmany.guir...@biocomp.cigb.edu.cu> wrote: > Hi, > When I send the full log I received this mail from the list. > > --------------------------------- > > > Your mail to 'gromacs.org_gmx-users' with the subject > > Re: [gmx-users] GPU problem with running gromacs.2018 > > Is being held until the list moderator can review it for approval. > > The reason it is being held: > > Message body is too big: 60010 bytes with a limit of 50 KB > > Either the message will get posted to the list, or you will receive > notification of the moderator's decision. If you would like to cancel > this posting, please visit the following URL: > > https://maillist.sys.kth.se/mailman/confirm/gromacs.org_gmx-users/1 > 29a1575b806c54484b39d65032d5862b41be235 > <https://maillist.sys.kth.se/mailman/confirm/gromacs.org_gmx-users/129a1575b806c54484b39d65032d5862b41be235> > > > > ---------------------------------- > > > > > > -----Original Message----- > From: Szilárd Páll <pall.szil...@gmail.com> > Reply-to: gmx-us...@gromacs.org > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] GPU problem with running gromacs.2018 > Date: Fri, 16 Feb 2018 20:06:05 +0100 > > Hi, > > Indeed, this is an issue introduced in the 2018 release which aborts > mdrun if an error is encountered during GPU detection; My first guess > is that one of your GPUs is in exclusive or prohibited mode. You can > use mdrun by skipping that GPU, i.e. setting the CUDA_VISIBLE_DEVICES > environment variable. > > BTW, what you shared is not your full log! It would have been (and > will be in the future) helpful if you actually shared the _full_ log > file so we get all information not just what you find useful to paste > in your reply; in this particular case seeing the hardware detection > report would have helped a bit. > > Cheers, > -- > Szilárd > > > On Fri, Feb 16, 2018 at 1:55 PM, Osmany Guirola Cruz > <osmany.guir...@biocomp.cigb.edu.cu> wrote: > > This is the output with gromacs 2018 and cuda 9 > > ----------------------------------------------------- > > --Program: gmx > > mdrun, version 2018Source file: src/gromacs/gpu_utils/gpu_utils.cu > > (line 735)Function: void findGpus(gmx_gpu_info_t*) > > Assertion failed:Condition: cudaSuccess == > > cudaPeekAtLastError()Should > > be cudaSuccess > > For more information and tips for troubleshooting, please check the > > GROMACSwebsite at http://www.gromacs.org/Documentation/Errors-------- > > -- > > ----------------------------------------------------- > > > > and this is the log > > Log file opened on Fri Feb 16 07:49:19 2018Host: draco pid: > > 20855 rank ID: 0 number of ranks: 1 :-) > > GROMACS - gmx mdrun, 2018 (-: > > GROMACS is written by: Emile > > Apol Rossen Apostolov Herman J.C. Berendsen Par > > Bjelkmar Aldert van Buuren Rudi van Drunen Anton > > Feenstra Gerrit Groenhof Christoph Junghans Anca > > Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter > > Kasson Jiri Kraus Carsten Kutzner Per Larsson > > Justin A. Lemkul Viveca Lindahl Magnus Lundborg Pieter > > Meulenhoff Erik Marklund Teemu Murtola Szilard > > Pall Sander Pronk Roland Schulz Alexey > > Shvetsov Michael Shirts Alfons Sijbers Peter > > Tieleman Teemu Virolainen Christian Wennberg Maarten > > Wolf and the project > > leaders: Mark > > Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > > Copyright (c) 1991-2000, University of Groningen, The > > Netherlands.Copyright (c) 2001-2017, The GROMACS development team > > atUppsala University, Stockholm University andthe Royal Institute of > > Technology, Sweden.check out http://www.gromacs.org for more > > information. > > GROMACS is free software; you can redistribute it and/or modify > > itunder > > the terms of the GNU Lesser General Public Licenseas published by the > > Free Software Foundation; either version 2.1of the License, or (at > > your > > option) any later version. > > GROMACS: gmx mdrun, version > > 2018Executable: /usr/local/gromacs/bin/gmxData > > prefix: /usr/local/gromacsWorking > > dir: /home/osmany/Downloads/RASCommand line: gmx mdrun -deffnm md > > GROMACS version: 2018Precision: singleMemory > > model: 64 bitMPI library: thread_mpiOpenMP > > support: enabled (GMX_OPENMP_MAX_THREADS = 64)GPU > > support: CUDASIMD instructions: SSE4.1FFT > > library: fftw- > > 3.3.7-sse2-avxRDTSCP usage: disabledTNG > > support: enabledHwloc support: hwloc-1.11.6Tracing > > support: disabledBuilt on: 2018-02-14 14:05:11Built > > by: osmany@draco [CMAKE]Build OS/arch: Linux 4.14.0-3- > > amd64 x86_64Build CPU vendor: IntelBuild CPU brand: Intel(R) > > Core(TM)2 Quad CPU Q9650 @ 3.00GHzBuild CPU family: 6 Model: > > 23 Stepping: 10Build CPU features: apic clfsh cmov cx8 cx16 intel > > lahf mmx msr pdcm pse sse2 sse3 sse4.1 ssse3C > > compiler: /usr/bin/gcc-6 GNU 6.4.0C compiler flags: - > > msse4.1 -O3 -DNDEBUG -funroll-all-loops -fexcess- > > precision=fast C++ compiler: /usr/bin/g++-6 GNU 6.4.0C++ > > compiler flags: -msse4.1 -std=c++11 -O3 -DNDEBUG -funroll-all- > > loops -fexcess-precision=fast CUDA compiler: /usr/lib/nvidia- > > cuda-toolkit/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright > > (c) 2005-2017 NVIDIA Corporation;Built on > > Fri_Sep__1_21:08:03_CDT_2017;Cuda compilation tools, release 9.0, > > V9.0.176CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;- > > gencode;arch=compute_35,code=sm_35;- > > gencode;arch=compute_37,code=sm_37;- > > gencode;arch=compute_50,code=sm_50;- > > gencode;arch=compute_52,code=sm_52;- > > gencode;arch=compute_60,code=sm_60;- > > gencode;arch=compute_61,code=sm_61;- > > gencode;arch=compute_70,code=sm_70;- > > gencode;arch=compute_70,code=compute_70;-use_fast_math;- > > D_FORCE_INLINES;; ;-msse4.1;-std=c++11;-O3;-DNDEBUG;-funroll-all- > > loops;-fexcess-precision=fast;CUDA driver: 9.0CUDA > > runtime: 9.0 > > ------------------------------------------------------------------- > > --- > > > > > > Osmany > > > > > > > > > > > > -----Original Message-----From: Szilárd Páll <pall.szil...@gmail.com> > > Re > > ply-to: gmx-users@gromacs.orgTo: Discussion list for GROMACS users > > <gmx > > -us...@gromacs.org>Subject: Re: [gmx-users] GPU problem with running > > gromacs.2018Date: Thu, 15 Feb 2018 18:23:05 +0100 > > Please provide a full log file output.--Szilárd > > > > On Thu, Feb 15, 2018 at 6:11 PM, Osmany Guirola Cruz<osmany.guirola@b > > io > > comp.cigb.edu.cu> wrote: > > > Hi > > > > > > I am having problems running mdrun command compiled with GPU > > > support(cuda 9.0). > > > here is the output of the mdrun command.... > > > > > > ........ > > > Using 1 MPI thread > > > Using 4 OpenMP threads > > > > > > 1 compatible GPU is present, with ID 0 > > > 1 GPU auto-selected for this run. > > > Mapping of GPU ID to the 1 PP rank in this node: 0 > > > > > > > > > WARNING: Just caught a previously occurred CUDA error (no kernel > > > image > > > is available for execution on the device), will try to continue. > > > > > > > > > ------------------------------------------------------- > > > Program: gmx mdrun, version 2016.4 > > > Source file: src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu (line 740) > > > > > > Fatal error: > > > cudaFuncSetCacheConfig failed: invalid device function > > > > > > For more information and tips for troubleshooting, please check the > > > GROMACS > > > website at http://www.gromacs.org/Documentation/Errors > > > ............... > > > > > > > > > Thanks. > > > Osmany > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at http://www.gromacs.org/Support/Maili > > > ng > > > _Lists/GMX-Users_List before posting! > > > > > > * Can't post? 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