[gmx-users] GPU problem with running gromacs.2018
Mark Abraham
mark.j.abraham at gmail.com
Fri Feb 16 20:57:38 CET 2018
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.guirola at 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.szilard at gmail.com>
> Reply-to: gmx-users at gromacs.org
> To: Discussion list for GROMACS users <gmx-users at 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.guirola at 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 at 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.szilard at gmail.com>
> > Re
> > ply-to: gmx-users at gromacs.orgTo: Discussion list for GROMACS users
> > <gmx
> > -users at 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 at 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? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > or
> > > send a mail to gmx-users-request at gromacs.org.
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/Support/Mailing
> > _Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users
mailing list