[gmx-developers] Gromacs 2018: orientation restraint regtest failing
Berk Hess
hess at kth.se
Fri Jan 12 12:10:24 CET 2018
Hi,
What error are you referring to? The main error was on OpenCL issue,
whereas you use CUDA.
Or are you referring to the -multi message? That occurs with all
invocations of mdrun, I have uploaded a fix for that.
Cheers,
Berk
On 2018-01-12 03:45, Jernej Zidar wrote:
> Hi,
>
> I'm able to replicate this error on two different Linux machines too.
> It does not depend on whether GPUs are used or not.
>
> One is running Centos, GCC 6.3.1-3, CUDA 9.1, the other one is running
> Debian Stretch, GCC 6.3.0, CUDA 9.1.
>
> It also seems there is one message displayed for every MPI task started.
>
> Jernej
>
> On Thu, Jan 11, 2018 at 9:37 PM, Erik Lindahl <erik.lindahl at gmail.com
> <mailto:erik.lindahl at gmail.com>> wrote:
>
> HI,
>
> We did have another similar report during the beta phase, and
> unfortunately that too appeared to be transient, which indicates
> it's a Mac OS bug rather than the software :-/
>
> Cheers,
>
> Erik
>
> On Thu, Jan 11, 2018 at 2:06 PM, Carlo Camilloni
> <carlo.camilloni at gmail.com <mailto:carlo.camilloni at gmail.com>> wrote:
>
> Hi Erik
>
> Yes the header file is there, and yes in scalar it works, and
> you know what is weird, that know also the parallel one works..
> And if I remove everything and I reinstall the parallel one it
> also works, so it probably doesn’t matter..
>
> Carlo
>
>
>
>
> > Date: Thu, 11 Jan 2018 12:38:14 +0100
> > From: Erik Lindahl <erik.lindahl at gmail.com
> <mailto:erik.lindahl at gmail.com>>
> > To: gmx-developers at gromacs.org
> <mailto:gmx-developers at gromacs.org>
> > Subject: Re: [gmx-developers] Gromacs 2018: orientation
> restraint
> > regtest failing
> > Message-ID:
> >
> <CAEJJM8GrNroV-XRjHCqjOdG0H3n=meOeqc4fDUSCyMn38dhReg at mail.gmail.com
> <mailto:meOeqc4fDUSCyMn38dhReg at mail.gmail.com>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi Carlo,
> >
> > Your hardware looks almost to identical to my macbook, and
> for me it works
> > without problems.
> >
> > Could you
> >
> > 1) Confirm that the header file in question is present in
> > /Users/carlo/Codes/gromacs-2018/exe/share/gromacs/opencl
> >
> > 2) Try compiling without MPI - this is the only obvious
> setup difference I
> > can see from what I tried.
> >
> > Cheers,
> >
> > Erik
> >
> > On Thu, Jan 11, 2018 at 12:16 PM, Carlo Camilloni
> <carlo.camilloni at gmail.com <mailto:carlo.camilloni at gmail.com>
> >> wrote:
> >
> >> Dear all,
> >>
> >> First of all once again congratulations for the new gromacs!
> >>
> >> I have just compiled it on my MacBook Pro with OpenCL and
> after running
> >> the regtests I got this single failing test;
> >>
> >> BTW there is this weird output always: 'No option -multi?
> >>
> >>
> >> :-) 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 at
> >> Uppsala University, Stockholm University and
> >> the 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 it
> >> under the terms of the GNU Lesser General Public License
> >> as published by the Free Software Foundation; either
> version 2.1
> >> of the License, or (at your option) any later version.
> >>
> >> GROMACS: gmx mdrun, version 2018
> >> Executable: /Users/carlo/Codes/gromacs-2018/exe/bin/gmx_mpi
> >> Data prefix: /Users/carlo/Codes/gromacs-2018/exe
> >> Working dir: /Users/carlo/Codes/gromacs-2018/build/tests/
> >> regressiontests-2018/complex/orientation-restraints
> >> Command line:
> >> gmx_mpi mdrun -notunepme
> >>
> >> Reading file topol.tpr, VERSION 2018 (single precision)
> >> Changing nstlist from 10 to 100, rlist from 2 to 2
> >>
> >> No option -multi
> >> Using 1 MPI process
> >> 1 GPU auto-selected for this run.
> >> Mapping of GPU IDs to the 1 GPU task in the 1 rank on this
> node:
> >> PP:0
> >> Compilation of source file /Users/carlo/Codes/gromacs-
> >> 2018/exe/share/gromacs/opencl/nbnxn_ocl_kernels.cl
> <http://nbnxn_ocl_kernels.cl> failed!
> >> -- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_
> >> -DGMX_OCL_FASTGEN_ADD_TWINCUT -DEL_EWALD_ANA
> -DEELNAME=_ElecEw -DLJ_COMB_LB
> >> -DVDWNAME=_VdwLJCombLB -DCENTRAL=22
> -DNBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER=8
> >> -DNBNXN_GPU_CLUSTER_SIZE=8 -DNBNXN_GPU_JGROUP_SIZE=4
> >> -DGMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY=4
> -DNBNXN_MIN_RSQ=3.82e-07f
> >> -DIATYPE_SHMEM -cl-fast-relaxed-math
> -I/Users/carlo/Codes/gromacs-
> >> 2018/exe/share/gromacs/opencl
> >> --------------LOG START---------------
> >> <program source>:80:10: fatal error:
> 'nbnxn_ocl_kernel_pruneonly.cl
> <http://nbnxn_ocl_kernel_pruneonly.cl>h'
> >> file not found
> >> #include "nbnxn_ocl_kernel_pruneonly.cl
> <http://nbnxn_ocl_kernel_pruneonly.cl>h"
> >> ^
> >> ---------------LOG END----------------
> >>
> >> -------------------------------------------------------
> >> Program: gmx mdrun, version 2018
> >> Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 502)
> >> Function: cl_program gmx::ocl::compileProgram(FILE *,
> const std::string
> >> &, const std::string &, cl_context, cl_device_id,
> ocl_vendor_id_t)
> >>
> >> Internal error (bug):
> >> Failed to compile NBNXN kernels for GPU #AMD Radeon Pro 460
> Compute Engine
> >> Could not build OpenCL program, error was
> CL_BUILD_PROGRAM_FAILURE
> >>
> >> For more information and tips for troubleshooting, please
> check the GROMACS
> >> website at http://www.gromacs.org/Documentation/Errors
> <http://www.gromacs.org/Documentation/Errors>
> >> -------------------------------------------------------
> >>
> --------------------------------------------------------------------------
> >> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> >> with errorcode 1.
> >>
> >> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
> processes.
> >> You may or may not see output from other processes,
> depending on
> >> exactly when Open MPI kills them.
> >> ?????????????????????????????????????
> >>
> >>
> >>
> >> This is the configuration from md.log:
> >>
> >>
> >> gmx_mpi mdrun -notunepme
> >>
> >> GROMACS version: 2018
> >> Precision: single
> >> Memory model: 64 bit
> >> MPI library: MPI
> >> OpenMP support: disabled
> >> GPU support: OpenCL
> >> SIMD instructions: AVX2_256
> >> FFT library: fftw-3.3.5-sse2-avx
> >> RDTSCP usage: enabled
> >> TNG support: enabled
> >> Hwloc support: hwloc-1.11.0
> >> Tracing support: disabled
> >> Built on: 2018-01-11 08:54:21
> >> Built by: carlo at dhcp-162-244.celoria26-
> >> 16000022-smfn_biodip.unimi.it
> <http://16000022-smfn_biodip.unimi.it> [CMAKE]
> >> Build OS/arch: Darwin 17.3.0 x86_64
> >> Build CPU vendor: Intel
> >> Build CPU brand: Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz
> >> Build CPU family: 6 Model: 94 Stepping: 3
> >> Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16
> f16c fma hle htt
> >> intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb
> popcnt pse rdrnd
> >> rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> >> C compiler:
> /Applications/Xcode.app/Contents/Developer/Toolchains/
> >> XcodeDefault.xctoolchain/usr/bin/cc AppleClang 9.0.0.9000039
> >> C compiler flags: -march=core-avx2 -Wno-unknown-pragmas
> -O3 -DNDEBUG
> >> C++ compiler:
> /Applications/Xcode.app/Contents/Developer/Toolchains/
> >> XcodeDefault.xctoolchain/usr/bin/c++ AppleClang 9.0.0.9000039
> >> C++ compiler flags: -march=core-avx2 -std=c++11
> -Wno-unknown-pragmas
> >> -O3 -DNDEBUG
> >> OpenCL include dir: /System/Library/Frameworks/OpenCL.framework
> >> OpenCL library: /System/Library/Frameworks/OPENCL.framework
> >> OpenCL version: 1.2
> >>
> >>
> >> Running on 1 node with total 8 cores, 8 logical cores, 1
> compatible GPU
> >> Hardware detected on host dhcp-162-244.celoria26-
> >> 16000022-smfn_biodip.unimi.it
> <http://16000022-smfn_biodip.unimi.it> (the node of MPI rank 0):
> >> CPU info:
> >> Vendor: Intel
> >> Brand: Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz
> >> Family: 6 Model: 94 Stepping: 3
> >> Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma
> hle htt intel
> >> lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt
> pse rdrnd rdtscp
> >> rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> >> Hardware topology: Only logical processor count
> >> GPU info:
> >> Number of GPUs detected: 2
> >> #0: name: AMD Radeon Pro 460 Compute Engine, vendor:
> AMD, device
> >> version: OpenCL 1.2 , stat: compatible
> >> #1: name: Intel(R) HD Graphics 530, vendor: Intel Inc.,
> device
> >> version: OpenCL 1.2 , stat: incompatible
> >>
> >>
> >> Best,
> >> Carlo
> >>
> >>
> >> --
> >> Gromacs Developers mailing list
> >>
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> >
> >
> >
> >
> > --
> > Erik Lindahl <erik.lindahl at dbb.su.se
> <mailto:erik.lindahl at dbb.su.se>>
> > Professor of Biophysics, Dept. Biochemistry & Biophysics,
> Stockholm
> > University
> > Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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> --
> Erik Lindahl <erik.lindahl at dbb.su.se <mailto:erik.lindahl at dbb.su.se>>
> Professor of Biophysics, Dept. Biochemistry & Biophysics,
> Stockholm University
> Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
>
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