[gmx-developers] Gromacs 2018: orientation restraint regtest failing
Jernej Zidar
jernej.zidar at gmail.com
Fri Jan 12 03:46:30 CET 2018
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>
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> 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>
>> > To: gmx-developers at gromacs.org
>> > Subject: Re: [gmx-developers] Gromacs 2018: orientation restraint
>> > regtest failing
>> > Message-ID:
>> > <CAEJJM8GrNroV-XRjHCqjOdG0H3n=meOeqc4fDUSCyMn
>> 38dhReg 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
>> >> 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 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_SUPER
>> CLUSTER=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.clh'
>> >> file not found
>> >> #include "nbnxn_ocl_kernel_pruneonly.clh"
>> >> ^
>> >> ---------------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
>> >> -------------------------------------------------------
>> >> ------------------------------------------------------------
>> --------------
>> >> 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 [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/Conte
>> nts/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/Conte
>> nts/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 (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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>> >> or send a mail to gmx-developers-request at gromacs.org.
>> >
>> >
>> >
>> >
>> > --
>> > Erik Lindahl <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>
> Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
> University
> Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
>
> --
> Gromacs Developers mailing list
>
> * Please search the archive at http://www.gromacs.org/
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>
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