[gmx-developers] Gromacs 2018: orientation restraint regtest failing
Jernej Zidar
jernej.zidar at gmail.com
Fri Jan 12 15:39:16 CET 2018
I was refering to the “-multi” error.
Thanks for uploading the fix!
Jernej
On Fri, 12 Jan 2018 at 19:10, Berk Hess <hess at kth.se> wrote:
> 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>
> 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=
>>> 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
>>> >> 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_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.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/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 (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>
>>> > 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/Support/Mailing_Lists/GMX-developers_List before
>> posting!
>>
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>
>
>
>
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>
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> posting!
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