<div dir="ltr">Hi,<div><br></div><div>I'm able to replicate this error on two different Linux machines too. It does not depend on whether GPUs are used or not. </div><div><br></div><div>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.</div><div><br></div><div>It also seems there is one message displayed for every MPI task started.</div><div><br></div><div>Jernej</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jan 11, 2018 at 9:37 PM, Erik Lindahl <span dir="ltr"><<a href="mailto:erik.lindahl@gmail.com" target="_blank">erik.lindahl@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">HI,<div><br></div><div>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 :-/</div><div><br></div><div>Cheers,</div><div><br></div><div>Erik </div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jan 11, 2018 at 2:06 PM, Carlo Camilloni <span dir="ltr"><<a href="mailto:carlo.camilloni@gmail.com" target="_blank">carlo.camilloni@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Erik<br>
<br>
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..<br>
And if I remove everything and I reinstall the parallel one it also works, so it probably doesn’t matter..<br>
<br>
Carlo<br>
<br>
<br>
<br>
<br>
> Date: Thu, 11 Jan 2018 12:38:14 +0100<br>
> From: Erik Lindahl <<a href="mailto:erik.lindahl@gmail.com" target="_blank">erik.lindahl@gmail.com</a>><br>
> To: <a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a><br>
> Subject: Re: [gmx-developers] Gromacs 2018: orientation restraint<br>
> regtest failing<br>
> Message-ID:<br>
> <CAEJJM8GrNroV-<wbr>XRjHCqjOdG0H3n=<a href="mailto:meOeqc4fDUSCyMn38dhReg@mail.gmail.com" target="_blank">meOeqc4fDUSCyMn<wbr>38dhReg@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
<span>><br>
> Hi Carlo,<br>
><br>
> Your hardware looks almost to identical to my macbook, and for me it works<br>
> without problems.<br>
><br>
> Could you<br>
><br>
> 1) Confirm that the header file in question is present in<br>
> /Users/carlo/Codes/gromacs-201<wbr>8/exe/share/gromacs/opencl<br>
><br>
> 2) Try compiling without MPI - this is the only obvious setup difference I<br>
> can see from what I tried.<br>
><br>
> Cheers,<br>
><br>
> Erik<br>
><br>
> On Thu, Jan 11, 2018 at 12:16 PM, Carlo Camilloni <<a href="mailto:carlo.camilloni@gmail.com" target="_blank">carlo.camilloni@gmail.com</a><br>
>> wrote:<br>
><br>
>> Dear all,<br>
>><br>
>> First of all once again congratulations for the new gromacs!<br>
>><br>
>> I have just compiled it on my MacBook Pro with OpenCL and after running<br>
>> the regtests I got this single failing test;<br>
>><br>
</span>>> BTW there is this weird output always: 'No option -multi?<br>
<div><div class="m_5908609438363287214h5">>><br>
>><br>
>> :-) GROMACS - gmx mdrun, 2018 (-:<br>
>><br>
>> GROMACS is written by:<br>
>> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par<br>
>> Bjelkmar<br>
>> Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof<br>
>> Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios<br>
>> Karkoulis<br>
>> Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson<br>
>> Justin A. Lemkul Viveca Lindahl Magnus Lundborg Pieter Meulenhoff<br>
>> Erik Marklund Teemu Murtola Szilard Pall Sander Pronk<br>
>> Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers<br>
>> Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf<br>
>> and the project leaders:<br>
>> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel<br>
>><br>
>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>
>> Copyright (c) 2001-2017, The GROMACS development team at<br>
>> Uppsala University, Stockholm University and<br>
>> the Royal Institute of Technology, Sweden.<br>
>> check out <a href="http://www.gromacs.org" rel="noreferrer" target="_blank">http://www.gromacs.org</a> for more information.<br>
>><br>
>> GROMACS is free software; you can redistribute it and/or modify it<br>
>> under the terms of the GNU Lesser General Public License<br>
>> as published by the Free Software Foundation; either version 2.1<br>
>> of the License, or (at your option) any later version.<br>
>><br>
>> GROMACS: gmx mdrun, version 2018<br>
>> Executable: /Users/carlo/Codes/gromacs-20<wbr>18/exe/bin/gmx_mpi<br>
>> Data prefix: /Users/carlo/Codes/gromacs-201<wbr>8/exe<br>
>> Working dir: /Users/carlo/Codes/gromacs-201<wbr>8/build/tests/<br>
>> regressiontests-2018/complex/o<wbr>rientation-restraints<br>
>> Command line:<br>
>> gmx_mpi mdrun -notunepme<br>
>><br>
>> Reading file topol.tpr, VERSION 2018 (single precision)<br>
>> Changing nstlist from 10 to 100, rlist from 2 to 2<br>
>><br>
>> No option -multi<br>
>> Using 1 MPI process<br>
>> 1 GPU auto-selected for this run.<br>
>> Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:<br>
>> PP:0<br>
>> Compilation of source file /Users/carlo/Codes/gromacs-<br>
>> 2018/exe/share/gromacs/opencl/<a href="http://nbnxn_ocl_kernels.cl" rel="noreferrer" target="_blank"><wbr>nbnxn_ocl_kernels.cl</a> failed!<br>
>> -- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_<br>
>> -DGMX_OCL_FASTGEN_ADD_TWINCUT -DEL_EWALD_ANA -DEELNAME=_ElecEw -DLJ_COMB_LB<br>
>> -DVDWNAME=_VdwLJCombLB -DCENTRAL=22 -DNBNXN_GPU_NCLUSTER_PER_SUPER<wbr>CLUSTER=8<br>
>> -DNBNXN_GPU_CLUSTER_SIZE=8 -DNBNXN_GPU_JGROUP_SIZE=4<br>
>> -DGMX_NBNXN_PRUNE_KERNEL_J4_CO<wbr>NCURRENCY=4 -DNBNXN_MIN_RSQ=3.82e-07f<br>
>> -DIATYPE_SHMEM -cl-fast-relaxed-math -I/Users/carlo/Codes/gromacs-<br>
>> 2018/exe/share/gromacs/opencl<br>
>> --------------LOG START---------------<br>
>> <program source>:80:10: fatal error: '<a href="http://nbnxn_ocl_kernel_pruneonly.cl">nbnxn_ocl_kernel_pruneonly.cl</a><wbr>h'<br>
>> file not found<br>
>> #include "<a href="http://nbnxn_ocl_kernel_pruneonly.cl">nbnxn_ocl_kernel_pruneonly.cl</a><wbr>h"<br>
>> ^<br>
>> ---------------LOG END----------------<br>
>><br>
>> ------------------------------<wbr>-------------------------<br>
>> Program: gmx mdrun, version 2018<br>
>> Source file: src/gromacs/gpu_utils/ocl_comp<wbr>iler.cpp (line 502)<br>
>> Function: cl_program gmx::ocl::compileProgram(FILE *, const std::string<br>
>> &, const std::string &, cl_context, cl_device_id, ocl_vendor_id_t)<br>
>><br>
>> Internal error (bug):<br>
>> Failed to compile NBNXN kernels for GPU #AMD Radeon Pro 460 Compute Engine<br>
>> Could not build OpenCL program, error was CL_BUILD_PROGRAM_FAILURE<br>
>><br>
>> For more information and tips for troubleshooting, please check the GROMACS<br>
>> website at <a href="http://www.gromacs.org/Documentation/Errors" rel="noreferrer" target="_blank">http://www.gromacs.org/Documen<wbr>tation/Errors</a><br>
>> ------------------------------<wbr>-------------------------<br>
>> ------------------------------<wbr>------------------------------<wbr>--------------<br>
>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD<br>
>> with errorcode 1.<br>
>><br>
>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br>
>> You may or may not see output from other processes, depending on<br>
>> exactly when Open MPI kills them.<br>
</div></div>>> ??????????????????????????????<wbr>???????<br>
<div><div class="m_5908609438363287214h5">>><br>
>><br>
>><br>
>> This is the configuration from md.log:<br>
>><br>
>><br>
>> gmx_mpi mdrun -notunepme<br>
>><br>
>> GROMACS version: 2018<br>
>> Precision: single<br>
>> Memory model: 64 bit<br>
>> MPI library: MPI<br>
>> OpenMP support: disabled<br>
>> GPU support: OpenCL<br>
>> SIMD instructions: AVX2_256<br>
>> FFT library: fftw-3.3.5-sse2-avx<br>
>> RDTSCP usage: enabled<br>
>> TNG support: enabled<br>
>> Hwloc support: hwloc-1.11.0<br>
>> Tracing support: disabled<br>
>> Built on: 2018-01-11 08:54:21<br>
>> Built by: carlo@dhcp-162-244.celoria26-<br>
>> <a href="http://16000022-smfn_biodip.unimi.it" rel="noreferrer" target="_blank">16000022-smfn_biodip.unimi.it</a> [CMAKE]<br>
>> Build OS/arch: Darwin 17.3.0 x86_64<br>
>> Build CPU vendor: Intel<br>
>> Build CPU brand: Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz<br>
>> Build CPU family: 6 Model: 94 Stepping: 3<br>
>> Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt<br>
>> intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd<br>
>> rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic<br>
>> C compiler: /Applications/Xcode.app/Conte<wbr>nts/Developer/Toolchains/<br>
>> XcodeDefault.xctoolchain/usr/b<wbr>in/cc AppleClang 9.0.0.9000039<br>
>> C compiler flags: -march=core-avx2 -Wno-unknown-pragmas -O3 -DNDEBUG<br>
>> C++ compiler: /Applications/Xcode.app/Conte<wbr>nts/Developer/Toolchains/<br>
>> XcodeDefault.xctoolchain/usr/b<wbr>in/c++ AppleClang 9.0.0.9000039<br>
>> C++ compiler flags: -march=core-avx2 -std=c++11 -Wno-unknown-pragmas<br>
>> -O3 -DNDEBUG<br>
>> OpenCL include dir: /System/Library/Frameworks/Ope<wbr>nCL.framework<br>
>> OpenCL library: /System/Library/Frameworks/OP<wbr>ENCL.framework<br>
>> OpenCL version: 1.2<br>
>><br>
>><br>
>> Running on 1 node with total 8 cores, 8 logical cores, 1 compatible GPU<br>
>> Hardware detected on host dhcp-162-244.celoria26-<br>
>> <a href="http://16000022-smfn_biodip.unimi.it" rel="noreferrer" target="_blank">16000022-smfn_biodip.unimi.it</a> (the node of MPI rank 0):<br>
>> CPU info:<br>
>> Vendor: Intel<br>
>> Brand: Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz<br>
>> Family: 6 Model: 94 Stepping: 3<br>
>> Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel<br>
>> lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp<br>
>> rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic<br>
>> Hardware topology: Only logical processor count<br>
>> GPU info:<br>
>> Number of GPUs detected: 2<br>
>> #0: name: AMD Radeon Pro 460 Compute Engine, vendor: AMD, device<br>
>> version: OpenCL 1.2 , stat: compatible<br>
>> #1: name: Intel(R) HD Graphics 530, vendor: Intel Inc., device<br>
>> version: OpenCL 1.2 , stat: incompatible<br>
>><br>
>><br>
>> Best,<br>
>> Carlo<br>
>><br>
>><br>
>> --<br>
>> Gromacs Developers mailing list<br>
>><br>
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><br>
><br>
><br>
><br>
> --<br>
> Erik Lindahl <<a href="mailto:erik.lindahl@dbb.su.se" target="_blank">erik.lindahl@dbb.su.se</a>><br>
> Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm<br>
> University<br>
> Science for Life Laboratory, Box 1031, 17121 Solna, Sweden<br>
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</span>> End of gromacs.org_gmx-developers Digest, Vol 165, Issue 7<br>
> ******************************<wbr>****************************<br>
<div class="m_5908609438363287214HOEnZb"><div class="m_5908609438363287214h5"><br>
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