<div><div dir="auto">I was refering to the “-multi” error.</div><div dir="auto"><br></div><div dir="auto">Thanks for uploading the fix!</div><div dir="auto"><br></div><div dir="auto">Jernej</div><br><div class="gmail_quote"><div>On Fri, 12 Jan 2018 at 19:10, Berk Hess <<a href="mailto:hess@kth.se">hess@kth.se</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<div class="m_7687218201365232832moz-cite-prefix">Hi,<br>
<br>
What error are you referring to? The main error was on OpenCL
issue, whereas you use CUDA.<br>
Or are you referring to the -multi message? That occurs with all
invocations of mdrun, I have uploaded a fix for that.<br>
<br>
Cheers,<br>
<br>
Berk</div></div><div text="#000000" bgcolor="#FFFFFF"><div class="m_7687218201365232832moz-cite-prefix"><br>
<br>
On 2018-01-12 03:45, Jernej Zidar wrote:<br>
</div></div><div text="#000000" bgcolor="#FFFFFF">
<blockquote type="cite">
<div>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><<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>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="m_7687218201365232832HOEnZb">
<div class="m_7687218201365232832h5">
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Jan 11, 2018 at 2:06
PM, Carlo Camilloni <span><<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-XRjHCqjOdG0H3n=<a href="mailto:meOeqc4fDUSCyMn38dhReg@mail.gmail.com" target="_blank">meOeqc4fDUSCyMn38dhReg@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-2018/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_7687218201365232832m_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-2018/exe/bin/gmx_mpi<br>
>> Data prefix:
/Users/carlo/Codes/gromacs-2018/exe<br>
>> Working dir:
/Users/carlo/Codes/gromacs-2018/build/tests/<br>
>> regressiontests-2018/complex/orientation-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">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_SUPERCLUSTER=8<br>
>> -DNBNXN_GPU_CLUSTER_SIZE=8
-DNBNXN_GPU_JGROUP_SIZE=4<br>
>> -DGMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY=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" target="_blank">nbnxn_ocl_kernel_pruneonly.cl</a>h'<br>
>> file not found<br>
>> #include "<a href="http://nbnxn_ocl_kernel_pruneonly.cl" target="_blank">nbnxn_ocl_kernel_pruneonly.cl</a>h"<br>
>> ^<br>
>> ---------------LOG
END----------------<br>
>><br>
>> -------------------------------------------------------<br>
>> Program: gmx mdrun, version 2018<br>
>> Source file:
src/gromacs/gpu_utils/ocl_compiler.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/Documentation/Errors</a><br>
>> -------------------------------------------------------<br>
>> --------------------------------------------------------------------------<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>
>> ?????????????????????????????????????<br>
<div>
<div class="m_7687218201365232832m_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:
<a class="m_7687218201365232832moz-txt-link-abbreviated" href="mailto:carlo@dhcp-162-244.celoria26" target="_blank">carlo@dhcp-162-244.celoria26</a>-<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/Contents/Developer/Toolchains/<br>
>> XcodeDefault.xctoolchain/usr/bin/cc
AppleClang 9.0.0.9000039<br>
>> C compiler flags:
-march=core-avx2 -Wno-unknown-pragmas -O3
-DNDEBUG<br>
>> C++ compiler:
/Applications/Xcode.app/Contents/Developer/Toolchains/<br>
>> XcodeDefault.xctoolchain/usr/bin/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/OpenCL.framework<br>
>> OpenCL library:
/System/Library/Frameworks/OPENCL.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>
>> * Please search the archive at <a href="http://www.gromacs.org/" rel="noreferrer" target="_blank">http://www.gromacs.org/</a><br>
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>><br>
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>><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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<div>
<div>
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<div>
<div>
<div>
<div>
<div>Erik Lindahl <<a href="mailto:erik.lindahl@dbb.su.se" target="_blank">erik.lindahl@dbb.su.se</a>></div>
<div>Professor of Biophysics, Dept.
Biochemistry & Biophysics,
Stockholm University</div>
<div>Science for Life Laboratory, Box
1031, 17121 Solna, Sweden</div>
</div>
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