[gmx-developers] Gromacs 2018: orientation restraint regtest failing

Erik Lindahl erik.lindahl at gmail.com
Thu Jan 11 12:40:46 CET 2018 

PS: Another thing is to try the compile manually (no line breaks, and make
sure there are no double spaces):

/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries/openclc
-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
/Users/carlo/Codes/gromacs-2018/exe/share/gromacs/opencl/
nbnxn_ocl_kernels.cl

What happens?





On Thu, Jan 11, 2018 at 12:38 PM, Erik Lindahl <erik.lindahl at gmail.com>
wrote:

> 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-201
>> 8/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-201
>> 8/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-2
>> 018/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.celoria26-1600002
>> 2-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
>



-- 
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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