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

Erik Lindahl erik.lindahl at gmail.com
Thu Jan 11 12:38:21 CET 2018 

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
>
>
> --
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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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