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

Carlo Camilloni carlo.camilloni at gmail.com
Thu Jan 11 12:16:14 CET 2018

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:
Compilation of source file /Users/carlo/Codes/gromacs-2018/exe/share/gromacs/opencl/nbnxn_ocl_kernels.cl failed!
--------------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
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
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


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