[gmx-users] Building Gromacs on a MacBook Pro with AMD Radeon Pro 560

[Michael Williams]

Hello, I’ve been having trouble building Gromacs 2018.3 on my MacBook Pro. I would like to be able to use OpenMP as well as the GPU (via OpenCL). I’ve searched for successful builds with similar systems described on this email list, but haven’t found anything that worked yet. 

Based on what I’ve read on this email list and various searches elsewhere, I am trying to build Gromacs 2018.3 using the OS X (10.14.3, Mojave) system default clang compiler (so that there is no compiler mismatch with the system OpenCL libraries). Since it does not have OpenMP support by default, I compiled libomp using the system’s clang. (As a side note, I built static libomp libraries). 

I installed the custom libomp with a prefix of $HOME/.local , which is mostly empty except for Cmake. When I built Gromacs, I used the following command: 

cmake .. -DGMX_BUILD_OWN_FFTW=ON \
-DCMAKE_INSTALL_PREFIX=/Users/michael/.local/apps/gromacs-2018.3-apple-clang-omp-ocl \
-DCMAKE_PREFIX_PATH=/Users/michael/.local \
-DREGRESSIONTEST_PATH=/Users/michael/.local/source/regressiontests-2018.3 \
-DCMAKE_C_FLAGS="-Xpreprocessor -fopenmp -lomp -I/Users/michael/.local/include -L/Users/michael/.local/lib” \
-DCMAKE_CXX_FLAGS="-Xpreprocessor -fopenmp -lomp -I/Users/michael/.local/include -L/Users/michael/.local/lib” \
-DGMX_GPU=ON \
-DGMX_USE_OPENCL=ON

Next I ran "make -j 4" and I didn’t get any errors during building (although I got the following warnings many times: clang: warning: -lomp: 'linker' input unused [-Wunused-command-line-argument]
clang: warning: argument unused during compilation: '-L/Users/michael/.local/lib' [-Wunused-command-line-argument]). 

However, when I ran "make check”, I got the errors pasted below. For the record, when I compiled the same version of Gromacs with the same configuration settings as above except with no GPU support, all of the tests passed. 

Any help or suggestions would be very much appreciated. Thanks kindly!

Mike


Errors during tests:

….
Using 1 MPI thread
Using 1 OpenMP thread 

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/michael/.local/source/gromacs-2018.3/src/gromacs/mdlib/nbnxn_ocl/nbnxn_ocl_kernels.cl failed!
-- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_ -DGMX_OCL_FASTGEN -DEL_CUTOFF -DEELNAME=_ElecCut -DLJ_COMB_GEOM -DVDWNAME=_VdwLJCombGeom -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 -cl-denorms-are-zero -I/Users/michael/.local/source/gromacs-2018.3/src/gromacs/mdlib/nbnxn_ocl
--------------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:     mdrun-test, version 2018.3
Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 507)
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 560 Compute Engine
  Could not build OpenCL program, error was CL_BUILD_PROGRAM_FAILURE

Followed by:

Abnormal return value for ' gmx mdrun -ntmpi 12      -notunepme >mdrun.out 2>&1' was 1
Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun -ntmpi 12    -ntomp 1  -notunepme >mdrun.out 2>&1' was 1
Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun -ntmpi 12    -ntomp 1  -notunepme >mdrun.out 2>&1' was 1
Retrying mdrun with better settings...
FAILED. Check mdrun.out, md.log file(s) in dd121 for dd121

Abnormal return value for ' gmx mdrun       -notunepme >mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in nbnxn_pme_order5 for nbnxn_pme_order5

Abnormal return value for ' gmx mdrun       -notunepme >mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in nbnxn_rzero for nbnxn_rzero

Abnormal return value for ' gmx mdrun -ntmpi 6      -notunepme >mdrun.out 2>&1' was 1
Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun -ntmpi 6    -ntomp 1  -notunepme >mdrun.out 2>&1' was 1
Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun -ntmpi 1      -notunepme >mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in orientation-restraints for orientation-restraints

Abnormal return value for ' gmx mdrun       -notunepme >mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in position-restraints for position-restraints

Abnormal return value for ' gmx mdrun       -notunepme >mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in pull_geometry_angle for pull_geometry_angle

Abnormal return value for ' gmx mdrun       -notunepme >mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in pull_geometry_angle-axis for pull_geometry_angle-axis
7 out of 51 complex tests FAILED

      Start 36: regressiontests/kernel
36/39 Test #36: regressiontests/kernel ...........   Passed   42.00 sec
      Start 37: regressiontests/freeenergy
37/39 Test #37: regressiontests/freeenergy .......***Failed    8.50 sec
                      :-) GROMACS - gmx mdrun, 2018.3 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar    Aldert van Buuren   Rudi van Drunen     Anton Feenstra  
  Gerrit Groenhof    Aleksei Iupinov   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:
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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 <http://www.gromacs.org/> for more information.

GROMACS is free software; you can redistribute it and/or modify it
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as published by the Free Software Foundation; either version 2.1
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GROMACS:      gmx mdrun, version 2018.3
Executable:   /Users/michael/.local/source/gromacs-2018.3/build-apple-clang-omp-ocl/bin/gmx
Data prefix:  /Users/michael/.local/source/gromacs-2018.3 (source tree)
Working dir:  /Users/michael/.local/source/regressiontests-2018.3
Command line:
  gmx mdrun -h


Thanx for Using GROMACS - Have a Nice Day


Abnormal return value for ' gmx mdrun       -notunepme >mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in expanded for expanded
1 out of 10 freeenergy tests FAILED

      Start 38: regressiontests/pdb2gmx
38/39 Test #38: regressiontests/pdb2gmx ..........   Passed   12.44 sec
      Start 39: regressiontests/rotation
39/39 Test #39: regressiontests/rotation .........   Passed    2.64 sec

92% tests passed, 3 tests failed out of 39