[gmx-users] 2019.2 build warnings

Alex nedomacho at gmail.com
Sat Apr 20 20:51:14 CEST 2019

Hi Mark,

Here you are:

                          :-) GROMACS - gmx, 2019.2 (-:

                             GROMACS is written by:
      Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. 
     Par Bjelkmar      Christian Blau   Viacheslav Bolnykh Kevin Boyd
  Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
   Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
   Aleksei Iupinov   Christoph Junghans     Joe Jordan Dimitrios Karkoulis
     Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
   Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
     Pascal Merz     Pieter Meulenhoff    Teemu Murtola Szilard Pall
     Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
    Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu 
  Christian Wennberg    Maarten Wolf
                            and the project leaders:
         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

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check out http://www.gromacs.org for more information.

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GROMACS:      gmx, version 2019.2
Executable: redacted/gmx2019.2_gpu/gromacs-2019.2/build/bin/./gmx
Data prefix:  redacted/gmx2019.2_gpu/gromacs-2019.2 (source tree)
Working dir:  redacted/gmx2019.2_gpu/gromacs-2019.2/build/bin
Command line:
   gmx -version

GROMACS version:    2019.2
Precision:          single
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:        CUDA
SIMD instructions:  AVX2_256
FFT library:        fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      hwloc-1.11.0
Tracing support:    disabled
C compiler:         /usr/bin/cc GNU 5.4.0
C compiler flags:    -mavx2 -mfma     -O3 -DNDEBUG -funroll-all-loops 
C++ compiler:       /usr/bin/c++ GNU 5.4.0
C++ compiler flags:  -mavx2 -mfma    -std=c++11   -O3 -DNDEBUG 
-funroll-all-loops -fexcess-precision=fast
CUDA compiler:      /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda 
compiler driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on 
Fri_Feb__8_19:08:17_PST_2019;Cuda compilation tools, release 10.1, V10.1.105
CUDA compiler 
CUDA driver:        10.10
CUDA runtime:       10.10

On 4/20/2019 12:38 PM, Mark Abraham wrote:
> Hi,
> Your experience looks unusual. What does gmx -version report?
> Mark
> On Fri., 19 Apr. 2019, 03:02 Alex, <nedomacho at gmail.com> wrote:
>> Can someone please confirm that my emails indeed reach this board? :)
>> Thank you.
>> On 4/16/2019 6:31 PM, Alex wrote:
>>> Okay, more interesting things are happening.
>>> At the end of 'make' I get a bunch of things like
>>> .................. nbnxn_cuda.cu <http://nbnxn_cuda.cu>(373): warning:
>>> variable "dim_grid" was declared but never referenced
>>> -bash: syntax error near unexpected token `373'
>>> More errors during 'make check' right after " Building NVCC (Device)
>>> object
>> src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o"
>>> then continues as if nothing happened.
>>> Finally, fails test #42 with what appears to be sarcasm:
>>> "...
>>> Thanx for Using GROMACS - Have a Nice Day
>>> Mdrun cannot use the requested (or automatic) number of ranks,
>>> retrying with 8.
>>> Abnormal return value for ' gmx mdrun    -nb cpu  -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 distance_restraints for
>>> distance_restraints
>>> 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  -notunepme >mdrun.out 2>&1' was -1
>>> FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron
>>> Re-running orientation-restraints using CPU-based PME
>>> Abnormal return value for ' gmx mdrun -ntmpi 1 -pme cpu    -notunepme
>>>> mdrun.out 2>&1' was -1
>>> FAILED. Check mdrun.out, md.log file(s) in
>>> orientation-restraints/pme-cpu for orientation-restraints-pme-cpu
>>> Re-running pull_geometry_angle using CPU-based PME
>>> Re-running pull_geometry_angle-axis using CPU-based PME
>>> Re-running pull_geometry_dihedral using CPU-based PME
>>> 3 out of 55 complex tests FAILED"
>>> Then finally quits for good. Your suggestions will be highly appreciated.
>>> Thank you,
>>> Alex
>> --
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