[gmx-users] gromacs 2018.1 installation

Wed Mar 21 22:18:36 CET 2018

bin/gmx -version:

                         :-) GROMACS - gmx, 2018.1 (-:

                            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:
        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, version 2018.1
Executable:   /home/syue/Packages/gromacs-2018.1/build/bin//gmx
Data prefix:  /home/syue/Packages/gromacs-2018.1 (source tree)
Working dir:  /home/syue/Packages/gromacs-2018.1/build/bin
Command line:
  gmx -version

GROMACS version:    2018.1
Precision:          single
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:        disabled
SIMD instructions:  AVX_512
FFT library:        fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      hwloc-1.11.0
Tracing support:    disabled
Built on:           2018-03-21 17:58:53
Built by:           syue at tigercpu.princeton.edu [CMAKE]
Build OS/arch:      Linux 3.10.0-693.17.1.el7.x86_64 x86_64
Build CPU vendor:   Intel
Build CPU brand:    Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
Build CPU family:   6   Model: 85   Stepping: 4
Build CPU features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl
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:         /opt/rh/devtoolset-6/root/usr/bin/cc GNU 6.3.1
C compiler flags:    -mavx512f -mfma     -O2 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast
C++ compiler:       /opt/rh/devtoolset-6/root/usr/bin/c++ GNU 6.3.1
C++ compiler flags:  -mavx512f -mfma    -std=c++11   -O2 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast

On Wed, Mar 21, 2018 at 5:04 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Thanks - we need some more information to be able to help. What does
> bin/gmx -version report?
>
> Mark
>
> On Wed, Mar 21, 2018, 19:28 Jo <jojo412202 at gmail.com> wrote:
>
> > Hello,
> >
> > I have had some errors with the v2018.1 installation make check.  Any
> > suggestions on what I can do?
> >
> >  8/39 Test  #8: TUnitTests .....................***Exception: SegFault
> > 0.01 sec
> > [==========] Running 14 tests from 4 test cases.
> > [----------] Global test environment set-up.
> > [----------] 2 tests from ManyFFTTest
> > [ RUN      ] ManyFFTTest.Complex1DLength48Multi5Test
> >
> > .
> > .
> > .
> >
> > 26/39 Test #26: CorrelationsTest .................***Exception: SegFault
> > 0.10 sec
> > [==========] Running 21 tests from 3 test cases.
> > [----------] Global test environment set-up.
> > [----------] 10 tests from AutocorrTest
> > [ RUN      ] AutocorrTest.EacNormal
> > [       OK ] AutocorrTest.EacNormal (79 ms)
> > [ RUN      ] AutocorrTest.EacNoNormalize
> >
> > .
> > .
> > .
> >
> > 95% tests passed, 2 tests failed out of 39
> >
> > Label Time Summary:
> > GTest              =   9.06 sec (33 tests)
> > IntegrationTest    =   6.36 sec (3 tests)
> > MpiTest            =   0.21 sec (3 tests)
> > UnitTest           =   2.70 sec (30 tests)
> >
> > Total Test time (real) = 163.71 sec
> >
> > The following tests FAILED:
> >   8 - FFTUnitTests (SEGFAULT)
> > 26 - CorrelationsTest (SEGFAULT)
> > Errors while running CTest
> > CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
> > 'CMakeFiles/run-ctest-nophys' failed
> > make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
> > CMakeFiles/Makefile2:1160: recipe for target
> > 'CMakeFiles/run-ctest-nophys.dir/all' failed
> > make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
> > CMakeFiles/Makefile2:971: recipe for target 'CMakeFiles/check.dir/rule'
> > failed
> > make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> > Makefile:546: recipe for target 'check' failed
> > make: *** [check] Error 2
> >
> >
> > Thanks,
> >
> > Jo
> > --
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> >
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