Re: [gmx-users] Make check not passing tests on 2018.5

2019-02-15 Thread Schulz, Roland
You compiled gcc from sources? From which sources (e.g. tgz or deb-src, any 
patches?) How did you compile gcc (your configure arguments)?
Could you try with GMX_FFT_LIBRARY=fftpack or with the fftw provided by the 
system by running cmake without GMX_BUILD_OWN_FFTW? Want to make sure it isn't 
FFTW with AVX512 where the issue is for you.

Roland

> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
> David Lister
> Sent: Friday, February 15, 2019 9:19 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Make check not passing tests on 2018.5
> 
> That's quite interesting, I wonder what it is about my system that is causing
> the issue. If it means anything, this is on a fresh install of Ubuntu 18.04.
> 
> I've had a chance to experiment with compilers on my system. GCC 8.2.0
> passes with avx-512. Using a freshly compiled version of GCC 7.3.0 and tried 
> it,
> but it showed the same behavior as before: failing make check with avx-512
> and passing with avx2-256.
> 
> Cheers,
> David
> 
> On Fri, Feb 15, 2019 at 7:53 AM Szilárd Páll  wrote:
> 
> > Forgot to get back, but same here, I checked on a Core i9 with gcc 7.3
> > (compiled from source though) and could not reproduce it.
> > --
> > Szilárd
> >
> >
> > On Thu, Feb 14, 2019 at 6:36 PM Schulz, Roland
> > 
> > wrote:
> >
> > > I can't reproduce this. For me the regressiontests pass with gcc
> > > 7.3, AVX_512, double.
> > >
> > > Roland
> > >
> > > > -Original Message-
> > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> > > > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On
> > > > Behalf
> > Of
> > > > David Lister
> > > > Sent: Tuesday, February 12, 2019 4:59 PM
> > > > To: gmx-us...@gromacs.org
> > > > Subject: Re: [gmx-users] Make check not passing tests on 2018.5
> > > >
> > > > I have yet to have a chance to test a different compiler. The
> > > > AVX_512
> > is
> > > > reproducible and showed the same error in 3 tests.
> > > >
> > > > I hope to check gcc 8 later this week.
> > > >
> > > > Cheers,
> > > > David
> > > >
> > > > On Mon, Feb 11, 2019 at 6:15 PM Szilárd Páll
> > > > 
> > > wrote:
> > > >
> > > > > What about the other checks I suggested? IS the failing test
> > > > > 100% reproducible with AVX_512?
> > > > > --
> > > > > Szilárd
> > > > >
> > > > > On Mon, Feb 11, 2019 at 9:15 PM David Lister 
> > > wrote:
> > > > > >
> > > > > > Hello,
> > > > > >
> > > > > > My bad, I copied my single precision build by mistake, this is
> > > > > > what was used originally for double precision:
> > > > > >
> > > > > > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -
> > > > DGMX_BUILD_OWN_FFTW=ON
> > > > > > -DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
> > > > > > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5 -
> > > > DGMX_DOUBLE=on
> > > > > >
> > > > > > Adding -DGMX_SIMD=AVX2_256 did resolve the problem, thank-
> you
> > > > > > for the
> > > > > help!
> > > > > > I did not test different compilers as I don't have any others
> > > > > > on my
> > > > > system
> > > > > > at the moment.
> > > > > >
> > > > > > Cheers,
> > > > > > David
> > > > > >
> > > > > > On Tue, Feb 5, 2019 at 7:15 AM Szilárd Páll <
> > pall.szil...@gmail.com>
> > > > > wrote:
> > > > > >
> > > > > > > On Fri, Feb 1, 2019 at 5:01 AM David Lister
> > > > > > > 
> > > wrote:
> > > > > > > >
> > > > > > > > Hello,
> > > > > > > >
> > > > > > > > I've compiled gromacs 2018.5 in double precision a couple
> > > > > > > > times now
> > > > > and
> > > > > > > it
> > > > > > > > keeps on failing the same tests every time. This is on
> > > > > > > > Ubuntu
> > > > > > > > 

Re: [gmx-users] Make check not passing tests on 2018.5

2019-02-15 Thread David Lister
That's quite interesting, I wonder what it is about my system that is
causing the issue. If it means anything, this is on a fresh install of
Ubuntu 18.04.

I've had a chance to experiment with compilers on my system. GCC 8.2.0
passes with avx-512. Using a freshly compiled version of GCC 7.3.0 and
tried it, but it showed the same behavior as before: failing make check
with avx-512 and passing with avx2-256.

Cheers,
David

On Fri, Feb 15, 2019 at 7:53 AM Szilárd Páll  wrote:

> Forgot to get back, but same here, I checked on a Core i9 with gcc 7.3
> (compiled from source though) and could not reproduce it.
> --
> Szilárd
>
>
> On Thu, Feb 14, 2019 at 6:36 PM Schulz, Roland 
> wrote:
>
> > I can't reproduce this. For me the regressiontests pass with gcc 7.3,
> > AVX_512, double.
> >
> > Roland
> >
> > > -Original Message-
> > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> > > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf
> Of
> > > David Lister
> > > Sent: Tuesday, February 12, 2019 4:59 PM
> > > To: gmx-us...@gromacs.org
> > > Subject: Re: [gmx-users] Make check not passing tests on 2018.5
> > >
> > > I have yet to have a chance to test a different compiler. The AVX_512
> is
> > > reproducible and showed the same error in 3 tests.
> > >
> > > I hope to check gcc 8 later this week.
> > >
> > > Cheers,
> > > David
> > >
> > > On Mon, Feb 11, 2019 at 6:15 PM Szilárd Páll 
> > wrote:
> > >
> > > > What about the other checks I suggested? IS the failing test 100%
> > > > reproducible with AVX_512?
> > > > --
> > > > Szilárd
> > > >
> > > > On Mon, Feb 11, 2019 at 9:15 PM David Lister 
> > wrote:
> > > > >
> > > > > Hello,
> > > > >
> > > > > My bad, I copied my single precision build by mistake, this is what
> > > > > was used originally for double precision:
> > > > >
> > > > > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -
> > > DGMX_BUILD_OWN_FFTW=ON
> > > > > -DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
> > > > > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5 -
> > > DGMX_DOUBLE=on
> > > > >
> > > > > Adding -DGMX_SIMD=AVX2_256 did resolve the problem, thank-you for
> > > > > the
> > > > help!
> > > > > I did not test different compilers as I don't have any others on my
> > > > system
> > > > > at the moment.
> > > > >
> > > > > Cheers,
> > > > > David
> > > > >
> > > > > On Tue, Feb 5, 2019 at 7:15 AM Szilárd Páll <
> pall.szil...@gmail.com>
> > > > wrote:
> > > > >
> > > > > > On Fri, Feb 1, 2019 at 5:01 AM David Lister 
> > wrote:
> > > > > > >
> > > > > > > Hello,
> > > > > > >
> > > > > > > I've compiled gromacs 2018.5 in double precision a couple times
> > > > > > > now
> > > > and
> > > > > > it
> > > > > > > keeps on failing the same tests every time. This is on Ubuntu
> > > > > > > 18.04
> > > > with
> > > > > > an
> > > > > > > i9 7900X.
> > > > > > >
> > > > > > > The cmake I used was:
> > > > > > > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on
> > > > > > -DGMX_BUILD_OWN_FFTW=ON
> > > > > > > -DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
> > > > > > > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5
> > > > > >
> > > > > > That couldn't have been the cmake invocation as it's not double
> > > > > > precision build (and -DGMX_GPU=on is not valid in a double
> > > > > > precision build).
> > > > > >
> > > > > > >
> > > > > > > The problem with make check is:
> > > > > > >
> > > > > > > 34/39 Test #34: regressiontests/simple ...   Passed
> > 3.01
> > > > sec
> > > > > > >   Start 35: regressiontests/complex
> > > > > > > 35/39 Test #35: regressiontests/complex ..***Failed
> >  34.69
> > > > sec
> > > > > > > Will test using exe

Re: [gmx-users] Make check not passing tests on 2018.5

2019-02-15 Thread Szilárd Páll
Forgot to get back, but same here, I checked on a Core i9 with gcc 7.3
(compiled from source though) and could not reproduce it.
--
Szilárd


On Thu, Feb 14, 2019 at 6:36 PM Schulz, Roland 
wrote:

> I can't reproduce this. For me the regressiontests pass with gcc 7.3,
> AVX_512, double.
>
> Roland
>
> > -Original Message-
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
> > David Lister
> > Sent: Tuesday, February 12, 2019 4:59 PM
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Make check not passing tests on 2018.5
> >
> > I have yet to have a chance to test a different compiler. The AVX_512 is
> > reproducible and showed the same error in 3 tests.
> >
> > I hope to check gcc 8 later this week.
> >
> > Cheers,
> > David
> >
> > On Mon, Feb 11, 2019 at 6:15 PM Szilárd Páll 
> wrote:
> >
> > > What about the other checks I suggested? IS the failing test 100%
> > > reproducible with AVX_512?
> > > --
> > > Szilárd
> > >
> > > On Mon, Feb 11, 2019 at 9:15 PM David Lister 
> wrote:
> > > >
> > > > Hello,
> > > >
> > > > My bad, I copied my single precision build by mistake, this is what
> > > > was used originally for double precision:
> > > >
> > > > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -
> > DGMX_BUILD_OWN_FFTW=ON
> > > > -DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
> > > > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5 -
> > DGMX_DOUBLE=on
> > > >
> > > > Adding -DGMX_SIMD=AVX2_256 did resolve the problem, thank-you for
> > > > the
> > > help!
> > > > I did not test different compilers as I don't have any others on my
> > > system
> > > > at the moment.
> > > >
> > > > Cheers,
> > > > David
> > > >
> > > > On Tue, Feb 5, 2019 at 7:15 AM Szilárd Páll 
> > > wrote:
> > > >
> > > > > On Fri, Feb 1, 2019 at 5:01 AM David Lister 
> wrote:
> > > > > >
> > > > > > Hello,
> > > > > >
> > > > > > I've compiled gromacs 2018.5 in double precision a couple times
> > > > > > now
> > > and
> > > > > it
> > > > > > keeps on failing the same tests every time. This is on Ubuntu
> > > > > > 18.04
> > > with
> > > > > an
> > > > > > i9 7900X.
> > > > > >
> > > > > > The cmake I used was:
> > > > > > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on
> > > > > -DGMX_BUILD_OWN_FFTW=ON
> > > > > > -DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
> > > > > > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5
> > > > >
> > > > > That couldn't have been the cmake invocation as it's not double
> > > > > precision build (and -DGMX_GPU=on is not valid in a double
> > > > > precision build).
> > > > >
> > > > > >
> > > > > > The problem with make check is:
> > > > > >
> > > > > > 34/39 Test #34: regressiontests/simple ...   Passed
> 3.01
> > > sec
> > > > > >   Start 35: regressiontests/complex
> > > > > > 35/39 Test #35: regressiontests/complex ..***Failed
>  34.69
> > > sec
> > > > > > Will test using executable suffix _d
> > > > > >  :-) GROMACS - gmx mdrun, 2018.5 (double precision)
> (-:
> > > > > >
> > > > > > GROMACS is written by:
> > > > > >  Emile Apol  Rossen Apostolov  Paul Bauer Herman
> J.C.
> > > > > Berendsen
> > > > > > Par BjelkmarAldert van Buuren   Rudi van Drunen Anton
> > > > > Feenstra
> > > > > >   Gerrit GroenhofAleksei Iupinov   Christoph Junghans   Anca
> > > Hamuraru
> > > > > >  Vincent Hindriksen Dimitrios KarkoulisPeter Kasson
> Jiri
> > > Kraus
> > > > > >   Carsten Kutzner  Per Larsson  Justin A. Lemkul
> Viveca
> > > > > Lindahl
> > > > > >   Magnus Lundborg   Pieter MeulenhoffErik Marklund  Teemu
> > > Murtola
> > > > > > Szila

Re: [gmx-users] Make check not passing tests on 2018.5

2019-02-14 Thread Schulz, Roland
I can't reproduce this. For me the regressiontests pass with gcc 7.3, AVX_512, 
double.

Roland

> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
> David Lister
> Sent: Tuesday, February 12, 2019 4:59 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Make check not passing tests on 2018.5
> 
> I have yet to have a chance to test a different compiler. The AVX_512 is
> reproducible and showed the same error in 3 tests.
> 
> I hope to check gcc 8 later this week.
> 
> Cheers,
> David
> 
> On Mon, Feb 11, 2019 at 6:15 PM Szilárd Páll  wrote:
> 
> > What about the other checks I suggested? IS the failing test 100%
> > reproducible with AVX_512?
> > --
> > Szilárd
> >
> > On Mon, Feb 11, 2019 at 9:15 PM David Lister  wrote:
> > >
> > > Hello,
> > >
> > > My bad, I copied my single precision build by mistake, this is what
> > > was used originally for double precision:
> > >
> > > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -
> DGMX_BUILD_OWN_FFTW=ON
> > > -DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
> > > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5 -
> DGMX_DOUBLE=on
> > >
> > > Adding -DGMX_SIMD=AVX2_256 did resolve the problem, thank-you for
> > > the
> > help!
> > > I did not test different compilers as I don't have any others on my
> > system
> > > at the moment.
> > >
> > > Cheers,
> > > David
> > >
> > > On Tue, Feb 5, 2019 at 7:15 AM Szilárd Páll 
> > wrote:
> > >
> > > > On Fri, Feb 1, 2019 at 5:01 AM David Lister  wrote:
> > > > >
> > > > > Hello,
> > > > >
> > > > > I've compiled gromacs 2018.5 in double precision a couple times
> > > > > now
> > and
> > > > it
> > > > > keeps on failing the same tests every time. This is on Ubuntu
> > > > > 18.04
> > with
> > > > an
> > > > > i9 7900X.
> > > > >
> > > > > The cmake I used was:
> > > > > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on
> > > > -DGMX_BUILD_OWN_FFTW=ON
> > > > > -DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
> > > > > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5
> > > >
> > > > That couldn't have been the cmake invocation as it's not double
> > > > precision build (and -DGMX_GPU=on is not valid in a double
> > > > precision build).
> > > >
> > > > >
> > > > > The problem with make check is:
> > > > >
> > > > > 34/39 Test #34: regressiontests/simple ...   Passed3.01
> > sec
> > > > >   Start 35: regressiontests/complex
> > > > > 35/39 Test #35: regressiontests/complex ..***Failed   34.69
> > sec
> > > > > Will test using executable suffix _d
> > > > >  :-) GROMACS - gmx mdrun, 2018.5 (double precision) (-:
> > > > >
> > > > > GROMACS is written by:
> > > > >  Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C.
> > > > Berendsen
> > > > > Par BjelkmarAldert van Buuren   Rudi van Drunen Anton
> > > > Feenstra
> > > > >   Gerrit GroenhofAleksei Iupinov   Christoph Junghans   Anca
> > Hamuraru
> > > > >  Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri
> > Kraus
> > > > >   Carsten Kutzner  Per Larsson  Justin A. LemkulViveca
> > > > Lindahl
> > > > >   Magnus Lundborg   Pieter MeulenhoffErik Marklund  Teemu
> > Murtola
> > > > > Szilard Pall   Sander Pronk  Roland Schulz Alexey
> > > > Shvetsov
> > > > >Michael Shirts Alfons Sijbers Peter TielemanTeemu
> > > > Virolainen
> > > > >  Christian WennbergMaarten 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

Re: [gmx-users] Make check not passing tests on 2018.5

2019-02-12 Thread David Lister
I have yet to have a chance to test a different compiler. The AVX_512 is
reproducible and showed the same error in 3 tests.

I hope to check gcc 8 later this week.

Cheers,
David

On Mon, Feb 11, 2019 at 6:15 PM Szilárd Páll  wrote:

> What about the other checks I suggested? IS the failing test 100%
> reproducible with AVX_512?
> --
> Szilárd
>
> On Mon, Feb 11, 2019 at 9:15 PM David Lister  wrote:
> >
> > Hello,
> >
> > My bad, I copied my single precision build by mistake, this is what was
> > used originally for double precision:
> >
> > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_OWN_FFTW=ON
> > -DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
> > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5 -DGMX_DOUBLE=on
> >
> > Adding -DGMX_SIMD=AVX2_256 did resolve the problem, thank-you for the
> help!
> > I did not test different compilers as I don't have any others on my
> system
> > at the moment.
> >
> > Cheers,
> > David
> >
> > On Tue, Feb 5, 2019 at 7:15 AM Szilárd Páll 
> wrote:
> >
> > > On Fri, Feb 1, 2019 at 5:01 AM David Lister  wrote:
> > > >
> > > > Hello,
> > > >
> > > > I've compiled gromacs 2018.5 in double precision a couple times now
> and
> > > it
> > > > keeps on failing the same tests every time. This is on Ubuntu 18.04
> with
> > > an
> > > > i9 7900X.
> > > >
> > > > The cmake I used was:
> > > > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on
> > > -DGMX_BUILD_OWN_FFTW=ON
> > > > -DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
> > > > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5
> > >
> > > That couldn't have been the cmake invocation as it's not double
> > > precision build (and -DGMX_GPU=on is not valid in a double precision
> > > build).
> > >
> > > >
> > > > The problem with make check is:
> > > >
> > > > 34/39 Test #34: regressiontests/simple ...   Passed3.01
> sec
> > > >   Start 35: regressiontests/complex
> > > > 35/39 Test #35: regressiontests/complex ..***Failed   34.69
> sec
> > > > Will test using executable suffix _d
> > > >  :-) GROMACS - gmx mdrun, 2018.5 (double precision) (-:
> > > >
> > > > GROMACS is written by:
> > > >  Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C.
> > > Berendsen
> > > > Par BjelkmarAldert van Buuren   Rudi van Drunen Anton
> > > Feenstra
> > > >   Gerrit GroenhofAleksei Iupinov   Christoph Junghans   Anca
> Hamuraru
> > > >  Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri
> Kraus
> > > >   Carsten Kutzner  Per Larsson  Justin A. LemkulViveca
> > > Lindahl
> > > >   Magnus Lundborg   Pieter MeulenhoffErik Marklund  Teemu
> Murtola
> > > > Szilard Pall   Sander Pronk  Roland Schulz Alexey
> > > Shvetsov
> > > >Michael Shirts Alfons Sijbers Peter TielemanTeemu
> > > Virolainen
> > > >  Christian WennbergMaarten 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 2018.5 (double precision)
> > > > Executable:   /home/david/gromacs-2018.5/build/bin/gmx_d
> > > > Data prefix:  /home/david/gromacs-2018.5 (source tree)
> > > > Working dir:
> > > /home/david/gromacs-2018.5/build/tests/regressiontests-2018.5
> > > > Command line:
> > > >   gmx_d mdrun -h
> > > >
> > > >
> > > > 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_d mdrun-nb cpu   -notunepme
> > > > >mdrun.out 2>&1' was 1
> > > > Retrying mdrun with better settings...
> > > > Mdrun cannot use the requested (or automatic) number of ranks,
> retrying
> > > with 8.
> > > >
> > > > Abnormal return value for ' gmx_d mdrun-nb cpu   -notunepme
> > > > >mdrun.out 2>&1' was 1
> > > > Retrying mdrun with better settings...
> > > > FAILED. Check checkpot.out (69 errors), checkforce.out (224 errors)
> > > > file(s) in distance_restraints for distance_restraints
> > > > Mdrun cannot use the requested (or automatic) number of ranks,
> retrying
> > > with 8.
> > > >
> > > > Abnormal return value for ' gmx_d mdrun-nb cpu   -notunepme
> > > > >mdrun.out 2>&1' was 1
> > > > Retrying mdrun with better settings...
> > > > Mdrun cannot 

Re: [gmx-users] Make check not passing tests on 2018.5

2019-02-11 Thread Szilárd Páll
What about the other checks I suggested? IS the failing test 100%
reproducible with AVX_512?
--
Szilárd

On Mon, Feb 11, 2019 at 9:15 PM David Lister  wrote:
>
> Hello,
>
> My bad, I copied my single precision build by mistake, this is what was
> used originally for double precision:
>
> cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_OWN_FFTW=ON
> -DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
> -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5 -DGMX_DOUBLE=on
>
> Adding -DGMX_SIMD=AVX2_256 did resolve the problem, thank-you for the help!
> I did not test different compilers as I don't have any others on my system
> at the moment.
>
> Cheers,
> David
>
> On Tue, Feb 5, 2019 at 7:15 AM Szilárd Páll  wrote:
>
> > On Fri, Feb 1, 2019 at 5:01 AM David Lister  wrote:
> > >
> > > Hello,
> > >
> > > I've compiled gromacs 2018.5 in double precision a couple times now and
> > it
> > > keeps on failing the same tests every time. This is on Ubuntu 18.04 with
> > an
> > > i9 7900X.
> > >
> > > The cmake I used was:
> > > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on
> > -DGMX_BUILD_OWN_FFTW=ON
> > > -DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
> > > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5
> >
> > That couldn't have been the cmake invocation as it's not double
> > precision build (and -DGMX_GPU=on is not valid in a double precision
> > build).
> >
> > >
> > > The problem with make check is:
> > >
> > > 34/39 Test #34: regressiontests/simple ...   Passed3.01 sec
> > >   Start 35: regressiontests/complex
> > > 35/39 Test #35: regressiontests/complex ..***Failed   34.69 sec
> > > Will test using executable suffix _d
> > >  :-) GROMACS - gmx mdrun, 2018.5 (double precision) (-:
> > >
> > > GROMACS is written by:
> > >  Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C.
> > Berendsen
> > > Par BjelkmarAldert van Buuren   Rudi van Drunen Anton
> > Feenstra
> > >   Gerrit GroenhofAleksei Iupinov   Christoph Junghans   Anca Hamuraru
> > >  Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus
> > >   Carsten Kutzner  Per Larsson  Justin A. LemkulViveca
> > Lindahl
> > >   Magnus Lundborg   Pieter MeulenhoffErik Marklund  Teemu Murtola
> > > Szilard Pall   Sander Pronk  Roland Schulz Alexey
> > Shvetsov
> > >Michael Shirts Alfons Sijbers Peter TielemanTeemu
> > Virolainen
> > >  Christian WennbergMaarten 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 2018.5 (double precision)
> > > Executable:   /home/david/gromacs-2018.5/build/bin/gmx_d
> > > Data prefix:  /home/david/gromacs-2018.5 (source tree)
> > > Working dir:
> > /home/david/gromacs-2018.5/build/tests/regressiontests-2018.5
> > > Command line:
> > >   gmx_d mdrun -h
> > >
> > >
> > > 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_d mdrun-nb cpu   -notunepme
> > > >mdrun.out 2>&1' was 1
> > > Retrying mdrun with better settings...
> > > Mdrun cannot use the requested (or automatic) number of ranks, retrying
> > with 8.
> > >
> > > Abnormal return value for ' gmx_d mdrun-nb cpu   -notunepme
> > > >mdrun.out 2>&1' was 1
> > > Retrying mdrun with better settings...
> > > FAILED. Check checkpot.out (69 errors), checkforce.out (224 errors)
> > > file(s) in distance_restraints for distance_restraints
> > > Mdrun cannot use the requested (or automatic) number of ranks, retrying
> > with 8.
> > >
> > > Abnormal return value for ' gmx_d mdrun-nb cpu   -notunepme
> > > >mdrun.out 2>&1' was 1
> > > Retrying mdrun with better settings...
> > > Mdrun cannot use the requested (or automatic) number of ranks, retrying
> > with 8.
> > >
> > > Abnormal return value for ' gmx_d mdrun   -notunepme >mdrun.out
> > 2>&1' was 1
> > > Retrying mdrun with better settings...
> > > Mdrun cannot use the requested (or automatic) number of ranks, retrying
> > with 8.
> > >
> > > Abnormal return value for ' gmx_d mdrun   -notunepme >mdrun.out
> > 2>&1' was 1
> > > Retrying mdrun with better settings...
> > > FAILED. Check checkpot.out (16 errors), 

Re: [gmx-users] Make check not passing tests on 2018.5

2019-02-11 Thread David Lister
Hello,

My bad, I copied my single precision build by mistake, this is what was
used originally for double precision:

cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_OWN_FFTW=ON
-DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5 -DGMX_DOUBLE=on

Adding -DGMX_SIMD=AVX2_256 did resolve the problem, thank-you for the help!
I did not test different compilers as I don't have any others on my system
at the moment.

Cheers,
David

On Tue, Feb 5, 2019 at 7:15 AM Szilárd Páll  wrote:

> On Fri, Feb 1, 2019 at 5:01 AM David Lister  wrote:
> >
> > Hello,
> >
> > I've compiled gromacs 2018.5 in double precision a couple times now and
> it
> > keeps on failing the same tests every time. This is on Ubuntu 18.04 with
> an
> > i9 7900X.
> >
> > The cmake I used was:
> > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on
> -DGMX_BUILD_OWN_FFTW=ON
> > -DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
> > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5
>
> That couldn't have been the cmake invocation as it's not double
> precision build (and -DGMX_GPU=on is not valid in a double precision
> build).
>
> >
> > The problem with make check is:
> >
> > 34/39 Test #34: regressiontests/simple ...   Passed3.01 sec
> >   Start 35: regressiontests/complex
> > 35/39 Test #35: regressiontests/complex ..***Failed   34.69 sec
> > Will test using executable suffix _d
> >  :-) GROMACS - gmx mdrun, 2018.5 (double precision) (-:
> >
> > GROMACS is written by:
> >  Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C.
> Berendsen
> > Par BjelkmarAldert van Buuren   Rudi van Drunen Anton
> Feenstra
> >   Gerrit GroenhofAleksei Iupinov   Christoph Junghans   Anca Hamuraru
> >  Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus
> >   Carsten Kutzner  Per Larsson  Justin A. LemkulViveca
> Lindahl
> >   Magnus Lundborg   Pieter MeulenhoffErik Marklund  Teemu Murtola
> > Szilard Pall   Sander Pronk  Roland Schulz Alexey
> Shvetsov
> >Michael Shirts Alfons Sijbers Peter TielemanTeemu
> Virolainen
> >  Christian WennbergMaarten 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 2018.5 (double precision)
> > Executable:   /home/david/gromacs-2018.5/build/bin/gmx_d
> > Data prefix:  /home/david/gromacs-2018.5 (source tree)
> > Working dir:
> /home/david/gromacs-2018.5/build/tests/regressiontests-2018.5
> > Command line:
> >   gmx_d mdrun -h
> >
> >
> > 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_d mdrun-nb cpu   -notunepme
> > >mdrun.out 2>&1' was 1
> > Retrying mdrun with better settings...
> > Mdrun cannot use the requested (or automatic) number of ranks, retrying
> with 8.
> >
> > Abnormal return value for ' gmx_d mdrun-nb cpu   -notunepme
> > >mdrun.out 2>&1' was 1
> > Retrying mdrun with better settings...
> > FAILED. Check checkpot.out (69 errors), checkforce.out (224 errors)
> > file(s) in distance_restraints for distance_restraints
> > Mdrun cannot use the requested (or automatic) number of ranks, retrying
> with 8.
> >
> > Abnormal return value for ' gmx_d mdrun-nb cpu   -notunepme
> > >mdrun.out 2>&1' was 1
> > Retrying mdrun with better settings...
> > Mdrun cannot use the requested (or automatic) number of ranks, retrying
> with 8.
> >
> > Abnormal return value for ' gmx_d mdrun   -notunepme >mdrun.out
> 2>&1' was 1
> > Retrying mdrun with better settings...
> > Mdrun cannot use the requested (or automatic) number of ranks, retrying
> with 8.
> >
> > Abnormal return value for ' gmx_d mdrun   -notunepme >mdrun.out
> 2>&1' was 1
> > Retrying mdrun with better settings...
> > FAILED. Check checkpot.out (16 errors), checkforce.out (1362 errors)
> > file(s) in orientation-restraints for orientation-restraints
> > 2 out of 51 complex tests FAILED
> >
> >   Start 36: regressiontests/kernel
> > 36/39 Test #36: regressiontests/kernel ...   Passed   55.12 sec
> >   Start 37: regressiontests/freeenergy
> > 37/39 Test #37: regressiontests/freeenergy ...   Passed9.27 sec
> >   Start 38: 

Re: [gmx-users] Make check not passing tests on 2018.5

2019-02-05 Thread Szilárd Páll
On Fri, Feb 1, 2019 at 5:01 AM David Lister  wrote:
>
> Hello,
>
> I've compiled gromacs 2018.5 in double precision a couple times now and it
> keeps on failing the same tests every time. This is on Ubuntu 18.04 with an
> i9 7900X.
>
> The cmake I used was:
> cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -DGMX_BUILD_OWN_FFTW=ON
> -DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
> -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5

That couldn't have been the cmake invocation as it's not double
precision build (and -DGMX_GPU=on is not valid in a double precision
build).

>
> The problem with make check is:
>
> 34/39 Test #34: regressiontests/simple ...   Passed3.01 sec
>   Start 35: regressiontests/complex
> 35/39 Test #35: regressiontests/complex ..***Failed   34.69 sec
> Will test using executable suffix _d
>  :-) GROMACS - gmx mdrun, 2018.5 (double precision) (-:
>
> GROMACS is written by:
>  Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C. 
> Berendsen
> Par BjelkmarAldert van Buuren   Rudi van Drunen Anton Feenstra
>   Gerrit GroenhofAleksei Iupinov   Christoph Junghans   Anca Hamuraru
>  Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus
>   Carsten Kutzner  Per Larsson  Justin A. LemkulViveca Lindahl
>   Magnus Lundborg   Pieter MeulenhoffErik Marklund  Teemu Murtola
> Szilard Pall   Sander Pronk  Roland Schulz Alexey Shvetsov
>Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen
>  Christian WennbergMaarten 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 2018.5 (double precision)
> Executable:   /home/david/gromacs-2018.5/build/bin/gmx_d
> Data prefix:  /home/david/gromacs-2018.5 (source tree)
> Working dir:  /home/david/gromacs-2018.5/build/tests/regressiontests-2018.5
> Command line:
>   gmx_d mdrun -h
>
>
> 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_d mdrun-nb cpu   -notunepme
> >mdrun.out 2>&1' was 1
> Retrying mdrun with better settings...
> Mdrun cannot use the requested (or automatic) number of ranks, retrying with 
> 8.
>
> Abnormal return value for ' gmx_d mdrun-nb cpu   -notunepme
> >mdrun.out 2>&1' was 1
> Retrying mdrun with better settings...
> FAILED. Check checkpot.out (69 errors), checkforce.out (224 errors)
> file(s) in distance_restraints for distance_restraints
> Mdrun cannot use the requested (or automatic) number of ranks, retrying with 
> 8.
>
> Abnormal return value for ' gmx_d mdrun-nb cpu   -notunepme
> >mdrun.out 2>&1' was 1
> Retrying mdrun with better settings...
> Mdrun cannot use the requested (or automatic) number of ranks, retrying with 
> 8.
>
> Abnormal return value for ' gmx_d mdrun   -notunepme >mdrun.out 2>&1' was 
> 1
> Retrying mdrun with better settings...
> Mdrun cannot use the requested (or automatic) number of ranks, retrying with 
> 8.
>
> Abnormal return value for ' gmx_d mdrun   -notunepme >mdrun.out 2>&1' was 
> 1
> Retrying mdrun with better settings...
> FAILED. Check checkpot.out (16 errors), checkforce.out (1362 errors)
> file(s) in orientation-restraints for orientation-restraints
> 2 out of 51 complex tests FAILED
>
>   Start 36: regressiontests/kernel
> 36/39 Test #36: regressiontests/kernel ...   Passed   55.12 sec
>   Start 37: regressiontests/freeenergy
> 37/39 Test #37: regressiontests/freeenergy ...   Passed9.27 sec
>   Start 38: regressiontests/pdb2gmx
> 38/39 Test #38: regressiontests/pdb2gmx ..   Passed   16.95 sec
>   Start 39: regressiontests/rotation
> 39/39 Test #39: regressiontests/rotation .   Passed3.60 sec
>
> 97% tests passed, 1 tests failed out of 39
>
> Label Time Summary:
> GTest  =   4.54 sec*proc (33 tests)
> IntegrationTest=   2.03 sec*proc (3 tests)
> MpiTest=   0.20 sec*proc (3 tests)
> UnitTest   =   2.51 sec*proc (30 tests)
>
> Total Test time (real) = 127.19 sec
>
> The following tests FAILED:
>  35 - regressiontests/complex (Failed)
> Errors while running CTest
> CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
> 

Re: [gmx-users] Make check not passing tests on 2018.5

2019-02-01 Thread David Lister
Hi Roland,

This is using gcc version 7.3.0.

The output of gmx_d --version is:

$ ./bin/gmx_d --version
   :-) GROMACS - gmx_d, 2018.5 (double precision) (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C. Berendsen
Par BjelkmarAldert van Buuren   Rudi van Drunen Anton Feenstra
  Gerrit GroenhofAleksei Iupinov   Christoph Junghans   Anca Hamuraru
 Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus
  Carsten Kutzner  Per Larsson  Justin A. LemkulViveca Lindahl
  Magnus Lundborg   Pieter MeulenhoffErik Marklund  Teemu Murtola
Szilard Pall   Sander Pronk  Roland Schulz Alexey Shvetsov
   Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen
 Christian WennbergMaarten 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_d, version 2018.5 (double precision)
Executable:   /home/david/gromacs-2018.5/build/./bin/gmx_d
Data prefix:  /home/david/gromacs-2018.5 (source tree)
Working dir:  /home/david/gromacs-2018.5/build
Command line:
  gmx_d --version

GROMACS version:2018.5
Precision:  double
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-3.3.8-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage:   enabled
TNG support:enabled
Hwloc support:  hwloc-1.11.6
Tracing support:disabled
Built on:   2019-02-01 03:19:10
Built by:   david@computer [CMAKE]
Build OS/arch:  Linux 4.15.0-45-generic x86_64
Build CPU vendor:   Intel
Build CPU brand:Intel(R) Core(TM) i9-7900X CPU @ 3.30GHz
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: /usr/bin/cc GNU 7.3.0
C compiler flags:-mavx512f -mfma -O3 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast
C++ compiler:   /usr/bin/c++ GNU 7.3.0
C++ compiler flags:  -mavx512f -mfma-std=c++11   -O3 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast

Cheers,

David


On Thu, Jan 31, 2019 at 11:28 PM Schulz, Roland 
wrote:

> Hi,
>
> What compiler are you using? Please also paste the output of "gmx
> -version".
>
> Roland
>
> > -Original Message-
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
> > David Lister
> > Sent: Thursday, January 31, 2019 8:00 PM
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] Make check not passing tests on 2018.5
> >
> > Hello,
> >
> > I've compiled gromacs 2018.5 in double precision a couple times now and
> it
> > keeps on failing the same tests every time. This is on Ubuntu 18.04 with
> an
> > i9 7900X.
> >
> > The cmake I used was:
> > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -
> > DGMX_BUILD_OWN_FFTW=ON -DCMAKE_BUILD_TYPE=Release -
> > DGMX_BUILD_UNITTESTS=ON
> > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5
> >
> > The problem with make check is:
> >
> > 34/39 Test #34: regressiontests/simple ...   Passed3.01 sec
> >   Start 35: regressiontests/complex
> > 35/39 Test #35: regressiontests/complex ..***Failed   34.69 sec
> > Will test using executable suffix _d
> >  :-) GROMACS - gmx mdrun, 2018.5 (double precision) (-:
> >
> > GROMACS is written by:
> >  Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C.
> Berendsen
> > Par BjelkmarAldert van Buuren   Rudi van Drunen Anton
> Feenstra
> >   Gerrit GroenhofAleksei Iupinov   Christoph Junghans   Anca Hamuraru
> >  Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus
> >   Carsten Kutzner  Per Larsson  Justin A. LemkulViveca
> Lindahl
> >   Magnus Lundborg   Pieter MeulenhoffErik Marklund  Teemu Murtola
> > Szilard Pall   Sander Pronk  Roland Schulz Alexey
> Shvetsov
> >Michael Shirts Alfons Sijbers Peter TielemanTeemu
> Virolainen
> >  Christian WennbergMaarten Wolf
> >

Re: [gmx-users] Make check not passing tests on 2018.5

2019-01-31 Thread Schulz, Roland
Hi,

What compiler are you using? Please also paste the output of "gmx -version".

Roland

> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
> David Lister
> Sent: Thursday, January 31, 2019 8:00 PM
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Make check not passing tests on 2018.5
> 
> Hello,
> 
> I've compiled gromacs 2018.5 in double precision a couple times now and it
> keeps on failing the same tests every time. This is on Ubuntu 18.04 with an
> i9 7900X.
> 
> The cmake I used was:
> cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -
> DGMX_BUILD_OWN_FFTW=ON -DCMAKE_BUILD_TYPE=Release -
> DGMX_BUILD_UNITTESTS=ON
> -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5
> 
> The problem with make check is:
> 
> 34/39 Test #34: regressiontests/simple ...   Passed3.01 sec
>   Start 35: regressiontests/complex
> 35/39 Test #35: regressiontests/complex ..***Failed   34.69 sec
> Will test using executable suffix _d
>  :-) GROMACS - gmx mdrun, 2018.5 (double precision) (-:
> 
> GROMACS is written by:
>  Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C. 
> Berendsen
> Par BjelkmarAldert van Buuren   Rudi van Drunen Anton Feenstra
>   Gerrit GroenhofAleksei Iupinov   Christoph Junghans   Anca Hamuraru
>  Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus
>   Carsten Kutzner  Per Larsson  Justin A. LemkulViveca Lindahl
>   Magnus Lundborg   Pieter MeulenhoffErik Marklund  Teemu Murtola
> Szilard Pall   Sander Pronk  Roland Schulz Alexey Shvetsov
>Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen
>  Christian WennbergMaarten 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 2018.5 (double precision)
> Executable:   /home/david/gromacs-2018.5/build/bin/gmx_d
> Data prefix:  /home/david/gromacs-2018.5 (source tree) Working dir:
> /home/david/gromacs-2018.5/build/tests/regressiontests-2018.5
> Command line:
>   gmx_d mdrun -h
> 
> 
> 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_d mdrun-nb cpu   -notunepme
> >mdrun.out 2>&1' was 1
> Retrying mdrun with better settings...
> Mdrun cannot use the requested (or automatic) number of ranks, retrying
> with 8.
> 
> Abnormal return value for ' gmx_d mdrun-nb cpu   -notunepme
> >mdrun.out 2>&1' was 1
> Retrying mdrun with better settings...
> FAILED. Check checkpot.out (69 errors), checkforce.out (224 errors)
> file(s) in distance_restraints for distance_restraints Mdrun cannot use the
> requested (or automatic) number of ranks, retrying with 8.
> 
> Abnormal return value for ' gmx_d mdrun-nb cpu   -notunepme
> >mdrun.out 2>&1' was 1
> Retrying mdrun with better settings...
> Mdrun cannot use the requested (or automatic) number of ranks, retrying
> with 8.
> 
> Abnormal return value for ' gmx_d mdrun   -notunepme >mdrun.out 2>&1'
> was 1
> Retrying mdrun with better settings...
> Mdrun cannot use the requested (or automatic) number of ranks, retrying
> with 8.
> 
> Abnormal return value for ' gmx_d mdrun   -notunepme >mdrun.out 2>&1'
> was 1
> Retrying mdrun with better settings...
> FAILED. Check checkpot.out (16 errors), checkforce.out (1362 errors)
> file(s) in orientation-restraints for orientation-restraints
> 2 out of 51 complex tests FAILED
> 
>   Start 36: regressiontests/kernel
> 36/39 Test #36: regressiontests/kernel ...   Passed   55.12 sec
>   Start 37: regressiontests/freeenergy
> 37/39 Test #37: regressiontests/freeenergy ...   Passed9.27 sec
>   Start 38: regressiontests/pdb2gmx
> 38/39 Test #38: regressiontests/pdb2gmx ..   Passed   16.95 sec
>   Start 39: regressiontests/rotation
> 39/39 Test #39: regressiontests/rotation .   Passed3.60 sec
> 
> 97% tests passed, 1 tests failed out of 39
> 
> Label Time Summary:
> GTest  =   4.54 sec*proc (33 tests)
> IntegrationTest=   2.03 sec*proc (3 tests)
> MpiTest=   0.20 sec*proc (3 tests)
> UnitTest   =   2.51 sec*proc (30 tests)
> 
>