[gmx-users] mac OS Catalina segmentation fault

[Daskalakis Vangelis]

Hi Paul,
Thank you for your e-mail. I forgot to note that without the plumed patch,
the situation remains still problematic. The vanilla versions produce the
same errors (segmentation faults), even without any specific input files.
Just running the command e.g. gmx(_mpi) grompp, or gmx(_mpi) trjconv
without any input files, a segmentation fault is produced, as it is in the
case also with specific input files. Some tools, like editconf (v. 2019.4),
just complain about missing input files, if none is given, but without a
segmentation fault, as it should be.
I attach the full CMake Config and log files.
I will try and open an issue on redmine.gromacs.org
thank you again,
Vangelis.

On Tue, Nov 5, 2019 at 11:30 PM Paul bauer <paul.bauer.q at gmail.com> wrote:

> Hello,
>
> could you try running first with an unmodified version of GROMACS, so we
> can check if the PLUMED modifications are responsible for the crashes
> (unlikely for the tools, but we need to make sure)?
> If the vanilla versions are still crashing, can you supply us with some
> log files and input files/run scripts for the failures and open a new
> issue on redmine.gromacs.org?
>
> Also, can you share the full CMakeConfig file?
>
> Cheers
>
> Paul
>
> On 05/11/2019 21:10, Daskalakis Vangelis wrote:
> > Dear all,
> > I am running Mac OS Catalina 10.15.1 (Xcode 11.2 11B52). I have
> > successfully compiled several versions of Gromacs (5.1.5, 2018.8, or
> > 2019.4) patched with plumed (v.2.4.6 for 5.1.5, or v.2.5.3 for 2018/2019
> > versions). The compilations are completed without any errors, employing
> the
> > configuration:
> > # cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=on
> > -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/gromacs -DCXX="$MPICXX"
> >
> > For example Gromacs v. 5.1.5 (but the same is happening on the other
> > versions), I get segmentation faults, when I just run some tools, like:
> >
> > [MacBook-Pro:33466] *** Process received signal ***
> > [MacBook-Pro:33466] Signal: Segmentation fault: 11 (11)
> > [MacBook-Pro:33466] Signal code:  (0)
> > [MacBook-Pro:33466] Failing at address: 0x0
> > [MacBook-Pro:33466] [ 0] 0   libsystem_platform.dylib
> >   0x00007fff69e47b1d _sigtramp + 29
> > [MacBook-Pro:33466] [ 1] 0   libdyld.dylib
> > 0x00007fff69c3730e dyld_stub_binder + 282
> > [MacBook-Pro:33466] [ 2] 0   libgromacs_mpi.1.5.0.dylib
> >   0x000000010dd60f2e _ZN3gmx24CommandLineModuleManager3runEiPPc + 798
> > [MacBook-Pro:33466] [ 3] 0   gmx_mpi
> > 0x000000010dcc39d1 main + 129
> > [MacBook-Pro:33466] [ 4] 0   libdyld.dylib
> > 0x00007fff69c462e5 start + 1
> > [MacBook-Pro:33466] [ 5] 0   ???
> > 0x0000000000000002 0x0 + 2
> > [MacBook-Pro:33466] *** End of error message ***
> > zsh: segmentation fault  gmx_mpi trjconv
> >
> > switching MPI support on/ off on the configuration/ compilation stage
> does
> > not change the situation. Some tools are running smoothly, as editconf.
> > However others, have segmentation faults. Grompp is running on v.5.1.5,
> but
> > gives a segmantation fault on v. 2019.4.
> >
> > I would appreciate some help,
> > thank you,
> > Vangelis.
>
>
> --
> Paul Bauer, PhD
> GROMACS Release Manager
> KTH Stockholm, SciLifeLab
> 0046737308594
>
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