Re: [gmx-users] mac OS Catalina segmentation fault
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 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 > > 0x7fff69e47b1d _sigtramp + 29 > > [MacBook-Pro:33466] [ 1] 0 libdyld.dylib > > 0x7fff69c3730e dyld_stub_binder + 282 > > [MacBook-Pro:33466] [ 2] 0 libgromacs_mpi.1.5.0.dylib > > 0x00010dd60f2e _ZN3gmx24CommandLineModuleManager3runEiPPc + 798 > > [MacBook-Pro:33466] [ 3] 0 gmx_mpi > > 0x00010dcc39d1 main + 129 > > [MacBook-Pro:33466] [ 4] 0 libdyld.dylib > > 0x7fff69c462e5 start + 1 > > [MacBook-Pro:33466] [ 5] 0 ??? > > 0x0002 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 > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mac OS Catalina segmentation fault
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 0x7fff69e47b1d _sigtramp + 29 [MacBook-Pro:33466] [ 1] 0 libdyld.dylib 0x7fff69c3730e dyld_stub_binder + 282 [MacBook-Pro:33466] [ 2] 0 libgromacs_mpi.1.5.0.dylib 0x00010dd60f2e _ZN3gmx24CommandLineModuleManager3runEiPPc + 798 [MacBook-Pro:33466] [ 3] 0 gmx_mpi 0x00010dcc39d1 main + 129 [MacBook-Pro:33466] [ 4] 0 libdyld.dylib 0x7fff69c462e5 start + 1 [MacBook-Pro:33466] [ 5] 0 ??? 0x0002 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] mac OS Catalina segmentation fault
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 0x7fff69e47b1d _sigtramp + 29 [MacBook-Pro:33466] [ 1] 0 libdyld.dylib 0x7fff69c3730e dyld_stub_binder + 282 [MacBook-Pro:33466] [ 2] 0 libgromacs_mpi.1.5.0.dylib 0x00010dd60f2e _ZN3gmx24CommandLineModuleManager3runEiPPc + 798 [MacBook-Pro:33466] [ 3] 0 gmx_mpi 0x00010dcc39d1 main + 129 [MacBook-Pro:33466] [ 4] 0 libdyld.dylib 0x7fff69c462e5 start + 1 [MacBook-Pro:33466] [ 5] 0 ??? 0x0002 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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
