Hi Paul, I checked using this command for a specific folder, and I used '-mpirun mdrun' rather '-mpirun mpirun':
./gmxtest.pl -mpirun mdrun -np 2 -noverbose rotation I get lot of these errors: topol.tpr file different from ./reference_s.tpr. Check files in flex for flex FAILED. Check checktpr.out, checktpr.err file(s) in flex for flex topol.tpr file different from ./reference_s.tpr. Check files in flex-t for flex-t FAILED. Check checktpr.out, checktpr.err file(s) in flex-t for flex-t topol.tpr file different from ./reference_s.tpr. Check files in flex2 for flex2 FAILED. Check checktpr.out, checktpr.err file(s) in flex2 for flex2 topol.tpr file different from ./reference_s.tpr. Check files in flex2-t for flex2-t FAILED. Check checktpr.out, checktpr.err file(s) in flex2-t for flex2-t .... so on A) the only suspicious thing I see in checktpr.err is possibly different software versions. Command line: gmx_mpi check -s1 ./reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 Note: When comparing run input files, default tolerances are reduced. Reading file ./reference_s.tpr, VERSION 5.0-beta2-dev-20140130-02adca5 (single precision) Note: file tpx version 96, software tpx version 116 Reading file topol.tpr, VERSION 2019.4 (single precision) B) And Only suspicious thing I see in checktpr.out is pasted below (I have removed the host ip number). Just to mention I use Amazon web services so probably the following error is related to instance when it was created and then stored as an image and then re-used with a different ip. May be am just talking silly! [[2115,1],0]: A high-performance Open MPI point-to-point messaging module was unable to find any relevant network interfaces: Module: OpenFabrics (openib) Host: ip-xxx-xx-xx-xxx Another transport will be used instead, although this may result in lower performance. NOTE: You can disable this warning by setting the MCA parameter btl_base_warn_component_unused to 0. On Wed, Oct 23, 2019 at 4:10 AM Paul bauer <paul.baue...@gmail.com> wrote: > Hello Dave, > > this is weird, no idea why it didn't work then. > You can try running the test suite manually in the folder you found with > > perl gmxtest.pl -mpirun mpirun -np X -noverbose > > That will show if the test binary works and should report any failing > tests. > Don't forget to source the GMXRC file before trying, though! > > Cheers > > Paul > > > On 23/10/2019 12:36, Dave M wrote: > > Hi Paul, > > > > Thanks for the 'mpirun -n X gmx_mpi mdrun'. It works now. > > > > Regarding tests, I found the folder here build/tests/regressiontests > > So I checked all the log using a simple script (searching keyword > > 'Finished') and it shows that all the log files have Finished properly > in > > their corresponding folders. So log files do not say anything here. > > > > On Wed, Oct 23, 2019 at 3:07 AM Paul Bauer <paul.baue...@gmail.com> > wrote: > > > >> Hello Dave, > >> > >> You need to use mpirun -n (number of processes) gmx_mpi mdrun to use a > MPI > >> enabled build of GROMACS. This is what the error message tries to tell > you, > >> but we might need to improve on this. > >> > >> There should be a regressiontests folder somewhere in your build tree > if it > >> downloaded the tests correctly. > >> > >> Cheers > >> > >> Paul > >> > >> On Wed, 23 Oct 2019, 12:02 Dave M, <dave.gro...@gmail.com> wrote: > >> > >>> Hi Paul, > >>> > >>> Thanks for your reply. > >>> a) I just checked there is no tests/regressiontests, some other folder > is > >>> there test/sphysicalvalidation > >>> There is no log file. > >>> b) Regarding thread-mpi I think it is not installed because when I use > >> some > >>> command like this: > >>> > >>> > >>> gmx_mpi mdrun -v -deffnm 03-run -rdd 2.0 -nt 2 > >>> > >>> I get an error: > >>> > >>> > >>> Fatal error: > >>> > >>> Setting the total number of threads is only supported with thread-MPI > and > >>> GROMACS was compiled without thread-MPI > >>> > >>> I think (please correct me) gmx_mpi is for external MPI openMPI in my > >> case > >>> so I tried just 'gmx mdrun' (not gmx_mpi) but then it says command not > >>> found. I am not sure what I missed in installation cmake flags. > >>> > >>> Dave > >>> > >>> On Wed, Oct 23, 2019 at 2:45 AM Paul Bauer <paul.baue...@gmail.com> > >> wrote: > >>>> Hello Dave, > >>>> > >>>> Did you have a look into the log files from the regression tests under > >>>> tests/regressiontests? > >>>> They might give us some insight into what is happening. > >>>> > >>>> The warning in respect to thread-MPI is harmless, it just tells you > >> that > >>>> you are using real MPI instead of thread-MPI. > >>>> > >>>> Cheers > >>>> Paul > >>>> > >>>> On Wed, 23 Oct 2019, 07:36 Dave M, <dave.gro...@gmail.com> wrote: > >>>> > >>>>> Hi All, > >>>>> > >>>>> Any hints/help much appreciated why am getting regression tests > >>> failure. > >>>>> Also to mention I think thread-mpi was not installed as I got an > >> error > >>>>> saying "MPI is not compatible with thread-MPI. Disabling thread-MPI". > >>> How > >>>>> to check the compatibility? > >>>>> > >>>>> Thanks. > >>>>> > >>>>> best regards, > >>>>> D > >>>>> > >>>>> On Sun, Oct 20, 2019 at 2:58 AM Dave M <dave.gro...@gmail.com> > >> wrote: > >>>>>> Hi All, > >>>>>> > >>>>>> I am trying to install gromacs2019.4 with: > >>>>>> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=on > >>>>>> -DGMX_MPI=on -DGMX_GPU=on > >>>>>> -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromacs2019_4 > >>>>>> -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_BUILD_TYPE=Debug > >>>>>> > >>>>>> But 5 tests (41 to 46) were failed copied below: > >>>>>> > >>>>>> > >>>>>> The following tests FAILED: > >>>>>> > >>>>>> 41 - regressiontests/simple (Failed) > >>>>>> > >>>>>> 42 - regressiontests/complex (Failed) > >>>>>> > >>>>>> 43 - regressiontests/kernel (Failed) > >>>>>> > >>>>>> 44 - regressiontests/freeenergy (Failed) > >>>>>> > >>>>>> 45 - regressiontests/rotation (Failed) > >>>>>> > >>>>>> 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/Makefile2:1392: recipe for target > >>>>>> 'CMakeFiles/run-ctest-nophys.dir/all' failed > >>>>>> > >>>>>> make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2 > >>>>>> > >>>>>> CMakeFiles/Makefile2:1172: recipe for target > >>>> 'CMakeFiles/check.dir/rule' > >>>>>> failed > >>>>>> > >>>>>> make[1]: *** [CMakeFiles/check.dir/rule] Error 2 > >>>>>> > >>>>>> Makefile:626: recipe for target 'check' failed > >>>>>> make: *** [check] Error 2 > >>>>>> > >>>>>> Not sure what could be wrong. Just to add I get some error/warning > >>>> during > >>>>>> installation which says "MPI is not compatible with thread-MPI. > >>>> Disabling > >>>>>> thread-MPI". I am using -DGMX_MPI=on and to have openMPI on ubuntu > >>>> 18.04 > >>>>> I > >>>>>> used "sudo apt-get install openmpi-bin openmpi-common > >> libopenmpi-dev" > >>>>>> Please let me know how I can fix this. > >>>>>> > >>>>>> best regards, > >>>>>> D > >>>>>> > >>>>>> > >>>>> -- > >>>>> 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. > >>>> > >>> -- > >>> 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. > >> > > -- > 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.