Thanks a lot Paul. best regards, D
On Wed, Oct 23, 2019 at 4:44 AM Paul bauer <paul.baue...@gmail.com> wrote: > Hello Dave, > > I thought it was something like that. > The error is harmless (just telling you that MPI is doing its job), and > the testing script gets confused because of the extra message in the > output file. > > So I think you are good to go (and we need to do something about the > testing script). > > Happy simulating! > > Cheers > > Paul > > On 23/10/2019 13:39, Dave M wrote: > > 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. > >> > > -- > 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? 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