Re: [gmx-users] regression test errors
Thanks a lot Paul. best regards, D On Wed, Oct 23, 2019 at 4:44 AM Paul bauer 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 > 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 > >> 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, 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'
Re: [gmx-users] regression test errors
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 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 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, 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 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, 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 wrote: Hi All, I am trying
Re: [gmx-users] regression test errors
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 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 > 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, 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 > >> 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, 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? > > > >
Re: [gmx-users] regression test errors
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 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, 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 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, 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 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
Re: [gmx-users] regression test errors
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 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, 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 > 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, 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 > 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
Re: [gmx-users] regression test errors
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, 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 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, 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 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.
Re: [gmx-users] regression test errors
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 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, 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 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.
Re: [gmx-users] regression test errors
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, 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 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.
Re: [gmx-users] regression test errors
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 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.
[gmx-users] regression test errors
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.
