Shi, reinstalling the mpi version using gmx 18.4 did not help........any ideas ? hms@rgb2 ~/Desktop/PVP20k $ mpirun -np 8 mdrun_mpi -deffnm PVP20k1.em :-) GROMACS - mdrun_mpi, VERSION 5.1.2 (-:
GROMACS: mdrun_mpi, VERSION 5.1.2 Executable: /usr/bin/mdrun_mpi.openmpi Data prefix: /usr Command line: mdrun_mpi -deffnm PVP20k1.em Back Off! I just backed up PVP20k1.em.log to ./#PVP20k1.em.log.5# Running on 1 node with total 64 cores, 64 logical cores Hardware detected on host rgb2 (the node of MPI rank 0): CPU info: Vendor: AuthenticAMD Brand: AMD Ryzen Threadripper 2990WX 32-Core Processor SIMD instructions most likely to fit this hardware: AVX_128_FMA SIMD instructions selected at GROMACS compile time: SSE2 Compiled SIMD instructions: SSE2, GROMACS could use AVX_128_FMA on this machine, which is better Reading file PVP20k1.em.tpr, VERSION 2018.4 (single precision) ------------------------------------------------------- Program mdrun_mpi, VERSION 5.1.2 Source code file: /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/fileio/tpxio.c, line: 3345 Fatal error: reading tpx file (PVP20k1.em.tpr) version 112 with version 103 program For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Sent from Mailspring (https://getmailspring.com/), the best free email app for work On Dec 19 2018, at 10:04 am, p buscemi <pbusc...@q.com> wrote: > here is the output from the gmx_mpi command. I would think the correct > version of mdrun would be installed. maybe I could point to it in my PATH ?? > ------------------------------------------------------------------------------------- > > hms@rgb2 ~/Desktop/PVP20k $ gmx_mpi > :-) GROMACS - gmx_mpi, 2019-beta1 (-: > GROMACS is written by: > et etc............. > GROMACS: gmx_mpi, version 2019-beta1 > Executable: /usr/local/gromacs/bin/gmx_mpi > Data prefix: /usr/local/gromacs > Working dir: /home/hms/Desktop/PVP20k > Command line: > gmx_mpi > > SYNOPSIS > gmx [-[no]h] [-[no]quiet] [-[no]version] [-[no]copyright] [-nice <int>] > [-[no]backup] > > > > On Dec 18 2018, at 9:51 pm, paul buscemi <pbusc...@q.com> wrote: > > Shi, Thanks fo the note > > > > Yes, somehow - there is a version of gromacs 5 that is being summoned. I’ve > > got clean up my act a bit. > > A suggestion was made to try to use the mpi version because of the CPU I am > > using. gmx v18.3 was installed , but I removed its build and built the 19.1 > > beta mpi version in a separate directory. Apparently there are some > > remnants being called. But v 5 has never been installed on this particular > > computer, so I have no idea were gromacs -5.1.2 is coming from. it may be > > easier purge everything and start again. > > Paul > > > On Dec 18, 2018, at 8:48 PM, Shi Li <sli...@g.uky.edu> wrote: > > > > > > > > Message: 3 > > > > Date: Tue, 18 Dec 2018 15:12:00 -0600 > > > > From: p buscemi <pbusc...@q.com> > > > > To: "=?utf-8?Q?gmx-users=40gromacs.org?=" <gmx-us...@gromacs.org> > > > > Subject: [gmx-users] error on opening gmx_mpi > > > > Message-ID: > > > > <1545164001.local-b6243977-9380-v1.5.3-420ce...@getmailspring.com> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > I installed 2019 beata gmx_mpi with: > > > > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON > > > > -DGMX_GPU=on -DCMAKE_CXX_COMPILER=/usr/bin/g++-7 > > > > -DCMAKE_C_COMPILER=/usr/bin/gcc-7 -DGMX_MPI=ON -DGMX_USE_OPENCL=ON > > > > > > > > The install completed with no errors. > > > > I need to take this step by step: in running minim. For minimization I > > > > used > > > > mpirun -np 8 mdrun_mpi -deffnm RUNname.em > > > > with the output: > > > > :-) GROMACS - mdrun_mpi, VERSION 5.1.2 (-: > > > > etc etc.... > > > > GROMACS: mdrun_mpi, VERSION 5.1.2 > > > > Executable: /usr/bin/mdrun_mpi.openmpi > > > > Data prefix: /usr > > > > > > > > > It looked like you didn’t run the new installed GROMACS. What is the > > > output when you input gmx_mpi? It should be version 2018 instead of 5.1.2. > > > Have you put the gromacs in your PATH or source the GMXRC? > > > > > > Shi > > > > > > > Command line: > > > > mdrun_mpi -deffnm PVP20k1.em > > > > > > > > Back Off! I just backed up PVP20k1.em.log to ./#PVP20k1.em.log.2# > > > > Running on 1 node with total 64 cores, 64 logical cores > > > > Hardware detected on host rgb2 (the node of MPI rank 0): > > > > CPU info: > > > > Vendor: AuthenticAMD > > > > Brand: AMD Ryzen Threadripper 2990WX 32-Core Processor > > > > SIMD instructions most likely to fit this hardware: AVX_128_FMA > > > > SIMD instructions selected at GROMACS compile time: SSE2 > > > > > > > > Compiled SIMD instructions: SSE2, GROMACS could use AVX_128_FMA on this > > > > machine, which is better > > > > Reading file PVP20k1.em.tpr, VERSION 2018.4 (single precision) > > > > ------------------------------------------------------- > > > > Program mdrun_mpi, VERSION 5.1.2 > > > > Source code file: > > > > /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/fileio/tpxio.c, line: > > > > 3345 > > > > > > > > Fatal error: > > > > reading tpx file (PVP20k1.em.tpr) version 112 with version 103 program > > > > For more information and tips for troubleshooting, please check the > > > > GROMACS > > > > website at http://www.gromacs.org/Documentation/Errors > > > > ------------------------------------------------------- > > > > > > > > Halting parallel program mdrun_mpi on rank 0 out of 8 > > > > -------------------------------------------------------------------------- > > > > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > > > > with errorcode 1. > > > > > > > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > > > You may or may not see output from other processes, depending on > > > > exactly when Open MPI kills them. > > > > ==== > > > > I see the fatal error but minim.ndp was used while in gmx_mpi - this is > > > > not covered in commor errors. > > > > and I see the note on AVX_128_FM.. but that can wait. Is it the version > > > > of the MPI files ( 103 ) that is the at fault? > > > > > > > > I need to create the proper tpr to continue > > > > > > > > ------------------------------ > > > -- > > > 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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