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? 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.