Justin, thank you very much for the rapid response. I read that the same way, but I’m a bit confused. Is "mdrun_mpi version 5.1.2 in /usr/bin” a result of an install of v5 of gromacs ( have not used that version ) or a result of an install of a v5 of mpi ? i.e. not sure where that came from. Do I simply need to reinstall the beta version ?
I do plan on reporting all of this when it’s up and running ! Regards Paul > On Dec 18, 2018, at 3:15 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > On Tue, Dec 18, 2018 at 4:12 PM p buscemi <pbusc...@q.com> wrote: > > There's nothing wrong with the .tpr file, but you're not using the mdrun > binary you want to be. You've installed the 2019 beta but then you're using > mdrun_mpi version 5.1.2 in /usr/bin. You should be calling the same GROMACS > version for everything. > > -Justin >> 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 >> 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? >> >> > There's nothing wrong with the .tpr file, but you're not using the mdrun > binary you want to be. You've installed the 2019 beta but then you're using > mdrun_mpi version 5.1.2 in /usr/bin. You should be calling the same GROMACS > version for everything. > > -Justin > > -- > > ========================================== > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > > ========================================== > -- > 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.