On Tue, Dec 18, 2018 at 4:12 PM p buscemi <pbusc...@q.com> wrote: > 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.