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? 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.
