Shi, Justin straightened me out regarding the command structure ; Used "mpirun -np 8 gmx_mpi mdrun -deffnm Run_file.nvt”
But for time being I’ve given up on two GPUs with the 32 core system. I am now just trying to make the single GPU work well. Paul > On Dec 19, 2018, at 5:51 AM, Shi Li <sli...@g.uky.edu> wrote: > >> >> >> ------------------------------ >> >> Message: 3 >> Date: Tue, 18 Dec 2018 21:51:41 -0600 >> From: paul buscemi <pbusc...@q.com> >> To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> >> Subject: Re: [gmx-users] error on opening gmx_mpi >> Message-ID: <ff9159e0-345c-4266-900a-bad9ba514...@q.com> >> Content-Type: text/plain; charset=utf-8 >> >> 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 > > Another way to solve this is to install the new version of GROMACS on a > prefix directory, instead of using the default. Then make an individual file > to source the new GMXRC in the prefixed directory as well as load all the > modules you used to install the program. So that you won’t have the problem > to confuse with different versions on your computer/cluster. > > Shi >> >>> 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. -- 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.
