[gmx-users] error on opening gmx_mpi

[paul buscemi]

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 <jalemkul at vt.edu> wrote:
> 
> On Tue, Dec 18, 2018 at 4:12 PM p buscemi <pbuscemi at 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
> 
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
> 
> 
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