[gmx-users] error on opening gmx_mpi

[paul buscemi]

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

> On Dec 18, 2018, at 8:48 PM, Shi Li <sli259 at g.uky.edu> wrote:
> 
>> 
>> Message: 3
>> Date: Tue, 18 Dec 2018 15:12:00 -0600
>> From: p buscemi <pbuscemi at q.com>
>> To: "=?utf-8?Q?gmx-users=40gromacs.org?=" <gmx-users at gromacs.org>
>> Subject: [gmx-users] error on opening gmx_mpi
>> Message-ID:
>> 	<1545164001.local-b6243977-9380-v1.5.3-420ce003 at 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
>> 
>> 
>> ------------------------------
>> 
> 
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