[gmx-users] error on opening gmx_mpi

Thu Dec 20 03:41:31 CET 2018

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 <sli259 at g.uky.edu> wrote:
> 
>> 
>> 
>> ------------------------------
>> 
>> Message: 3
>> Date: Tue, 18 Dec 2018 21:51:41 -0600
>> From: paul buscemi <pbuscemi at q.com>
>> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] error on opening gmx_mpi
>> Message-ID: <FF9159E0-345C-4266-900A-BAD9BA514F81 at 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 <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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