[gmx-users] Thread-MPI error in GROMACS-2018

Mark Abraham mark.j.abraham at gmail.com
Fri Jun 1 12:25:15 CEST 2018


That error is a strong indicator of a code problem. There was a similar
report on here a few days ago about a tMPI error. Please do open an issue
at https://redmine.gromacs.org/ and attach those files above and your .tpr
so we can reproduce the issue and try to find and fix its cause.


On Fri, Jun 1, 2018 at 4:12 AM Siva Dasetty <sdasett at g.clemson.edu> wrote:

> Hello,
> I have come across an error that causes GROMACS (2018/2018.1) to crash. The
> message is:
> "tMPI error: Receive buffer size too small for transmission (in valid comm)
> Aborted"
> The error seems to only occur immediately following a LINCS or SETTLE
> warning. The error is reproducible across different systems. A simple
> example system is running an energy minimization on a box of 1000 rigid
> TIP4P/Ice water molecules generated with gmx solvate. When SETTLE is used
> as the constraint algorithm,  there are several SETTLE warnings in the
> early steps of the energy minimization, and GROMACS will crash with the
> above error message. If I replace SETTLE with LINCS, GROMACS crashes with
> the same error message following a LINCS warning. Other systems that have
> produced this error are -OH terminated self assembled monolayer surfaces
> (h-bonds constrained by LINCS), and mica surfaces (h-bonds constrained by
> LINCS).  Naturally, reducing -ntmpi to 1 eliminates the error for all
> cases.
> The problem does appear to be hardware dependent. Specifically, the tested
> node(s) on the cluster contains K20/K40 GPUs with Intel Xeon E5-2680v3
> processor (20/24 cores). I used GCC/5.4.0 and CUDA/8.0.44 compilers for
> installing GROMACS. An installation on my desktop machine with with very
> similar options does not have the thread MPI error.
> Example of procedure that causes error:
> # Node contains 24 cores and 2 K40 GPUs
> gmx solvate -cs tip4p -o box.gro -box 3.2 3.2 3.2 -maxsol 1000
> gmx grompp -f em.mdp -c box.gro -p tip4pice.top -o em
> export OMP_NUM_THREADS=6
> gmx mdrun -v -deffnm em -ntmpi 4 -ntomp 6 -pin on
> Attached are the relevant topology (tip4pice.top), mdp (em.mdp), and log
> (em.log) files.
> Thanks in advance for any ideas as to what might be causing this problem,
> Siva Dasetty
>  tip4pice.top
> <
> https://drive.google.com/a/g.clemson.edu/file/d/13e_rxBMNaizR1GvCVklc3IlQ1gcCTat_/view?usp=drive_web
> >
> ​​
>  em.mdp
> <
> https://drive.google.com/a/g.clemson.edu/file/d/1A1592_cB7jfwdBOcezkfsFnT4xPqksNB/view?usp=drive_web
> >
> ​​
>  em.log
> <
> https://drive.google.com/a/g.clemson.edu/file/d/15iU3364SwxpEx3popQf7elZ9_3p2r6v9/view?usp=drive_web
> >
>> --
> 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-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list