[gmx-users] Gromacs + Plumed parallel

nikolaev at spbau.ru nikolaev at spbau.ru
Fri Feb 3 15:01:18 CET 2017

Hello, everyone!

I have one problem with running gromacs with plumed using more than one
processor. When I install plumed, and patch gromacs with it, it writes
that everything is OK:
You are patching in runtime mode
Be warned that when you will run MD you will use the PLUMED version
pointed at
by the PLUMED_KERNEL environment variable

PLUMED is compiled with MPI support so you can configure gromacs-5.1.2
with MPI """

But when I try to run smth like this:

/home/nikolaev_d/JACK/gromacs-5.1.2/build/bin/gmx_d mdrun -deffnm md_1 -v
-ntmpi 2 -ntomp 4 -plumed plumed.dat

There is an error:

********** STACK DUMP **********
/home/nikolaev_d/JACK/gromacs-5.1.2/build/bin/gmx_d(do_md+0x254e) [0x41b62e]
/home/nikolaev_d/JACK/gromacs-5.1.2/build/bin/gmx_d() [0x433d54]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x80a4) [0x7f2b400e70a4]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x6d) [0x7f2b3f36e62d]
******** END STACK DUMP ********

+++ Internal PLUMED error
+++ file Communicator.cpp, line 102
+++ message: assertion failed initialized(), you are trying to use an MPI
function, but MPI is not initialized

However, when I try to run
/home/nikolaev_d/JACK/gromacs-5.1.2/build/bin/gmx_d mdrun -deffnm md_1 -v
-ntmpi 1 -ntomp 1 -plumed plumed.dat

everything works fine.

What's the problem? I've read that it might be the incompatibility of some
some parallelization parameters. But I tried to install gromacs in
different ways. In the last time I used:

-DCMAKE_INSTALL_PREFIX=/home/nikolaev_d/JACK for that.

Here I attach the config.log and the Makefile.conf of the PLUMED..

Thank you in advace,

More information about the gromacs.org_gmx-users mailing list