[gmx-users] Fwd: Trouble with mpirun gmx- 2/2 machines not sharing correctly

Jacob Nowatzke jn681 at humboldt.edu
Thu Mar 10 07:24:27 CET 2016

I've recently installed OpenMPI 1.10.2 alongside GROMACS 5.1.2. I've read
all over the web about how to, but I'm having issues left and right. I've
finally gotten to a point where *gmx* works, but in an odd way. I'll try to
explain without too much detail.

CPU: 8-core AMD FX9590
GPU: AMD HD8990 (dual-core)

CPU: 6-core AMD FX6120
GPU: AMD R9 Nano (single-core)

Machines are networked by LAN, which cat I don't remember (may be reason
for slow mdrun described soon?). I have added so many $PATH variables on
and off- I'm tired of it. I do have to ask if I have to add
usr/local/gromacs/bin to the $PATH and $LD_PATH in .bashrc? When I did this
is when the machines started picking up on eachother, as they would not
when only OMPI was specified in .bashrc. What's going on here?

My issue- besides understanding it all, this is the point where I've got
things somewhat working- is that I run something like "mpirun --hosts
Machine1,Machine2 --path usr/local/gromacs/bin gmx mdrun -v -deffnm nvt"
from Machine2 over ssh from separate laptop, everything seems to be going
smoothly... except this is only being run on Machine1(8990 is also
detected), with Machine2 components not being detected. Essentially, I'm
running gmx mdrun on Machine1 as if I was using ssh from Machine2.
Obviously, this isn't what I want to do. I'd like to see each machine with
their respective GPUs being utilized for gmx mdrun and the such.

If Machine1 is actually being utilized, then why is it performing steps at
a much slower rate than if I had used the same machine from ssh?

To top off this issue, when I run gmx grompp (or genion) it freezes before
bringing me back to the command line.

Obviously, I'm new, so I want to say that I really appreciate any help
here. Learning GROMACS has been a pleasure so far and I'm hoping to get
details down to utilize for homology modeling. Thanks for your help


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