Justin Kat wrote:
Dear gmx users,
I have installed the parallel version 4.0.7 of gromacs on one of the
nodes of my cluster. Here is the steps I've done through root:
first, the normal installation:
./configure
make
make install
make links
then issued commands below for the mpi build:
./configure |--enable-mpi|
make mdrun
make install-mdrun
make links
I dont see any errors and everything seems to install fine.
I then switch to a normal user to do my work and then after issuing the
grompp_md command as usual, I entered the command below:
mpirun -np 8 mdrun_mpi -s *.tpr -o *.tpr -c *_after_md -v >& output.mdrun_md
however, output.mdrun_md gives:
mpirun was unable to launch the specified application as it could not find an
executable:
Executable: mdrun_mpi
Node: node3.reyclus.loc
while attempting to start process rank 0.
Was the installation procedure incorrect? Or do I need to go through a
separate installation for the mdrun_mpi executable? Please guide me on
what is wrong.
No, the commands you gave should have built mdrun_mpi, as long as they finished
successfully. Were there errors in the installation?
With "make links" you should have links to all the Gromacs executables in
/usr/local/bin - are they there? You don't need to make links, instead you can
follow the steps here:
http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation
-Justin
Thanks,
Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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