[ESPResSo] Finally... ESPResSo working with openmpi in Fedora13
From:
Salvador Herrera Velarde
Subject:
[ESPResSo] Finally... ESPResSo working with openmpi in Fedora13
Date:
Sat, 11 Sep 2010 02:43:36 -0500
Dear All,
Finally I could compile ESPResSo in parallel using openmpi in Fedora13
I would like to share some information, that hopefully could be useful for someone in a similar situation.
---------------------------- a) According to http://fedoraproject.org/wiki/Fedora_13_Alpha_release_notes#User_level_MPI User level MPI The compilers, runtimes and any software compiled against them are installed in separate directories outside the $PATH.
b) It seems that in Fedora13 the relevant paths are in : (installing openmpi with: yum -y install openmpi openmpi-devel) /usr/lib64/openmpi/lib/ /usr/lib64/openmpi/bin/
c) Now in: http://forums.fedoraforum.org/showthread.php?t=194688 It seems like they forgot to link mpicc to /usr/bin, or add it to the PATH variable or whatever. so, to fix this, just add to your ~/.bashrc the following lines:
# for OpenMPI LIBRARY_PATH=/usr/lib64/openmpi/lib:$LIBRARY_PATH export LIBRARY_PATH
PATH=/usr/lib64/openmpi/bin/:$PATH export PATH
d) To use mpi see: http://fedoraforum.org/forum/showthread.php?t=243202 Under F12,F13, you can let the environmental modules take care of the env. variable management. module load openmpi-ARCH # where ARCH is the architecture of the machine, e.g. i686 or x86_64
e) So, I run the next command in the built directory: >> module load openmpi-x86_64
f) Then, I compiled ESPResSo with the command: >> /home/espresso-2.1.5/configure --with-myconfigure=New-config.h --with-mpi=openmpi CC=mpicc (Finally it works!!)
g) Add the following line to your ~/.bashrc export ESPRESSO_SCRIPTS=/YOUR_PATH/espresso-2.1.5/scripts
h) However to run the simulations with mpi, I always have to use the command: >> module load openmpi-x86_64 (I am not sure if it is a good idea to add this command in .bashrc)
Then,
mpirun -np 4 /YOUR_PATH_to/Espresso_bin script.tcl or ln -s ~/YOUR_PATH_to/Espresso_bin (it creates a link) mpirun -np 4 ./Espresso_bin script.tcl