== Building MPI Yourself ==

MPI does not require any special system privileges to set up or use on most clusters. There are many variants of MPI, and different users may
need different versions. In the case of EMAN2, OpenMPI, the most widely used MPI distribution, works well in almost all situations, but there
are some version-specific issues. We currently recommend version 1.4.3. This page describes how you can compile and install OpenMPI yourself
in your own account.

Beware! Even if you compile MPI yourself, you will still need to install '''pydusa'''.
By installing pydusa ''first'', you *might* be able to avoid compiling your own MPI, so... try it: Install pydusa for EMAN2/SPARX ; [[EMAN2/Parallel/PyDusa]]

 * For '''Independent OpenMPI compilation''', download the version of OpenMPI you want or need to use (for example, ''openmpi-1.4.3.tar.gz''; you can find any given OpenMPI version by searching for it on google), transfer the tar/zip file to your home directory on the cluster of interest, and untar/unzip it (ask someone who already has MPI working for them what version of MPI they recommend). Once you untar it, you should see a directory with all the OpenMPI source files (for example, ''openmpi-1.4.3'').
 * To compile, you will need to __create a separate folder within your come directory where OpenMPI will be built__. For example:

 {{{
 mkdir openmpi
 }}}

 * Then go to the source files directory
 {{{
 cd openmpi-1.4.3
 }}}
 
 * Once you're in there, run the __''configure'' file__, specifying that you want to use your own OpenMPI build (this is usually done through the ''--prefix'' option, which you have to set equal to your compilation directory, which is the __''openmpi'' directory__ you were instructed to create in this example; the ''--prefix'' option might be called something different depending on what version of OpenMPI you're building, but you can always check by typing ''./configure --help''). You also have to specify ''--disable-dlopen''

 {{{
 ./configure --prefix=/raid/jgalaz/openmpi --disable-dlopen
 }}}
 
 * Still within the source directory (''openmpi-1.4.3'') run the following commands:

 {{{
 make
 make install
 }}}

 * If it complies successfully, now you have to add mpi to your PATH by modifying your __''.bashrc'' file__, which is an invisible file that should be inside your home directory. You can easily open it with the __text editor ''vi''__ which comes with Linux and OSX by default

 {{{
 cd ~
 vi .bashrc
 }}}
 
 * Note that THE ORDER in which you add directories to your PATH variable *MATTERS*. You want the system to find your build of MPI *first*, so add the directory at the beginning of your PATH (or the following lines before any other lines that contain the word "export" on your .bashrc file):

  * export PATH=$HOME/openmpi/bin:$PATH:/usr/local/bin
  * export LD_LIBRARY_PATH=$HOME/openmpi/lib:$LD_LIBRARY_PATH

 * Once this is correctly set, go to the __''~/EMAN2/mpi_eman/'' directory__ and run ''Makefile.linux2'' to compile the __''mpi_eman_c'' library__.

 {{{
 cd ~/EMAN2/mpi_eman/
 make -f Makefile.linux2 install
 }}}
 
 If run successfully, two new files should have been generated: 
  * mpi_eman_c.o
  * mpi_eman_c.so

 * Copy the __''mpi_eman_c.so'' file__ to ~/EMAN2/lib/
 {{{
 cp mpi_eman_c.so ~/EMAN2/lib/
 }}}

 * You should now be able to run the test scripts that come within the ''~/EMAN2/mpi_eman/'' directory on the main [[EMAN2/Parallel/Mpi]] page.

If you're getting errors running your jobs on a cluster using mpi, '''please''' *DO* remember to clear the cache:

 {{{
 cexec rm -rf /scratch/username
 }}}