LifeV @ mox

Please refer to the proper tutorial for how to set up your account to work with LifeV at MOX.

Check out and mantain the source code via ECLIPSE IDE

Refer to the LifeV&Eclipse guides:

• obtaining the code;
• configure and build;
  
• synchronizing with the repository;
• use the Eclipse text editor.
  

Configure and build the library

First of all refer to the generic introduction. Then consider the following set up, specific to MOX.

We use OpenMPI at MOX, therefore you have to explicitly list the libraries needed at linking time, when running the C++ compiler mpicxx. This information is provided to the configure script through the --with-mpi-link-libs flag.

$ ../lifev-src/configure --enable-debug --prefix=LIFEV_INSTALL_DIR \
--with-mpi-link-libs="-L/u/software/Repository/opt/openmpi_1_2_4/64//lib -lmpi_cxx -lmpi \
-lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl"

You can see the libraries needed by your MPI compiler by invoking it with the option -show:

$ mpicxx -show
g++ -I/u/software/Repository/opt/openmpi_1_2_4/64//include -pthread \
-L/u/software/Repository/opt/openmpi_1_2_4/64//lib -lmpi_cxx \
-lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl

When configuring the library to be built in (compiler-)optimized mode, please consider linking against the optimized version of the linear algebra package Trilinos, available in the MOX software repository:

../lifev-src/configure --enable-opt2 --prefix=LIFEV_INSTALL_DIR \
--with-mpi-link-libs="-L/u/software/Repository/opt/openmpi_1_2_4/64//lib -lmpi_cxx -lmpi \
-lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl \
--with-trilinos=/u/software/Repository/opt/trilinos_9_0_2/64/opt-openmpi/"

Keep in mind that when not using the --with-trilinos flag, you are implicitly selecting the debug version of Trilinos, available in

/u/software/Repository/opt/trilinos_9_0_2/64/debug-openmpi/

Running a test 

We want now to run a LifeV program as a parallel job. First of all, choose the machine(s) on which you plan to work, and list them in a file (e. g. $HOME/machinefile.txt)

$ head $HOME/machinefile.txt
mactaris slots=4
dougga slots=4

shown here, the MPI launcher will try to run up to 4 jobs on mactaris, and (if needed) other jobs (up to 4) on dougga.