Compiling and running DOUAR

Prerequisites

In order to run DOUAR, you will need to have the following software installed.

• C and Fortran 77/90 compilers (Intel compilers strongly preferred)
• An MPI implementation (MPICH2, MVAPICH2 or Intel MPI seem to work best)
• The Watson Sparse Matrix Package (WSMP)
• An implementation of the Basic Linear Algebra Subprograms (BLAS). Intel MKL comes with the compilers as is preferred, but alternative options are listed in the WSMP documentation

Obtaining DOUAR

DOUAR is not currently open source. Requests for use of the code should be made to the main author, Jean Braun.

Compiling DOUAR

There are several steps to compiling DOUAR. Please perform these carefully.

1. Extract the code and place the source code directory somewhere sensible. If you're working on a cluster like the Taito cluster administered by the Finnish CSC, you should note that some storage locations are preferred for source code compilation due to filesystem performance.

2. Create symbolic link between system-specific Makefile.inc.<system.compiler.mpi> and Makefile.inc in the DOUAR/src directory.

   System	Makefile
   taito.csc.fi	ln -s Makefile.inc.taito.intel.mvapich2 Makefile.inc

3. If you haven't already done so, grab a copy of WSMP from the WSMP website and extract it someplace sensible.

4. Ensure a copy of the WSMP license file is installed where it can be read. On Taito the WSMP license file is installed at

   /homeappl/home/dwhipp/software/wsmp/wsmp.lic

5. Set the following WSMP environment variables in your .bashrc file:

   export MALLOC_TRIM_THRESHOLD_=100000000
   export MALLOC_MMAP_MAX_=0
   export WSMPLICPATH=<path/to/WSMP/license>

6. Set the following system-specific options in the .bashrc file:

   module unload intelmpi
   module load mvapich2
   export MKL_NUM_THREADS=1

7. In the Makefile.inc for the given system, review the compiler flags to ensure they read as follows for standard compilation:

   Standard compilation

   # Define FORTRAN compiler flags.......................
   #
   # For the Intel Fortran compiler
   F90FLAGS  = -O2 -heap-arrays 10
   F77FLAGS  = -O2 -heap-arrays 10
   # Define C compiler flags.............................
   #
   #CFLAGS  = -O2 -fp-model precise -fp-model source -I.
   CFLAGS  = -O2 -I.

   Debugging

   # Define FORTRAN compiler flags.......................
   #
   # For the Intel Fortran compiler
   F90FLAGS  = -O0 -fp-model strict -g -debug all -traceback -heap-arrays 10
   F77FLAGS  = -O0 -fp-model strict -g -debug all -traceback -heap-arrays 10
   # Define C compiler flags.............................
   #
   CFLAGS  = -O0 -I. -fp-model strict -g -debug all -traceback

8. At this point, the code can be compiled in the DOUAR/src directory by typing

   make distclean
   make all
   make install

9. To compile the post-processor, navigate to the DOUAR/src/VTK directory and type

   make all

Running DOUAR

Files needed to run DOUAR

• Input file
• Job submission script for Taito

If the stars have properly aligned, you should have a functional DOUAR-WSMP install. You can use this input file to run the code on the respective systems listed below. Note the test jobs should be run on at least 8 cores. On Taito, you can modify this example job submission script as needed. Jobs can be submitted on Taito by typing

Additional information on job submission, monitoring and configuration can be found on the Taito user guide.