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Compiling OGS with PETSc

To setup OGS-PETSc, please first get PETSc codes (v3.4) from the below link if you haven't installed it yet

http://www.mcs.anl.gov/petsc/download/index.html

and compile it with commands like

export PETSC_DIR=/home/me/foo/petsc-3.4.3
./configure PETSC_ARCH=linux-gnu --download-f2cblaslapack=1 -with-debugging=0 --download-superlu_dist --download-hypre=1 --download-ml=1 --download-parmetis --download-metis --prefix=/usr/lib/petsc
make install

where --prefix= is the target directory, where PETSc is installed.

To compile OGS with PETSc,

mkdir build
cd build
cmake ../sources/ -DOGS_FEM_PETSC=ON -DPETSC_DIR=/usr/lib/petsc -DPETSC_ARCH=linux-gnu -DOGS_ONLY_TH=ON
make

you may add -DPETSC_EXECUTABLE_RUNS=YES if multi-pass check with PETSc fails. If all compilation works well, you can test an attached example with the following command

mpirun -np 4 ./ogs t3d &> ogs.log

In case you have already prepared a mesh, the next step is partitioning the mesh for parallelization. To do that, you need to install metis and partmesh. Metis can be downloaded from

http://glaros.dtc.umn.edu/gkhome/metis/metis/download

For partmesh, please get source codes from the below repository

https://github.com/norihiro-w/mesh_partition

and compile it as

mkdir build & cd build
cmake ../sources
make

you will find "partmesh" in build/bin.

Assuming you have foo.msh, a partitioned mesh for 8 CUPs can be created by the following commands

partmesh --ogs2metis foo
mpmetis foo.mesh 8
partmesh --metis2ogs -np 8 -n foo

At the end, foo_partitioned_8.msh will be generated. You need to rename it to foo_partitioned.msh for simulations. For mechanical simulations, you need to add "-q" option to partmesh to prepare a partitioned mesh with quadratic nodes.