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install_moose.md

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#Reference

Preparation

  • load the module of gcc and MPI accordingly
  • export CC=mpicc; export CXX=mpicxx ; export F77=mpif77 ; export FC=mpif90;
  • export OPTFLAGS="-O3 -march=native -mtune=native -DNDEBUG"

PETSC install

./configure \
 COPTFLAGS="$OPTFLAGS" CXXOPTFLAGS="$OPTFLAGS" FOPTFLAGS="$OPTFLAGS" CUDAOPTFLAGS="$OPTFLAGS" \
--prefix=/opt/petsc/3.12.2_4moose \
--with-debugging=0 \
--with-ssl=0 \
--with-pic=1 \
--with-openmp=1 \
--with-mpi=1 \
--with-shared-libraries=1 \
--with-cxx-dialect=C++11 \
--with-fortran-bindings=0 \
--with-sowing=0 \
--download-hypre=/opt/petsc/externals/hypre-2.15.1.zip \
--download-fblaslapack=/opt/petsc/externals/fblaslapack-3.1.1.tar.gz \
--download-metis=/opt/petsc/ANL/metis.tar.gz \
--download-ptscotch=/opt/petsc/externals/scotch_6.0.9.tar.gz \
--download-parmetis=/opt/petsc/externals/parmetis-4.0.3.tar.gz \
--download-superlu_dist=/opt/petsc/externals/superlu_dist-6.2.0.zip \
--with-scalapack-dir=/opt/scalapack/2.1_gcc53 \
--download-mumps=/opt/petsc/externals/MUMPS_5.2.1.tar.gz \
--download-slepc=/opt/petsc/externals/slepc-3.12.2.tar.gz \
PETSC_DIR=`pwd` PETSC_ARCH=linux-opt
  • This didn't work. unpack those libraries at petsc/linux-opt/externalpackages/ and rename them such as metis-** to petsc-pkg-metis
  • In particular, metis, parmetis, MUMPS may need to be from ftp.anl. New version may not work.
  • Scalapack didnt' work. Install scalapack as a stand-alone then coupling using --with-scalapack-dir
    • ccmake ..; setup blas and lapack using existing libraries. dynamic (.so) only
    • make -j22; make install
  • make PETSC_DIR=/opt/petsc/petsc-3.12.2 PETSC_ARCH=linux-opt all # took less than 5 min
  • make PETSC_DIR=/opt/petsc/petsc-3.12.2 PETSC_ARCH=linux-opt install
  • make PETSC_DIR=/opt/petsc/petsc-3.12.2 PETSC_ARCH=linux-opt test # testing with MPI
Running test examples to verify correct installation  
Using PETSC_DIR=/share/apps/7/petsc/petsc-3.12.2 and PETSC_ARCH=linux-opt  
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI process  
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2 MPI processes  
C/C++ example src/snes/examples/tutorials/ex19 run successfully with hypre  
C/C++ example src/snes/examples/tutorials/ex19 run successfully with mumps  
C/C++ example src/snes/examples/tutorials/ex19 run successfully with superlu_dist  
Completed test examples

Installing moose

  • VTK might be necesssary. Install or skip VTK in the moose (actually libmesh) configuration
  • Will need the info of PETSC location. DO export PETSC_DIR=/opt/petsc/3.12.2_4moose
  • Define VTKLIB_DIR and VTKINCLUDE_DIR if ncessary
  • Download moose
    • If moose-master.zip is downloaded from github webpage, it will not contain 1) libmesh and 2) metaphysicL
    • Download each of them and upack libmesh at moose/libmesh. Unpack metaphysicL at moose/libmesh/contrib/metaphysicl
      • go to moose/libmesh/contrib/metaphysicl and run bootstrap script
      • go to moose/libmesh/contrib/timpi and run bootstrap script
  • cd moose; ./scripts/update_and_rebuild_libmesh.sh
    • This will very slow. Or hack the script and edit as make -j 10
  • For peacock, download vtk from pypi and pip install or conda install
    • For rhel7, opengl version is too low and will not work.
    • Compile vtk 7.1.1 from source using VTK_RENDERING_BACKEND=OpenGL (default is OpenGL2). Wrap with available python
    • After make;make install, copy vtk/lib/python3.x/site-packages/vtk folder into $PYTHON_HOME/lib/python3.x/site-packages
    • when libhdf.so.10X is missing error is found, re-install conda
    • check if import vtk works fromk python3 environment
    • Go to moose/test and re-run make hit and then run python3 ../python/peacock/peacock

Running tests

  • mkdir ~/project ; cd ~project ; cp -r /opt/moose/moose-next moose
  • cd ~/projects/moose/test
  • make -j 10 # took several minutes
  • make hit
  • Edit ~/.config/matplotlib/matplotlibrc as "backend : TkAgg"
  • ./run_tests -j 10