______           _  _____ _____
        |  _  \         | ||_   _|_   _|
        | | | |___  __ _| |  | |   | |
        | | | / _ \/ _| | |  | |   | |
        | |/ /  __/ (_| | |__| |_ _| |_
        |___/ \___|\__,_|_(_)___/ \___/

This is a shell with modules and PATHs set to work with Deal.II.
All external libraries and deal.II itself are located in 

    /Applications/deal.II.app/Contents/Resources/spack/

If you want to set up your daily Terminal to work with deal.II, add
these lines to your ~/.profile file (the first line turns off this message):

   export DEAL_II_CONF_SILENT=ON
   # DEAL_II_USE_LMOD=ON # if you want to use lmod instead of tcl module
   # DEAL_II_ENABLE_VIEW=ON # if you want to set CMAKE_PREFIX_PATH to a view of
   . /Applications/deal.II.app/Contents/MacOS/dealii.conf

deal.II and all its dependencies were installed using spack, and are available
through the spack and module or lmod commands, e.g.:

    module load dealii

The default interactive shell is now zsh.
To update your account to use zsh, please run `chsh -s /bin/zsh`.
For more details, please visit https://support.apple.com/kb/HT208050.
bash-3.2$ cd Desktop/GitHub-repos/CompLimb-biomech/
bash-3.2$ module load dealii
Loading dealii/9.2.0-openblas-py2-py3
  Loading requirement: zlib/1.2.11 xz/5.2.5 openblas/0.3.10 metis/5.1.0 suite-sparse/5.3.0-openblas libc/1.0 libxml2/2.9.10
    hwloc/1.11.11 openmpi/3.1.6 parmetis/4.0.3 netlib-scalapack/2.0.2-openblas hdf5/1.10.6 netcdf-c/4.7.3 mumps/5.2.0-openblas
    matio/1.5.13 hypre/2.18.2-openblas glm/0.9.7.1 bzip2/1.0.8 boost/1.73.0 trilinos/12.18.1-openblas tetgen/1.5.0 gmp/6.1.2
    mpfr/4.0.2 mpc/1.1.0 symengine/0.6.0 superlu-dist/6.3.0-openblas sundials/3.2.1 petsc/3.13.1-openblas-py2-py3
    arpack-ng/3.7.0-openblas slepc/3.13.3-openblas-py2-py3 p4est/2.2 intel-tbb/2020.2 oce/0.18.3 netgen/5.3.1 netcdf-cxx/4.2
    nanoflann/1.2.3 muparser/2.2.6.1 gsl/2.5 gmsh/4.5.4-openblas ginkgo/1.1.0 assimp/4.0.1 adol-c/2.7.2
bash-3.2$ cmake .
-- The C compiler identification is AppleClang 11.0.3.11030032
-- The CXX compiler identification is AppleClang 11.0.3.11030032
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc - works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/openmpi-3.1.6-ch3xlssbdriiio4hygk3xhnxclncjvze/bin/mpic++
-- Check for working CXX compiler: /Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/openmpi-3.1.6-ch3xlssbdriiio4hygk3xhnxclncjvze/bin/mpic++ - works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Autopilot invoked
###
#
#  Project  complimb-biomech  set up with  deal.II-9.2.0  found at
#      /Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/dealii-9.2.0-yv7ehpigjxtbrhqi7y4menbu532z6rxi
#
#  CMAKE_BUILD_TYPE:          Debug
#
#  You can now run
#       $ make                - to compile and link the program
#       $ make run            - to (compile, link and) run the program
#
#       $ make sign           - to sign the executable with the supplied OSX developer key
#
#       $ make debug          - to switch the build type to 'Debug'
#       $ make release        - to switch the build type to 'Release'
#
#       $ make edit_cache     - to change (cached) configuration variables
#                               and rerun the configure and generate phases of CMake
#
#       $ make strip_comments - to strip the source files in this
#                               directory off their comments; this is irreversible
#       $ make clean          - to remove the generated executable as well as
#                               all intermediate compilation files
#       $ make runclean       - to remove all output generated by the program
#       $ make distclean      - to clean the directory from _all_ generated
#                               files (includes clean, runclean and the removal
#                               of the generated build system)
#       $ make info           - to view this message again
#
#  Have a nice day!
#
###
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/ecomellas/Desktop/GitHub-repos/CompLimb-biomech
bash-3.2$ make debug
Scanning dependencies of target debug
[100%] Switching CMAKE_BUILD_TYPE to Debug
-- Autopilot invoked
-- Run   $ make info  to print a detailed help message
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/ecomellas/Desktop/GitHub-repos/CompLimb-biomech
***
*** Switched to Debug mode. Now recompile with:  $ make
***
[100%] Built target debug
bash-3.2$ make
Scanning dependencies of target complimb-biomech
[ 50%] Building CXX object CMakeFiles/complimb-biomech.dir/complimb-biomech.cc.o
[100%] Linking CXX executable complimb-biomech
ld: warning: directory not found for option '-L/Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/zlib-1.2.11-rqiqrujgg5aemhk7eqjk3asbaukff'
[100%] Built target complimb-biomech
bash-3.2$ mpirun -np 4 -wdir ./run ../complimb-biomech

Triangulation:
  Number of active cells: 1024 (by partition: 281+263+258+222)
  Number of degrees of freedom: 27644 (by partition: 8122+6856+7350+5316)
  Number of degrees of freedom per block: [n_u, n_p_fluid] = [26451, 1193]

Setting up quadrature point data...

Solver:
  CST     = make constraints
  ASM_SYS = assemble system
  SLV     = linear solver 

Timestep 1 @ 0.0001s
________________________________________________________________________________________________________________________

       SOLVER STEP      |    SYS_RES         RES_NORM     RES_U      RES_P           NU_NORM     NU_U       NU_P 
________________________________________________________________________________________________________________________

  0  CST  ASM_SYS  SLV