Building and Installing TDycore

To build TDycores, you need

• CMake version 3.10+
• GNU Make
• Decent C, C++, and Fortran compilers
• PETSc, release 3.14 (tagged v3.14), installed as described below, with PETSC_DIR and PETSC_ARCH environment variables set accordingly.
• autoconf and automake for Pnetcdf. On Mac you can use Homebrew to get these.

For the purposes of illustration, let's assume you're using the gcc, g++, and gfortran compilers.

Installing PETSc and Dependencies

TDycore relies on PETSc to provide several required libraries. Here's how you can properly configure and install PETSc on your system.

1. Clone the PETSc repo somewhere in your workspace.

   git clone https://gitlab.com/petsc/petsc.git
   

2. Set the repo to the correct revision.

   cd petsc
   git checkout v3.14
   

3. Set PETSC_DIR and PETSC_ARCH, and then run PETSc's configure script. The value of PETSC_ARCH doesn't matter--it's just a name for your build configuration. It might be good to name it debug or opt, for example, depending on how you're configuring it.

   export PETSC_DIR=$PWD    # (e.g. if you're using bash)
   export PETSC_ARCH=debug   # (for debug config)
   ./configure \
     --with-cc=mpicc \
     --with-cxx=mpicxx \
     --with-fc=mpif90 \
     --CFLAGS='-g -O0' --CXXFLAGS='-g -O0' --FFLAGS='-g -O0 -Wno-unused-function' \
     --with-clanguage=c \
     --with-debug=1  \
     --with-shared-libraries=0 \
     --download-hdf5 \
     --download-metis \
     --download-parmetis \
     --download-exodusii \
     --download-netcdf \
     --download-pnetcdf \
     --download-zlib \
     --download-fblaslapack
   

4. Build PETSc.

   make all
   

5. Run PETSc's tests to make sure it's properly built.

   make test
   

We're building PETSc in a debug configuration above, for use in development. To build a "production" version of PETSc for performant simulations, run configure with --with-debug=0 instead.

Troubleshooting

If you get errors about undefined symbols during the configuration/build process, you can try to fix it using the --LIBS flag to pass arguments to the linker. For example, you might need --LIBS='-ldl -lz' to get some of the I/O libraries to install properly.

On some systems, it may be easier to use shared libraries instead of static libraries (--with-shared-libraries=1).

Look here for more information on getting PETSc to build successfully in various configurations.

Building TDycore

When you've successully installed PETSc, you can build TDycore with make from the top-level source directory:

make -j V=1

Here, V=1 isn't strictly needed--it just provides verbose reporting of compiler and linker activity, for those of us who like to know that things are happening.

Running the Regression Tests

You can run TDycore's regression test suite with make from the top-level source directory:

make test