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README_SPECFEM2D_DG.md

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SPECFEM2D-DG Configuration and Installation

First Installation

1. Select the right Makefile for SCOTCH

  1. Check your architecture: uname -a
  2. Go into SCOTCH's src: cd ./src/meshfem2D/scotch/src
  3. Copy the appropriate Makefile from the Make.inc folder. E.g.: cp Make.inc/Makefile.inc.i686_mac_darwin10 Makefile.inc
  4. Go back to root: cd ../../../../

2. Configure SCOTCH

  1. Use the configurator: ./config_scotch.sh

  • Known error:

    library_random_f.c:75:3: error: implicit declaration of function 'SCOTCH_randomProc' is invalid in C99
      [-Werror,-Wimplicit-function-declaration]
  SCOTCH_randomProc (*procnum);
  ^

  • Solution: Edit ./src/meshfem2D/scotch/src/libscotch/scotch.h. Add the following line to it (preferably around line 270, where it would make sense): void SCOTCH_randomProc (int);. Go into SCOTCH's src: cd ./src/meshfem2D/scotch/src. Re-make SCOTCH with this edit (do no re-run "./config_scotch.sh"): make. Go back to root and continue installation: cd ../../../../.

  • Cause: For some reason, ./config_scotch.sh replaces the content of ./src/meshfem2D/scotch/src/libscotch/scotch.h at each run, but with a file that does not have the explicit declaration for SCOTCH_randomProc. I could not find the source file used for that. If the source is found, simply add the line above to it and everything should work well.

  • Known error:

    undefined reference to `clock_gettime'

  • Solution: Check the glibc version installed on the system: ldd --version. If the version is < 2.17, a link to the real-time library might be needed. Add -lrt to the list of libraries in SCOTCH's Makefile. To do so, edit ./src/meshfem2D/scotch/src/Makefile.inc and add "-lrt" at the end of the libraries' line ("LDFLAGS").

  • Cause: ??

  • Known error:

    /usr/bin/ld: cannot find -lz

  • Solution: Install the "zlib-dev" package.

  • Other tips: Check that the symbolic link "scotch" aims at the (last version) provided SCOTCH folder: readlink -f scotch. If not, make it be: ln -s -T ./scotch_X.X.X ./scotch

3. Configure SPECFEM

  1. Install an OpenMPI development package. Load its module. Check the module is indeed loaded ("module list" on Unix).
  2. Configure SPECFEM with GNU compilers by running: ./configure FC=gfortran CC=gcc MPIFC=mpif90 --with-mpi --enable-double-precision or with Intel compilers by running: ./configure FC=ifort CC=icc MPIFC=mpif90 --with-mpi --enable-double-precision

  • Known error:

    configure: error: MPI header not found; try setting MPI_INC.

  • Solution: Make sure you have an mpi package installed and loaded. Make sure you load the module corresponding to the compile you're using, e.g. with: load openmpi/intel.

  • Known error:

    configure: error: Fortran compiler cannot create executables

  • Solution: Make sure you have the right compilers installed (gcc, icc, gfortran, fort, etc.). On clusters, load the relevant package to have them available, e.g. with: load intel/compiler

  • Known error:

    ld: library not found for -lSystem

  • Solution: Re-install your compilers just in case. On MacOS and using HomeBrew, try brew reinstall gcc and brew reinstall gfortran. Make sure your library path contains the stdlib. On MacOS:

    export LIBRARY_PATH="$LIBRARY_PATH:/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"

    It might be useful to add that export line (or the one that works for you) in your login script.

4. Compile SPECFEM-DG

  1. Compile SPECFEM-DG: make clean; make all

  • Known error:

    undefined reference to `clock_gettime'"

  • Solution: Check the glibc version installed on the system: ldd --version. If the version is < 2.17, a link to the real-time library might be needed. Add -lrt to the list of libraries in SCOTCH's Makefile. To do so, edit specfem-dg/src/meshfem2D/scotch/src/Makefile.inc and add "-lrt" at the end of the libraries' line ("LDFLAGS").

  • Known error:

    Error: Array 'some_array' at (1) is larger than limit set by '-fmax-stack-var-size=', moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider using '-frecursive', or increase the '-fmax-stack-var-size=' limit, or change the code to use an ALLOCATABLE array. [-Werror=surprising]

Solution: Edit ./Makefile (SPECFEM's main makefile). Add "-frecursive" to the list "FLAGS_CHECK". Recompile (do not re-run "./configure FC=..."): make clean; make all.

Next Installations

Now, SPECFEM2D-DG is configured for your machine. If you modify the source code, you only need to recompile it with:

  make

or

  make clean; make all

Running SPECFEM2D-DG Simulations

The simulations' method of execution varies whether you are on a local machine or on a cluster. On a local machine, running the script provided in the folders which are under "./EXAMPLES" should be enough. On a cluster, please refer to its documentation.

Preparing a Run

Configure your own simulation case in the "./EXAMPLES/" folder.

  1. Configure global parameters in the file "./EXAMPLES/my_simulation/PARFILE".
  2. Adapt the mesh in the file "./EXAMPLES/my_simulation/INTERFACESFILE"
  3. Configure source parameters in the file "./EXAMPLES/my_simulation/SOURCEFILE"
  4. Note: the names of the files "PARFILE", "INTERFACESFILE", and "SOURCEFILE" may vary, depending of what's inside the "./EXAMPLES/my_simulation/run_this_example.sh" script.
  5. Run the simulation using the "./EXAMPLES/my_simulation/run_this_example.sh" script.