This is an attempt at listing the steps required to install Chombo on a unix system. It likely contains various holes where I forgot I had done something to get it working - please send any additions or corrections to [jamie.nosp@m..par.nosp@m.kinso.nosp@m.n@gm.nosp@m.ail.c.nosp@m.om], thanks.

To start with, you'll need to satisfy the prerequisites listed in Chombo/doc/ChomboDesign.pdf. In particular, you'll need Fortran compilers and C++ compilers that are sufficiently up to date.

Fortran

gfortran works well on Ubuntu, my installation looks like

parkinsonjl@atmlxlap005:~$ gfortran --version

GNU Fortran (Ubuntu 4.8.4-2ubuntu1~14.04.4) 4.8.4

C++ compiler

Make sure you have a sufficient compiler version. Mine looks like

parkinsonjl@atmlxlap005:~$ mpicc --version

gcc (Ubuntu 4.8.4-2ubuntu1~14.04.4) 4.8.4

HDF5

The latest version of hdf5 (1.10.xx) doesn't seem to work with Chombo at the moment. You can download the source code for version 1.8.21 from [https://portal.hdfgroup.org/display/support/HDF5+1.8.21#files], which does work. There are decent install instructions in release_docs/INSTALL_parallel. Download the files, extract them, then install like

$ cd /path/to/hdf5-1.8.21/
$ ./configure --enable-parallel --prefix=/home/parkinsonj/soft/hdf5/
$ make
$ make check
$ make install

Make sure you use the --enable-parallel option with configure.

Once installed make sure you set the evironment variable

LD_LIBRARY_PATH=/path/to/hdf5/lib/ e.g. LD_LIBRARY_PATH=/home/parkinsonj/soft/hdf5/lib/.

Do this in your .bashrc or whatever gets called whenever you open a terminal so it's always there.

Chombo

Chombo download instructions are available at [https://anag-repo.lbl.gov/chombo-3.2/access.html]. You need to register for an account, then you can get the code using svn:

$ svn --username username co https://anag-repo.lbl.gov/svn/Chombo/trunk/ /your/path/to/chombo/

Then you need to make a /lib/mk/Make.defs.local file for your system. I am using the following options:

DIM           = 2            # 3 also works
DEBUG         = FALSE        # true also works
OPT           = TRUE         # false also works
FC            = gfortran
MPI           = TRUE
MPICXX        = mpiCC
HDFINCFLAGS= -I/usr/local/hdf5-1.8.21p-v18/include
HDFLIBFLAGS= -L/usr/local/hdf5-1.8.21p-v18/lib -lhdf5 -lz 
USE_HDF       = TRUE
HDFMPIINCFLAGS= -I/usr/local/hdf5-1.8.21p-v18/include
HDFMPILIBFLAGS= -L/usr/local/hdf5-1.8.21p-v18/lib -lhdf5 -lz 
flibflags     = -lblas -llapack -lgfortran 
LAPACKLIBS = -L/usr/lib -L/usr/lib/lapack -L/usr/lib/libblas -llapack  -lblas

If the blas or lapack packages don't exist, you may need to run something like sudo apt-get install libblas-dev liblapack-dev. These are tools for mainly doing linear algebra (inverting matrices etc.) very quickly.

Visit

Visit is very useful for quickly visualising data. Download Visit from [https://wci.llnl.gov/simulation/computer-codes/visit/source]. There are good install instructions supplied with the source code/on their website. Add your visit install location to your PATH.

doxygen

Doxygen let's you build documentation from the source code (and the comments within it). It can be downloaded from [http://www.doxygen.nl/download.html]. Then go to the /path/to/mushy-layer/doc directory and run doxygen in a terminal - it should pick up the Doxyfile already there, which specifies how to build the documentation.