The packages required for the Fortran code are:
Note that often, default installations of HDF5 and MPI packages do not include support for Fortran - this has to be explicitly enabled as described below.
The first dependency is a Fortran compiler. In addition to commercial compilers (e.g. ifort, pgfortran, ...), there are a couple of free ones, the most common of which is gfortran. If you don’t already have a compiler installed, you can install gfortran via package managers on Linux machines, or from MacPorts or binary installers on Mac (e.g. http://gcc.gnu.org/wiki/GFortranBinaries). If you are unsure about how to do this, speak to your system administrator.
If you do not have root access to the machine you are using, then replace /usr/local in the following instructions by e.g. $HOME/usr. In addition, you should never include sudo in any of the commands.
Note
You only need to follow this section if you do not have HDF5 or MPI already installed
The easiest way to install these dependencies correctly is to use the installation script provided with Hyperion. First, make sure you have downloaded the latest tar file from here, then expand it with:
tar xvzf hyperion-x.x.x.tar.gz
cd hyperion-x.x.x
Then, go to the deps/fortran directory and run the automated install script provided:
cd deps/fortran
python install.py <prefix>
where <prefix> is the folder in which you want to install the MPI and HDF5 libraries. To avoid conflicting with existing installed versions (that may not have Fortran support), it is best to install these in a dedicated directory such as /usr/local/hyperion:
python install.py /usr/local/hyperion
and the libraries will be installed in the lib, include, etc. directories inside /usr/local/hyperion. Once the installation is complete, the installer will instruct you to add certain commands to your startup files.
Note
if you are installing to a location outside your user directory, you will need to run the command with sudo, i.e.:
sudo python install.py <prefix>
Next, open a new terminal and ensure that the following commands:
which mpif90
which h5fc
return a path that is inside the installation path you specified, for example:
$ which mpif90
/usr/local/hyperion/bin/mpif90
$ which h5fc
/usr/local/hyperion/bin/h5fc
If you get command not found then you have probably not set up your $PATH correctly.
The installation script has a number of options (e.g. to set the compilers) that can be seen with:
python install.py --help
If the installation fails, a log will be posted to the Pastebin service. Copy the URL and report it either by email or on the Github Issues.
If the installation succeeds, you can ignore the rest of this document, and move on to the Python code dependencies.
Note
You only need to follow this section if you do not have MPI already installed.
In order to use the parallel version of the radiation transfer code, you will need an installation of MPI that supports Fortran. By default, MacOS X ships with OpenMPI, but the Fortran bindings are not included. In this section, I have included instructions to install the MPICH2 library with support for Fortran (though you can in principle use any MPI distribution).
Note
If you encounter any errors at any stage, see the Troubleshooting section.
First, download the source for the latest stable release of MPICH2 from the MPI downloads page. Once downloaded, unpack the file and then go into the source directory:
cd mpich2-x.x.x
and configure the installation:
./configure --enable-fc --prefix=/usr/local/mpich2
In practice, you will probably want to use a specific fortran compiler, which you can specify using the F77 and FC variables as follows:
./configure F77=ifort FC=ifort --enable-fc --prefix=/usr/local/mpich2
Once the configure script has successfully run, you can then proceed to build the MPI library:
make
If the build is successful, then you can install the library into place using:
sudo make install
Finally, you will need to add the MPICH2 /usr/local/mpich2/bin directory to your $PATH. To check that the installation was successful, type:
which mpif90
and you should get:
/usr/local/mpich2/bin/mpif90
If this is not the case, then the installation was unsuccessful.
If you get the following error when running ./configure:
configure: error: **** Incompatible Fortran and C Object File Types! ****
F77 Object File Type produced by "ifort -O2" is : : Mach-O 64-bit object x86_64.
C Object File Type produced by "gcc -O2" is : : Mach-O object i386.
then you are probably using the 64-bit Intel Fortran Compiler on MacOS 10.5.x, but the 32-bit version of gcc. To fix this, you will need to switch to using the 32-bit Intel Fortran Compiler. First, clean up the installation so far with:
make clean
Then, rerun configure and build using:
./configure F77="ifort -m32" FC="ifort -m32" --enable-fc --prefix=/usr/local/mpich2
make
sudo make install
Note
You only need to follow this section if you do not have HDF5 already installed.
Note
If you encounter any errors at any stage, see the Troubleshooting section.
To compile the Fortran part of the radiation transfer code, you will need the HDF5 library v1.8.5 or later, with support for Fortran enabled. While package managers such as Fink and MacPorts include HDF5, they often do not include the Fortran bindings. Therefore, it is best to install the HDF5 library manually from source.
To start with, download the source code from the HDF5 downloads page, then go into the source code directory:
cd hdf5-x.x.x
and configure the installation:
./configure --enable-fortran --enable-hl --prefix=/usr/local/hdf5_fortran
In practice, you will probably want to use a specific fortran compiler, which you can specify using the FC variable as follows:
./configure --enable-fortran --enable-hl --prefix=/usr/local/hdf5_fortran FC=ifort
Once the configure script has successfully run, you can then proceed to build the HDF5 library:
make
If the build is successful, then you can install the library into place using:
sudo make install
Finally, you will need to add the HDF5 /usr/local/hdf5_fortan/bin directory to your $PATH. To check that the installation was successful, type:
which h5fc
and you should get:
/usr/local/hdf5_fortran/bin/h5fc
If this is not the case, then the installation was unsuccessful.
Note
The reason we install HDF5 in hdf5_fortran as opposed to simply hdf5 is so as not to conflict with a possible installation of the library without the Fortran bindings.
If you get the following error when running make:
...
H5f90proto.h:1211: warning: previous declaration of 'H5_FC_FUNC_' was here
H5f90proto.h:1216: error: 'H5_FC_FUNC_' declared as function returning a function
H5f90proto.h:1216: warning: redundant redeclaration of 'H5_FC_FUNC_'
H5f90proto.h:1213: warning: previous declaration of 'H5_FC_FUNC_' was here
H5f90proto.h:1218: error: 'H5_FC_FUNC_' declared as function returning a function
H5f90proto.h:1218: warning: parameter names (without types) in function declaration
H5f90proto.h:1218: warning: redundant redeclaration of 'H5_FC_FUNC_'
H5f90proto.h:1216: warning: previous declaration of 'H5_FC_FUNC_' was here
make[3]: *** [H5f90kit.lo] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1
then you are probably using the 64-bit Intel Fortran Compiler on MacOS 10.5.x, but the 32-bit version of gcc. To fix this, you will need to switch to using the 32-bit Intel Fortran Compiler. First, clean up the installation so far with:
make clean
Then, rerun configure and build using:
./configure --enable-fortran --enable-hl --prefix=/usr/local/hdf5_fortran FC="ifort -m32"
make
sudo make install
If this does not work, try cleaning again, and setup the 32-bit ifort using the scripts provided with ifort. For example, if you are using ifort 11.x, you can do:
make clean
source /opt/intel/Compiler/11.0/056/bin/ia32/ifortvars_ia32.sh
./configure --enable-fortran --enable-hl --prefix=/usr/local/hdf5_fortran FC=ifort
make
sudo make install
If you get the following error when running make:
Error: H5fortran_types.f90, line 39: KIND value (8) does not specify a valid representation method
Errors in declarations, no further processing for H5FORTRAN_TYPES
[f95 error termination]
make[3]: *** [H5fortran_types.lo] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1
you are using the NAG f95 compiler, which by default does not like statements like real(8) :: a. To fix this, you will need to specify the -kind=byte option for the f95 compiler. First, clean up the installation so far with:
make clean
Then, rerun configure and build using:
./configure --enable-fortran --enable-hl --prefix=/usr/local/hdf5_fortan FC="ifort -kind=byte"
make
sudo make install