2. Installation

2.1. Getting the code

The code is available on a git repository, hosted on github: https://github.com/ita-solar/rh. If you don’t have git installed and just want to get started, the easiest way is to download a zip file with the latest revision: https://github.com/ita-solar/rh/archive/master.zip. If you have git installed and would like to be up-to-date with the repository, you can do a git clone:

or using SSH (only for contributors):

git clone git@github.com:ita-solar/rh.git

Whether you unpack the zip file or do one of the above it will create a directory called rh in your current path. This directory will have the following subdirectories:

Directory Contents
rh Main RH source
rh/Atmos Used to keep atmosphere files
rh/Atoms_example Used to keep atom files, line and wavelength lists (example)
rh/idl Old RH IDL routines, not used
rh/Molecules Used to keep molecule files
rh/python Utility Python programs
rh/rh15d_mpi Source files for RH 1.5D
rh/rhf1d Source files for 1D geometry
rh/rhsc2d Source files for 2D geometry, not used
rh/rhsc3d Source files for 3D geometry, not used
rh/rhsphere Source files for spherical geometry, not used
rh/tools Associate C programs for RH, not tested.

2.2. Dependencies

RH 1.5D makes use of the HDF5 library to read the atmosphere files and write the output. It is not possible to run the code without this library. RH 1.5D requires HDF5 version 1.8.1 or newer (versions from branch 1.10.x do not currently work).

Note

RH 1.5D previously made use of the netCDF4 library for its output (which in turn also required HDF5). The latest changes mean RH 1.5D needs only HDF5. Because netCDF4 files are also HDF5 files, the output is still readable in the same way as before and input files in netCDF version 4 format can still be read in the same way by RH 1.5D. If you used input atmospheres in netCDF version 3 format, then these will have to be converted to HDF5. It is recommended that new atmosphere files be created in HDF5 only.

Because HDF5 is commonly used in high-performance computing, many supercomputers already have them available. In Hexagon, they can be loaded as:

module load cray-hdf5-parallel

in Pleiades:

module load hdf5/1.8.7/gcc/mpt

and at ITA’s Linux system:

module load hdf5/Intel/openmpi/1.8.18

2.3. Compilation

Compilation of RH 1.5D consists of two steps:

  1. Compilation of the geometry-independent main libraries (librh.a and librh_f90.a)
  2. Compilation of the rh15d_mpi tree and main binaries

RH 1.5D has been compiled in a variety of architectures and compilers, including gcc, the Intel compilers, and clang. As for MPI implementations, it has been tested with SGI’s mpt, OpenMPI, mpich, mvapich, and Intel’s MPI.

2.3.1. Main libraries

First, one needs to set the environment variables OS and CPU:

export CPU=`uname -m`
export OS=`uname -s`

Note

All the shell commands given in this manual are for bash, so you’ll have to modify them if using another shell.

The main Makefile will then look for an architecture-dependent Makefile in rh/makefile.$CPU.$OS. If a Makefile for your system combination does not exist, you’ll have to create a new Makefile and adapt it to your configuration. You need to make sure that the architecture-dependent Makefile reflects your system’s configuration (i.e., compiler names and flags).

After setting the correct compiler, just build the main libraries with make on the rh directory. If successful, the compilation will produce the two library files librh.a and librh_f90.a.

2.3.2. Program binaries

Go to the rh/rh15d_mpi/ directory and update the Makefile with your compiler and flags. You will need to set CC to the MPI alias (e.g. mpicc). The path to the HDF5 library needs to be explicitly set in HDF5_DIR. In Hexagon this is already stored in the HDF5_DIR environment variable.

If your version of HDF5 was not built as a shared binary, you need to link HDF5 and other used libraries directly. Set the LDFLAGS accordingly, and update the LIBS variable to contain all the other libraries. For Pleiades, make sure your Makefile contains the following:

OTHER_LIBRARY_DIR = /path/to/library
HDF5_DIR = /path/to/hdf5
LDFLAGS = -L../ -L$(OTHER_LIBRARY_DIR)/lib/  -L$(HDF5_DIR)/lib/
LIBS = -lrh -lrh_f90 $(ARCHLIBS) -lhdf5_hl -lhdf5 -lz -lm

Once the Makefile is updated, compilation is achieved with make. The following executables will be created:

File Description
rh15d_ray_pool Main RH 1.5D binary, uses a job pool (see Binaries and execution)
rh15d_ray Alternative RH 1.5D binary. Deprecated. This program runs much slower than rh15d_ray_pool and is kept for backwards compatibility only. Will be removed in a future revision.
rh15d_lteray Special binary for running in LTE

2.4. Run directory

Once compiled, you can copy or link the binaries to a run directory. This directory will contain all the necessary input files, and it should contain two subdirectories called output and scratch.

Warning

If the subdirectories output and scratch do not exist in the directory where the code is run, the code will crash with an obscure error message.

The run directory can be located anywhere, but it must have a directory called Atoms two levels below (i.e. ../../Atoms/) with the Barklem_*data.dat files. This is because these relative paths are hardcoded in barklem.c. The input files in the run directory must obviously point to existing path names.