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:
git clone https://github.com/ita-solar/rh.git
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, deprecated, do not use |
| rh/rhsc2d | Source files for 2D geometry, deprecated, do not use |
| rh/rhsc3d | Source files for 3D geometry, deprecated, do not use |
| rh/rhsphere | Source files for spherical geometry, deprecated, do not use |
| rh/tools | Associate C programs for RH, not tested. |
Warning
The source code directories for different geometries (rhf1d, rhsc2d, rhsc3d, rhsphere) are still in the code tree, but they are deprecated and will be removed soon. With the latest changes related to rh15d, they are not guaranteed to work or even run. Do not use.
2.2. Dependencies¶
2.2.1. HDF5¶
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 Fram, they can be loaded as (also loading the intel compilers):
module load HDF5/1.8.18-intel-2017a intel/2017a
in Pleiades:
module load hdf5/1.8.7/gcc/mpt
in Hexagon:
module load cray-hdf5-parallel
and at ITA’s Linux system:
module load hdf5/Intel/1.8.19
2.2.2. MPI¶
RH 1.5D is parallelised via MPI, therefore an MPI library is necessary even if running with only one CPU. These are readily available in supercomputers and clusters, but not always in individual workstations. In such cases, users will have to manually install both MPI and HDF5 libraries (HDF5 should be compiled with the MPI library so that the parallel I/O module works).
If using Linux or MacOS, the easiest way to install both MPI and HDF5 with parallel support is via the Anaconda Python distribution. Once you install Anaconda (version 3.6 or above), you can install the hdf5-parallel package, which installs both MPI and HDF5 and has been tested with RH 1.5D:
conda install -c spectraldns hdf5-parallel
Warning
If you obtain pre-compiled binaries or packages for HDF5, you need to make sure they have parallel support enabled. Most available packages do not have parallel support. This includes typical packages from Linux distributions and the hdf5 Anaconda package (but not the above hdf5-parallel package).
2.3. Compilation¶
Compilation of RH 1.5D consists of two steps:
- Compilation of the geometry-independent main libraries (
librh.aandlibrh_f90.a) - Compilation of the
rh15d_mpitree 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 Fram and Hexagon this is already stored in the HDF5_DIR environment variable.
If you are using HDF5 parallel from Anaconda, you need to set HDF5_DIR to your Anaconda directory plus include/ (e.g. ~/anaconda/include).
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.