Commander is an Optimal Monte-carlo Markov chAiN Driven EstimatoR which implements fast and efficient end-to-end CMB posterior exploration through Gibbs sampling.
| Main features | Installation | Usage | License | Projects | Citation |
The latest version - Commander3
- brings together critical features such as:
- Modern Linear Solver
- Map Making
- Parallelism
- Sky and instrumental modelling
- CMB Component Separation
Commander3
is written using modern Fortran
standards such as modules, sub modules, and object oriented derived types. The code is highly tuned and optimized to run on High Performance Computing (HPC) facilities, but it can also be run on your local machine.
The previous incarnation of Commander, - Commander2
- is now an internal part of Commander3
, while the first version of the code, - Commander1
- is used mainly for debugging and/or legacy purposes. However, Commander1
has not been officially released; thus, it doesn't support CMake installation, as described in official documentation.
For the complete installation guide please refer to the official documentation, where you can find how to compile and run Commander
on different platforms, including HPCs such as NERSC, UNINETT Sigma2, OWLs etc. Below you can find the short summary of how to compile it from source.
To successfully run Commander, you need the following libraries:
- MPI - required regardless of installation type;
- OpenMP - required regardless of installation type;
- BLAS - required regardless of installation type;
- LAPACK - required regardless of installation type;
- HDF5 - required only if compiled via
Makefile
; - FFTW - required only if compiled via
Makefile
; - Sharp2 - required only if compiled via
Makefile
; - Healpix - required only if compiled via
Makefile
; - CFitsio - required only if compiled via
Makefile
;
In addition you may want to install/update the following packages:
- Automake version 1.16 or higher - required regardless of installation type;
- Autoconf version 2.69 or higher - required regardless of installation type;
- Libtool version 2.4.6 or higher - required regardless of installation type;
CMake is a tool which allows you to compile your code on various platform, via generation of build files (e.g. on Linux are Makefiles
). It is configured to scan your system and identify present/missing libraries to download and install the missing ones. So, please install CMake before proceeding by this installation type.
Once CMake is installed, the Commander3
installation procedure is quite simple and consists of the following steps:
$ git clone https://github.com/hke/Commander.git
$ cd Commander
$ mkdir build
$ cd build
then to configure Commander3
compillation with, e.g. Intel Fortran compilers, use:
$ cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort ..
wait while configuration is finished and then run:
$ cmake --build . -j n
where n
is the amount of processors you wish to use to speed up the installation.
Because Commander3
is usually run on HPCs, where users do not have the sudo
/root
previleges, the default installation path is configured to be inside /path/to/cloned/repo/Commander/build/install/
, where Commander3
binary can be found inside
bin
folder, under the name commander3
.
After you cloned the latest version of the repo, you need to do the following:
- Determine the locations of your MPI compilers (mpif90, mpif77, mpicc, etc), and ensure that they function correctly.
- Determine the locations of the CFITSIO and LAPACK libraries, and how to link to these libraries.
- Look in the
config/
directory and see if a configuration already exists which is similar to your machine. Copy theconfig
(or theconfig.example
) to a new file in the same directory. Call this new fileconfig.<machine>
where<machine>
is the name of the system you will be building the software on. - Edit the
config
file and specify all the options for your system. cd
into the top level commander directory and set theCOMMANDER
environment variable to the string you used above as the<machine>
. For example, if your config is namedconfig.mylaptop
, then you would set the environment variable in.bashrc
as:- For Bourne-like shells
$ export COMMANDER=mylaptop
- For csh-like shells
% setenv COMMANDER mylaptop
- To view some additional help about the available make targets:
$ make help
- To build and install the software:
$ make
$ make install
In short, to run Commander3
, you need to:
$ export OMP_NUM_THREADS=1
then create the chain directory as specified in parameter file:
$ mkdir chains_dir
copy parameter file into it:
$ cp param_file.txt chains_dir/
and, finally, run Commander3
via following command:
$ mpirun -np num_proc ~/Commander/src/commander/commander param_file.txt 2>&1 | tee chains_dir/slurm.txt
Here, num_proc
is the number of processors to use, slurm.txt
is the file to store output logs.
As stated previously, Commander1
has not been officially released and is used primarily for debugging. If you wish to run it, however, you can compile it with Makefile
using:
$ cd commander1
$ make
and then run the follwoing command:
$ mpirun -n num_proc ~/Commander/commander1/src/commander/commander param_file.txt 2>&1 | tee chains_dir/slurm.txt
Commander framework is part of the following projects:
This work has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreements No 776282 (COMPET-4; BeyondPlanck), 772253 (ERC; bits2cosmology) and 819478 (ERC; Cosmoglobe).
If used for published results, please cite these papers: