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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 |

Main Features

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.

Installation

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.

Prerequisites

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;

Compile using CMake

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.

Compile from source

After you cloned the latest version of the repo, you need to do the following:

  1. Determine the locations of your MPI compilers (mpif90, mpif77, mpicc, etc), and ensure that they function correctly.
  2. Determine the locations of the CFITSIO and LAPACK libraries, and how to link to these libraries.
  3. Look in the config/ directory and see if a configuration already exists which is similar to your machine. Copy the config (or the config.example) to a new file in the same directory. Call this new file config.<machine> where <machine> is the name of the system you will be building the software on.
  4. Edit the config file and specify all the options for your system.
  5. cd into the top level commander directory and set the COMMANDER environment variable to the string you used above as the <machine>. For example, if your config is named config.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
  6. To view some additional help about the available make targets:
$ make help
  1. To build and install the software:
$ make
$ make install

Usage

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

License

Coming soon...

Projects

Coming soon...

Citation

If used for published results, please cite these papers:

  • Jewell et al. 2004, ApJ, 609, 1
  • Wandelt et al. 2004, Phys. Rev. D, 70, 083511
  • Eriksen et al. 2004, ApJS, 155, 227 (Commander)
  • Eriksen et al. 2008, ApJ, 676, 10 (Joint FG + CMB)