Pulsar Timing Environments

This repository offers a centeralized location for the IPTA Pulsar Timing & Data Combination Teams' environment.

Currently, this repository presents the following:

• An Anaconda Environment for Pulsar Science (anaconda_env.yml)
• Singularity/Apptainer Container for HPC Resources (containers/Singularity)

Installation of the Conda Environment

Please note, we highly encourage using a fresh install of Mambaforge or MicroMambaover a default install of Anaconda/Miniconda. If you must use an Anaconda/Miniconda installation, from a fresh environment install the Mamba Environment & Package Handler via conda install -c conda-forge mamba.

Note: As of conda version 22.11, libmamba can be used as a solver to speed up basic Anaconda installs (though there are growing pains). You can find out more at the official posting.

To install this environment in your flavor of Anaconda, proceed through the following steps:

1. Clone this directory: git clone https://github.com/ipta/pulsar-env.git
2. Enter the cloned directory: cd pulsar-env
3. Using mamba, install the environment: mamba env create -f anaconda-env.yml
4. Activate the environment: mamba activate IPTA_Env

MacOS installation

Same as above; but try with:

1. micromamba env create --platform osx-64 --file anaconda-env.yml

Important Note Regarding the Included OpenMPI

For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default. To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before launching your MPI processes. Equivalently, you can set the MCA parameter in the command line: mpiexec --mca opal_cuda_support 1 ...

In addition, the UCX support is also built but disabled by default. To enable it, first install UCX (conda install -c conda-forge ucx). Then, set the environment variables OMPI_MCA_pml="ucx" and OMPI_MCA_osc="ucx" before launching your MPI processes. Equivalently, you can set the MCA parameters in the command line: mpiexec --mca pml ucx --mca osc ucx ...

Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX. Please consult UCX's documentation for detail.