Updating Singularity/Apptainer definition file and README

containers/README.md

@@ -0,0 +1,26 @@
+# Apptainer/Singularity
+
+Apptainer (former name: Singularity) is a program to build virtual machines (containers) with desired OS and programs. These can be easily deployed and ran on other computers. 
+Containers are build based on the recipies called "definition files", here we provide a definition file `Singularity`. Note, sometimes definition files have an extension `.def`, which we also refer to in the instructions below.
+
+The current definition file contains `tempo2`, `enterprise`, and other primary packages for IPTA DR3 data analyses.
+
+## To build a container:
+
+`sudo apptainer build new_sif_file_name.sif def_file.def`
+
+## To browse container content:
+
+`apptainer shell --bind "/virtual_home_directory/:$HOME"  pulsarenv_official_20240220.sif`
+
+Where `/virtual_home_directory/` is a path on your local machine 
+
+## For building containers inside Windows WSL Ubuntu (Ubuntu for Windows)
+
+In Windows Store, there is Ubuntu app that allows to run Ubuntu shell in Windows. However, by default, it is based on WSL1. Make sure to upgrade from WSL1 to WSL2. This requires also updating settings in BIOS.
+
+To be able to use graphical interface (PGPLOT) in tempo2 plk plugin, a proper display redirection is required:
+
+1. In .bashrc in Ubuntu, `export DISPLAY=172.26.32.1:0.0`, where the IP address (v4) can be obtained in Windows command line prompt by running `ipconfig`.
+2. Install Xming for Windows.
+3. Run Xming with `-ac` argument via XLaunch. Then open Ubuntu.

containers/Singularity

@@ -58,6 +58,8 @@ From: ubuntu:22.04
     apt-get -y --no-install-recommends install libgeos++-dev libgeos3.10.2 libgeos-c1v5 libgeos-dev libgeos-doc
     apt-get -y --no-install-recommends install python3.10-dev libhdf5-dev libsuitesparse-dev cargo rustc proj-bin
 
+    apt-get install -y openmpi-bin libopenmpi-dev # OpenMPI for PolyChord sampler
+
     update-alternatives --install /usr/bin/python python /usr/bin/python3.10 1000
     update-alternatives --set python /usr/bin/python3.10
 
@@ -94,6 +96,12 @@ From: ubuntu:22.04
     python3.10 -m pip install -U emcee chainconsumer
     python3.10 -m pip install -U pdflatex
 
+    python3.10 -m pip install ipdb
+    python3.10 -m pip install tqdm
+    python3.10 -m pip install scikit-learn
+    python3.10 -m pip install bilby
+    python3.10 -m pip install mpi4py # for MPI support in PyPolyChord
+
     #tempo2
     rm -rf /tmp/tempo2
     rm -rf /var/tmp/tempo2
@@ -120,7 +128,8 @@ From: ubuntu:22.04
     python3.10 -m pip install git+https://github.com/nanograv/pint_pal@main
     python3.10 -m pip install git+https://github.com/nanograv/enterprise@dev
     python3.10 -m pip install git+https://github.com/nanograv/enterprise_extensions@dcbusyweek
-
+    python3.10 -m pip install git+https://github.com/bvgoncharov/enterprise_warp
+
     apt-get clean
     apt-get -y autoremove