Merge pull request #81 from LSSTDESC/integration

Merge Integration updates into Main

Dockerfile

@@ -26,7 +26,7 @@ ARG LSST_GROUP=lsst
 USER lsst
 
 WORKDIR $LSST_STACK_DIR
-   
+
 RUN echo "Environment: \n" && env | sort && \
     curl -LO https://ls.st/lsstinstall && \
     bash ./lsstinstall ${LSST_TAG:+"-X"} $LSST_TAG && \
@@ -41,7 +41,7 @@ RUN echo "Environment: \n" && env | sort && \
     mkdir -p /tmp/gh && \
     cd /tmp/gh && \
     git clone https://github.com/LSSTDESC/td_env && \
-    cd td_env && \ 
+    cd td_env && \
     git checkout $GH_SHA 
 
 USER root 
@@ -52,11 +52,12 @@ RUN cd /tmp/gh/td_env && \
 USER lsst
 RUN cd /tmp/gh/td_env/conda && \
     bash /tmp/gh/td_env/docker/update-docker.sh w_2022_10 && \
+    bash post-conda-build.sh && \
     echo "source $LSST_STACK_DIR/loadLSST.bash" >> ~/.bashrc && \
     echo "setup lsst_distrib" >> ~/.bashrc && \
     rm -Rf /tmp/gh
-    
-    
+
+
 ENV HDF5_USE_FILE_LOCKING FALSE
 ENV PYTHONSTARTUP ''
 

README.md

@@ -21,6 +21,13 @@ Defines, builds and installs a conda environment including the LSST Science Pipe
 ## Current Stable Release
 https://github.com/LSSTDESC/td_env/releases/latest
 
+## Running cosmosis + firecrown
+Cosmosis is available in the td_env integration builds. Users are encouraged to try this out. 
+
+The default `setup_td_int.sh` will prepare the environment by settting $CSL_DIR, $FIRECROWN_DIR, $FIRECROWN_SITE_PACKAGES variables which points to the current integration build directory. Currently the default setup does NOT entirely complete the cosmosis set up and does not run `source cosmosis-configure`. However, this can be enabled by doing:  `source setup_td_int.sh -c`.
+
+To run a test of cosmosis + firecrown after doing `source setup_td_int.sh` please try: `cosmosis $FIRECROWN_DIR/examples/des_y1_3x2pt/des_y1_3x2pt.ini`
+
 ## To Request Additional Packages, Report Problems, or Submit Questions
 Please [open an issue](https://github.com/LSSTDESC/td_env/issues) on this repository.
 

conda/build-nersc.sh

@@ -48,6 +48,7 @@ fi
 
 mkdir -p $curBuildDir
 cp conda/packlist.txt $curBuildDir
+cp conda/post-conda-build.sh $curBuildDir
 cp conda/piplist.txt $curBuildDir
 cp nersc/setup_td_env.sh $curBuildDir
 cp nersc/sitecustomize.py $curBuildDir
@@ -79,6 +80,18 @@ cd resspect
 python setup.py install
 cd ..
 
+# Grab firecrown source so we have the examples subdirectory
+firecrown_ver=$(conda list firecrown | grep firecrown|tr -s " " | cut -d " " -f 2)
+echo $firecrown_ver
+curl -LO https://github.com/LSSTDESC/firecrown/archive/refs/tags/v$firecrown_ver.tar.gz
+tar xvzf v$firecrown_ver.tar.gz
+# Set up a common directory name without version info to set FIRECROWN_DIR more easily
+ln -s firecrown-$firecrown_ver firecrown
+
+# Additional build steps
+bash ./post-conda-build.sh
+
+
 python -m compileall $curBuildDir
 
 # Hard-coding this for now for building at NERSC

conda/packlist.txt

@@ -3,6 +3,8 @@ celerite
 cmdstan
 cmdstanpy
 coloredlogs
+cosmosis>=2.2.2
+cosmosis-build-standard-library>=1.2
 emcee
 extinction
 f90nml
@@ -27,4 +29,3 @@ multiprocess>=0.70.8
 nestcheck
 pymultinest
 pyxdg
-

conda/post-conda-build.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+# Project- or dependency-specific setup commands to be
+# run after a conda installation, for example to download
+# additional data files
+
+
+# Download and build the CosmoSIS standard library
+# in a directory under the CosmoSIS python directory
+cosmosis-build-standard-library -i

docker/update-docker.sh

@@ -18,6 +18,9 @@ conda clean -y -a
 # Import of ligo.em_bright to cause associated data files to be downloaded into the image
 # python -c "import ligo.em_bright"
 
+# Additional build steps
+bash ./post-conda-build.sh
+
 conda env export --no-builds > /opt/lsst/software/stack/td_env-image-nobuildinfo.yml
 conda env export > /opt/lsst/software/stack/td_env-image.yml
 

nersc/setup_td_env.sh

@@ -54,3 +54,8 @@ else
   source $DESC_LSST_INSTALL_DIR/loadLSST.zsh
 fi
 setup lsst_distrib
+
+# For cosmosis and firecrown.  Should try to find a better way to set these
+export CSL_DIR=$CONDA_PREFIX/lib/python3.8/site-packages/cosmosis/cosmosis-standard-library
+export FIRECROWN_SITE_PACKAGES=$CONDA_PREFIX/lib/python3.8/site-packages
+export FIRECROWN_DIR=$DESC_LSST_INSTALL_DIR/firecrown

nersc/setup_td_int.sh

@@ -17,6 +17,7 @@ SCRIPT=${BASH_SOURCE[0]}
 usage() {  # Function: Print a help message.
   echo -e \\n"Help documentation for ${BOLD}${SCRIPT}"\\n
   echo "Command line switches are optional. The following switches are recognized."
+  echo "-c  --Setup cosmosis."
   echo "-k  --Setup the env without doing module purge."
   echo "-n  --Setup the env without the LSST Sci Pipelines."
   echo "-s  --Setup the env for shifter."
@@ -28,9 +29,10 @@ usage() {  # Function: Print a help message.
 # -h help
 # -n Do not setup the LSST Sci Pipelines
 #while getopts e:n: flag
-while getopts "hkns" flag
+while getopts "chkns" flag
 do
     case "${flag}" in
+        c) cosmosis=1;;
         h) usage;;
         k) keepenv=1;;
         n) nolsst=1;;
@@ -120,6 +122,13 @@ case $NERSC_HOST in
         export SNANA_SCRATCH="/global/cscratch1/sd/kessler"
         ;;
 esac
+
+
+if [[ "$cosmosis" ]];
+then
+  source cosmosis-configure 
+fi
+
 export SNANA_LSST_SIM="$SNANA_SCRATCH/SNANA_LSST_SIM"
 
 export SCRATCH_SIMDIR="$SNANA_LSST_SIM"