Merge pull request #113 from helenkirk/new_casa66

New casa66

science-containers/Dockerfiles/casa/ubuntu22.04/Dockerfile

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+FROM ubuntu:22.04
+
+#This Dockerfile creates a local version of the Ubuntu 22.04 OS, along with
+# standard software/libraries that CASA versions need to run.  This container
+# is stored on harbor for to assist with long term stability
+
+
+RUN apt update && \
+    apt upgrade -y && \
+    apt install -y libsm6 libxi6 libxrender1 libxrandr2 \
+        libxfixes3 libxcursor1 libxinerama1 fontconfig \
+        imagemagick xterm && \
+    apt install -y perl autoconf autoconf graphviz xz-utils \
+        gfortran libcanberra-gtk-module libsnl-dev && \
+    apt install -y libxslt1.1 xauth xorg xvfb dbus && \
+    apt install -y libfuse2  && \
+    apt install -y gcc libgsl-dev libfftw3-dev && \
+    apt install -y sssd acl && \
+    apt install -y tcsh && \
+    apt install -y wget
+
+
+

science-containers/Dockerfiles/casa/ubuntu22.04/Makefile

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+
+VERSIONS = \
+	22.04
+
+
+DOCKER_REPO_BASE=images.canfar.net/skaha/ubuntu
+
+.PHONY: build clean run 
+
+all: build
+
+build: 
+	@- $(foreach V,$(VERSIONS), \
+		docker build -t ${DOCKER_REPO_BASE}:$(V) .; \
+    	)
+
+clean:
+	@- $(foreach V,$(VERSIONS), \
+	  docker rmi ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+
+upload: build
+	@- $(foreach V,$(VERSIONS), \
+	  docker push ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+clean_all: clean
+upload_all: upload

science-containers/Dockerfiles/casa/ubuntu22.04/init.sh

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+#!/bin/bash
+
+echo "INIT START"
+echo "sourcing admit_start.sh"
+source /opt/admit/admit_start.sh
+echo "setting up analysisUtils path"
+echo 'import sys' > $HOME/.casa/init.py
+echo 'sys.path.append("/opt/casa/analysisUtils/analysis_scripts/")' >> $HOME/.casa/init.py
+echo 'import analysisUtils as au' >> $HOME/.casa/init.py
+echo 'import analysisUtils as AU' >> $HOME/.casa/init.py
+echo "INIT DONE"

science-containers/Dockerfiles/casa/ubuntu22.04/nsswitch.conf

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+#
+# /etc/nsswitch.conf
+#
+# An example Name Service Switch config file. This file should be
+# sorted with the most-used services at the beginning.
+#
+# The entry '[NOTFOUND=return]' means that the search for an
+# entry should stop if the search in the previous entry turned
+# up nothing. Note that if the search failed due to some other reason
+# (like no NIS server responding) then the search continues with the
+# next entry.
+#
+# Valid entries include:
+#
+#	nisplus			Use NIS+ (NIS version 3)
+#	nis			Use NIS (NIS version 2), also called YP
+#	dns			Use DNS (Domain Name Service)
+#	files			Use the local files
+#	db			Use the local database (.db) files
+#	compat			Use NIS on compat mode
+#	hesiod			Use Hesiod for user lookups
+#	[NOTFOUND=return]	Stop searching if not found so far
+#
+
+# To use db, put the "db" in front of "files" for entries you want to be
+# looked up first in the databases
+#
+# Example:
+#passwd:    db files nisplus nis
+#shadow:    db files nisplus nis
+#group:     db files nisplus nis
+
+passwd:     sss files
+shadow:     files sss
+group:      sss files
+
+#hosts:     db files nisplus nis dns
+hosts:      files dns
+
+# Example - obey only what nisplus tells us...
+#services:   nisplus [NOTFOUND=return] files
+#networks:   nisplus [NOTFOUND=return] files
+#protocols:  nisplus [NOTFOUND=return] files
+#rpc:        nisplus [NOTFOUND=return] files
+#ethers:     nisplus [NOTFOUND=return] files
+#netmasks:   nisplus [NOTFOUND=return] files
+
+bootparams: nisplus [NOTFOUND=return] files
+
+ethers:     files
+netmasks:   files
+networks:   files
+protocols:  files
+rpc:        files
+services:   files
+
+netgroup:   nisplus
+
+publickey:  nisplus
+
+automount:  files nisplus
+aliases:    files nisplus

science-containers/Dockerfiles/casa/ubuntu22.04/update-data.patch

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+#!/usr/bin/perl
+##
+## move rsync point from svn.cv.nrao.edu to casa.nrao.edu
+##
+use File::Find;
+
+if ( scalar(@ARGV) < 1 ) { die "$0 requires path to CASA installation to be patched..." }
+if ( scalar(@ARGV) > 1 ) { die "$0 requires only one parameter which is the path to CASA installation to be patched..." }
+
+unless ( -d $ARGV[0] ) { die "$0 requires path to CASA installation (which should be a directory) to be patched..." }
+
+sub locate_script {
+    if ( -f $_ && $_ eq "update-data" ) {
+        print "substituting $File::Find::dir/$_\n";
+        open( CONTENTS, "< $_" );
+        my @contents = <CONTENTS>;
+        close( CONTENTS );
+        open( CONTENTS, "> $_" );
+        foreach my $x ( @contents ) {
+            $x =~ s@(?:rsync://svn.cv.nrao.edu/casa-data|rsync://casa.nrao.edu/casa-data)@rsync://casa-rsync.nrao.edu/casa-data@g;
+            print CONTENTS "$x";
+        }
+        close( CONTENTS );
+    }
+}
+
+find( { wanted => \&locate_script }, $ARGV[0] );

science-containers/Dockerfiles/casa/version-6.6/Dockerfile

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+FROM images.canfar.net/skaha/ubuntu:22.04
+
+# setup all required env variables
+ARG CASA_RELEASE
+ENV CASA_RELEASE=${CASA_RELEASE}
+ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/casa/bin
+
+# unpack and move casa databundle to container
+ADD ${CASA_RELEASE}.tar.xz /opt/
+
+# chown because the untarred casa has wrong owner/group
+##NB: commands below revert back to the pre-CASA6.4 terminology, as the version of python AND el7 (etc) is now specified everywhere in the full path.
+##NB2: pipelines may be an exception. 
+## (the %%-py* string removes the -py3.X part of the CASA_RELEASE variable name for the directory structure)
+#RUN chown -R root:root /opt/${CASA_RELEASE%%-py*} && ln -s /opt/${CASA_RELEASE%%-py*} /opt/casa
+RUN chown -R root:root /opt/${CASA_RELEASE} && ln -s /opt/${CASA_RELEASE} /opt/casa
+
+#
+## add the admit enhancement (issue #25)
+RUN mkdir /opt/admit
+ADD admit /opt/admit
+RUN cd /opt/admit && \
+    autoconf && ./configure --with-casa-root=/opt/${CASA_RELEASE}
+
+# Allow runtime symlink creation to the casa-data-repository
+# Create a dangling symlink to casa-data-repository so that after deployment
+# the symlink will link to the actual casa-data-repository in storage.
+RUN mkdir -p /arc/projects/casa-data-repository && \
+    rm -rf /opt/${CASA_RELEASE}/data && \
+    ln -s /arc/projects/casa-data-repository/ /opt/${CASA_RELEASE}/data && \
+    chmod 777 /opt/${CASA_RELEASE} && \
+    cd /opt/${CASA_RELEASE} && \
+    REPLACED_DATA=`find lib -name __data__` && \
+    chmod 777 ${REPLACED_DATA}/.. && \
+    rm -rf ${REPLACED_DATA} && \
+    ln -s /arc/projects/casa-data-repository/ /opt/${CASA_RELEASE}/${REPLACED_DATA} && \
+    rm -rf /arc
+
+#Add in analysisUtils package
+RUN mkdir /opt/casa/analysisUtils && \
+    cd /opt/casa/analysisUtils && wget ftp://ftp.cv.nrao.edu/pub/casaguides/analysis_scripts.tar && tar -xvf analysis_scripts.tar
+#(if above doesn't work, can manually download the package and add as below)
+#ADD ./analysis_scripts.tar /opt/casa/analysisUtils/
+#NB: the analysisUtils path is added to the CASA startup file in the init.sh script
+# (needs access to user's $HOME)
+
+##NEW for CASA6.*: explicitly add in astropy
+##Instructions here: https://casadocs.readthedocs.io/en/latest/notebooks/frequently-asked-questions.html
+RUN /opt/${CASA_RELEASE}/bin/pip3 install astropy && \
+#also add astroquery (astroquery.readthedocs.io/en/latest/)
+    /opt/${CASA_RELEASE}/bin/python3 -m pip install --pre astroquery[all]
+
+
+
+RUN mkdir /skaha
+ADD init.sh /skaha/
+
+# generate missing dbus uuid (issue #47)
+RUN dbus-uuidgen --ensure
+
+ADD nsswitch.conf /etc/
+
+WORKDIR /opt
+COPY extract-casaviewer.sh .
+#below suggested by Seb to help with viewer script & variables, doesn't work
+# here for some reason, and generally hasn't been effective
+#ENV PYTHONPATH /opt/${CASA_RELEASE%%-py*}/lib/py/lib/python3.8/site-packages
+RUN bash extract-casaviewer.sh && rm extract-casaviewer.sh
+
+RUN chmod 777 -R /opt/squashfs-root /opt/squashfs-root/usr /opt/squashfs-root/usr/*
+
+CMD [ "/skaha/init.sh" ]

science-containers/Dockerfiles/casa/version-6.6/Makefile

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+# NB: before using, uncomment the version to be built
+# NB2: One manual edit is also required in the extract_casaviewer.sh script,
+# about halfway down, to again select the command associated with setting up
+# plotms for the desired version of CASA
+
+
+VERSIONS_PIPELINE = \
+#	casa-6.1.1-15-pipeline-2020.1.0.40
+
+#!NB >casa6.5.6 versions have a different directory naming structure again
+VERSIONS = \
+	casa-6.6.3-22-py3.8.el7 
+#	casa-6.6.0-20-py3.8.el7
+#	casa-6.5.6-22-py3.8.el7
+
+DOCKER_REPO_BASE=images.canfar.net/casa-6/casa
+
+.PHONY: build clean run 
+
+all: build-pipeline build
+
+build-pipeline: 
+	@- $(foreach V,$(VERSIONS_PIPELINE), \
+                ./download.sh $(V) pipeline ; \
+                docker build --build-arg CASA_RELEASE=$(V) -t ${DOCKER_REPO_BASE}:$(V) .; \
+	)
+
+build: 
+	@- $(foreach V,$(VERSIONS), \
+                ./download.sh $(V) current ; \
+                docker build --build-arg CASA_RELEASE=$(V) -t ${DOCKER_REPO_BASE}:$(V) .; \
+	)
+
+clean-pipeline:
+	@- $(foreach V,$(VERSIONS_PIPELINE), \
+                docker rmi ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+clean:
+	@- $(foreach V,$(VERSIONS), \
+                docker rmi ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+clean-all: clean-old clean-pipeline clean 
+
+upload-pipeline: build-pipeline
+	@- $(foreach V,$(VERSIONS_PIPELINE), \
+                docker push ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+upload: build
+	@- $(foreach V,$(VERSIONS), \
+                docker push ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+upload-all: upload-pipeline upload