CASA6.1-6.4 updates

science-containers/Dockerfiles/casa/centos7/CentOS-Base.repo

@@ -0,0 +1,25 @@
+[base]
+name=CentOS-$releasever - Base
+# mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=os&infra=$infra
+# baseurl=http://mirror.centos.org/centos/$releasever/os/$basearch/
+baseurl=https://vault.centos.org/7.9.2009/os/$basearch/
+gpgcheck=1
+gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7
+
+# released updates
+[updates]
+name=CentOS-$releasever - Updates
+# mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=updates&infra=$infra
+# baseurl=http://mirror.centos.org/centos/$releasever/updates/$basearch/
+baseurl=https://vault.centos.org/7.9.2009/updates/$basearch/
+gpgcheck=1
+gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7
+
+# additional packages that may be useful
+[extras]
+name=CentOS-$releasever - Extras
+# mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=extras&infra=$infra
+# baseurl=http://mirror.centos.org/centos/$releasever/extras/$basearch/
+baseurl=https://vault.centos.org/7.9.2009/extras/$basearch/
+gpgcheck=1
+gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7

science-containers/Dockerfiles/casa/centos7/Dockerfile

@@ -2,15 +2,21 @@ FROM centos:7
 #This dockerfile makes a centos7 container with library dependencies needed
 # for casa versions
 
-RUN yum clean all -y
-RUN yum makecache -y
-RUN yum update -y
-RUN yum install -y freetype libSM libXi libXrender libXrandr \
+# Override old repo info with current urls
+RUN rm /etc/yum.repos.d/CentOS-Base.repo
+ADD CentOS-Base.repo /etc/yum.repos.d/
+
+RUN yum clean all -y && \
+    yum makecache -y && \
+    yum update -y && \
+    yum install -y freetype libSM libXi libXrender libXrandr \
 	libXfixes libXcursor libXinerama fontconfig \
         libxslt xauth xorg-x11-server-Xvfb dbus-x11 \
-	tkinter ImageMagick-c++ xterm perl autoconf python-sphinx graphviz xz
-
-RUN yum install -y firefox
-
-RUN yum install -y sssd-client acl
+	tkinter ImageMagick-c++ xterm perl autoconf python-sphinx graphviz xz && \
+    yum install -y firefox && \
+    yum install -y sssd-client acl && \
+#for admit:
+    yum install -y tcsh && \ 
+#for analysisUtils:
+    yum install -y wget 
 

science-containers/Dockerfiles/casa/ubuntu20.04/Dockerfile

@@ -4,21 +4,20 @@ FROM ubuntu:20.04
 # 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
-RUN apt upgrade -y
-
-RUN apt install -y libsm6 libxi6 libxrender1 libxrandr2 \
+RUN apt update && \
+    apt upgrade -y && \
+    apt install -y libsm6 libxi6 libxrender1 libxrandr2 \
         libxfixes3 libxcursor1 libxinerama1 fontconfig \
-        imagemagick xterm
-RUN apt install -y perl autoconf autoconf graphviz xz-utils \
-        gfortran libcanberra-gtk-module libsnl0
+        imagemagick xterm && \
+    apt install -y perl autoconf autoconf graphviz xz-utils \
+        gfortran libcanberra-gtk-module libsnl0 && \
 #NB: for 20.04, need libsnl0 not libsnl-dev
-RUN apt install -y libxslt1.1 xauth xorg xvfb dbus
-
-RUN apt install -y libfuse2 
-
+    apt install -y libxslt1.1 xauth xorg xvfb dbus && \
+#
+    apt install -y libfuse2  && \
 #Add in firefox and library dependency
-RUN apt install -y firefox libpci3
-
-RUN apt install -y sssd acl
-
+    apt install -y firefox libpci3 && \
+    apt install -y sssd acl && \
+    apt install -y wget && \
+#add in tcsh for admit installation
+    apt install -y tcsh

science-containers/Dockerfiles/casa/version-6.1-6.4/Dockerfile → science-containers/Dockerfiles/casa/version-6.1/Dockerfile

@@ -1,8 +1,13 @@
 FROM images.canfar.net/skaha/centos:7
+#NB: CASA 6.1.X needs glibc2.29 and does not work with ubuntu20.04 which 
+# has glibc2.31. 
+#xterm dependency is an extra to get the casa shell in the display
+#perl was added for casa later than 5
 
-# xterm dependency is an extra to get the casa shell in the display
-# perl was added for casa later than 5
 
+##additional packages for UVmultifit
+#RUN yum install -y gcc gcc-c++ gsl-devel fftw-devel
+
 # setup all required env variables
 ARG CASA_RELEASE
 ENV CASA_RELEASE=${CASA_RELEASE}
@@ -11,39 +16,38 @@ ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/casa/
 # unpack and move casa databundle to container
 ADD ${CASA_RELEASE}.tar.xz /opt/
 
-# ADD does not untar xz automatically
-# RUN unxz /opt/${CASA_RELEASE}.tar.xz
-# RUN tar -xf /opt/${CASA_RELEASE}.tar
-
 # 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 is now specified everywhere in the full path.
+##NB2: exception is pipeline6.5.3, which does not specify -py3.8 and thus has a different naming structure to that below.
+## (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
 
-
-# add the admit enhancement (issue #25)
-RUN yum install -y tcsh
+## add the admit enhancement (issue #25)
 RUN mkdir /opt/admit
 ADD admit /opt/admit
 RUN cd /opt/admit && \
-    autoconf && ./configure --with-casa-root=/opt/${CASA_RELEASE%%-py*}
+    autoupdate && autoconf && \
+    ./configure --with-casa-root=/opt/${CASA_RELEASE%%-py*}
 
 # 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
-RUN rm -rf /opt/${CASA_RELEASE%%-py*}/data && \
-    ln -s /arc/projects/casa-data-repository/ /opt/${CASA_RELEASE%%-py*}/data
-RUN chmod 777 /opt/${CASA_RELEASE%%-py*}
-RUN cd /opt/${CASA_RELEASE%%-py*} && \
+RUN mkdir -p /arc/projects/casa-data-repository && \
+    rm -rf /opt/${CASA_RELEASE%%-py*}/data && \
+    ln -s /arc/projects/casa-data-repository/ /opt/${CASA_RELEASE%%-py*}/data && \
+    chmod 777 /opt/${CASA_RELEASE%%-py*} && \
+    cd /opt/${CASA_RELEASE%%-py*} && \
     REPLACED_DATA=`find lib -name __data__` && \
     chmod 777 ${REPLACED_DATA}/.. && \
     rm -rf ${REPLACED_DATA} && \
-    ln -s /arc/projects/casa-data-repository/ /opt/${CASA_RELEASE%%-py*}/${REPLACED_DATA}
-RUN rm -rf /arc
+    ln -s /arc/projects/casa-data-repository/ /opt/${CASA_RELEASE%%-py*}/${REPLACED_DATA} && \
+    rm -rf /arc
 
-#AnalysisUtils package
-RUN mkdir /opt/casa/analysisUtils
-RUN yum install -y wget
-RUN cd /opt/casa/analysisUtils && wget ftp://ftp.cv.nrao.edu/pub/casaguides/analysis_scripts.tar && tar -xvf analysis_scripts.tar
+#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
@@ -57,8 +61,12 @@ ADD init.sh /skaha/
 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/*

science-containers/Dockerfiles/casa/version-6.1/Makefile

@@ -0,0 +1,53 @@
+# 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 = \
+ 	casa-6.1.0-118# \
+
+VERSIONS_PIPELINE = \
+#	casa-6.1.1-15-pipeline-2020.1.0.40
+
+DOCKER_REPO_BASE=images.canfar.net/casa-6/casa
+
+.PHONY: build clean run 
+
+all: build build-pipeline
+
+build: 
+	@- $(foreach V,$(VERSIONS), \
+		./download.sh $(V) current ; \
+		docker build --build-arg CASA_RELEASE=$(V) -t ${DOCKER_REPO_BASE}:$(V) .; \
+	)
+
+build-pipeline: 
+	@- $(foreach V,$(VERSIONS_PIPELINE), \
+                ./download.sh $(V) pipeline ; \
+                docker build --build-arg CASA_RELEASE=$(V) -t ${DOCKER_REPO_BASE}:$(V) .; \
+	)
+
+
+clean:
+	@- $(foreach V,$(VERSIONS), \
+		docker rmi ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+clean-pipeline:
+	@- $(foreach V,$(VERSIONS_PIPELINE), \
+                docker rmi ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+clean-all: clean clean-pipeline 
+
+upload: build
+	@- $(foreach V,$(VERSIONS), \
+	  docker push ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+upload-pipeline: build-pipeline
+	@- $(foreach V,$(VERSIONS_PIPELINE), \
+                docker push ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+upload-all: upload upload-pipeline

science-containers/Dockerfiles/casa/version-6.1/extract-casaviewer.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+#NB: needs to be edited for casa version in first coding line below
+# AppImage fix applies now too casaviewer, casaplotms
+# and new: casalogger, casaplotserver, casatablebrowser, casafeather
+
+casavers=casa-6.1.0-118
+#casavers=casa-6.1.1-15-pipeline-2020.1.0.40
+
+pyvers=python3.6
+
+pushd /opt
+#below command was original way of structuring this, but not working anymore
+#manually inputting casavers above to get around this
+#casaviewer=$(python3 -m casaviewer --app-path 2> /dev/null | grep casaviewer)
+#echo ${casaviewer}
+casaviewer=/opt/${casavers}/lib/py/lib/${pyvers}/site-packages/casaviewer/__bin__/casaviewer-x86_64.AppImage
+${casaviewer} --appimage-extract 2> /dev/null
+
+mv /opt/casa/bin/casaviewer /opt/casa/bin/casaviewer.old
+ln -s /opt/squashfs-root/AppRun /opt/casa/bin/casaviewer
+
+#additional steps courtesy of CASA helpdesk
+#NB: casa6.5 and higher use python3.8, only option
+mv /opt/casa/lib/py/lib/${pyvers}/site-packages/casaviewer/__bin__/casaviewer-x86_64.AppImage /opt/casa/lib/py/lib/${pyvers}/site-packages/casaviewer/__bin__/casaviewer-x86_64.AppImage.orig
+ln -s /opt/squashfs-root/usr/bin/casaviewer /opt/casa/lib/py/lib/${pyvers}/site-packages/casaviewer/__bin__/casaviewer-x86_64.AppImage
+
+#Apply similar process for other packages
+#1) extract AppImage
+/opt/${casavers}/lib/py/lib/${pyvers}/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage --appimage-extract 2> /dev/null
+/opt/${casavers}/lib/py/lib/${pyvers}/site-packages/casalogger/__bin__/casalogger-x86_64.AppImage --appimage-extract 2> /dev/null
+/opt/${casavers}/lib/py/lib/${pyvers}/site-packages/casafeather/__bin__/casafeather-x86_64.AppImage --appimage-extract 2> /dev/null
+/opt/${casavers}/lib/py/lib/${pyvers}/site-packages/casaplotserver/__bin__/casaplotserver-x86_64.AppImage --appimage-extract 2> /dev/null
+/opt/${casavers}/lib/py/lib/${pyvers}/site-packages/casatablebrowser/__bin__/casatablebrowser-x86_64.AppImage --appimage-extract 2> /dev/null
+
+#2a) move old AppImage
+mv /opt/casa/lib/py/lib/${pyvers}/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage /opt/casa/lib/py/lib/${pyvers}/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage.orig
+mv /opt/casa/lib/py/lib/${pyvers}/site-packages/casalogger/__bin__/casalogger-x86_64.AppImage /opt/casa/lib/py/lib/${pyvers}/site-packages/casalogger/__bin__/casalogger-x86_64.AppImage.orig
+mv /opt/casa/lib/py/lib/${pyvers}/site-packages/casafeather/__bin__/casafeather-x86_64.AppImage /opt/casa/lib/py/lib/${pyvers}/site-packages/casafeather/__bin__/casafeather-x86_64.AppImage.orig
+mv /opt/casa/lib/py/lib/${pyvers}/site-packages/casaplotserver/__bin__/casaplotserver-x86_64.AppImage /opt/casa/lib/py/lib/${pyvers}/site-packages/casaplotserver/__bin__/casaplotserver-x86_64.AppImage.orig
+mv /opt/casa/lib/py/lib/${pyvers}/site-packages/casatablebrowser/__bin__/casatablebrowser-x86_64.AppImage /opt/casa/lib/py/lib/${pyvers}/site-packages/casatablebrowser/__bin__/casatablebrowser-x86_64.AppImage.orig
+
+#2b) link to new one
+ln -s /opt/squashfs-root/usr/bin/casaplotms /opt/casa/lib/py/lib/${pyvers}/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage
+ln -s /opt/squashfs-root/usr/bin/casalogger /opt/casa/lib/py/lib/${pyvers}/site-packages/casalogger/__bin__/casalogger-x86_64.AppImage
+ln -s /opt/squashfs-root/usr/bin/casafeather /opt/casa/lib/py/lib/${pyvers}/site-packages/casafeather/__bin__/casafeather-x86_64.AppImage
+ln -s /opt/squashfs-root/usr/bin/casaplotserver /opt/casa/lib/py/lib/${pyvers}/site-packages/casaplotserver/__bin__/casaplotserver-x86_64.AppImage
+ln -s /opt/squashfs-root/usr/bin/casatablebrowser /opt/casa/lib/py/lib/${pyvers}/site-packages/casatablebrowser/__bin__/casatablebrowser-x86_64.AppImage
+
+
+popd

science-containers/Dockerfiles/casa/version-6.1/init.sh

@@ -0,0 +1,12 @@
+#!/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/startup.py
+echo 'sys.path.append("/opt/casa/analysisUtils/analysis_scripts/")' >> $HOME/.casa/startup.py
+echo 'import analysisUtils as au' >> $HOME/.casa/startup.py
+echo 'import analysisUtils as AU' >> $HOME/.casa/startup.py
+echo "INIT DONE"
+echo "INIT DONE"

science-containers/Dockerfiles/casa/version-6.2-6.4/Dockerfile

@@ -0,0 +1,83 @@
+FROM images.canfar.net/skaha/ubuntu:20.04
+
+# xterm dependency is an extra to get the casa shell in the display
+# perl was added for casa later than 5
+
+##additional packages for UVmultifit
+#RUN yum install -y gcc gcc-c++ gsl-devel fftw-devel
+#
+#
+# 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 ${CASA_RELEASE}.tar.xz /opt/
+
+# chown because the untarred casa has wrong owner/group
+##NB: commands below revert back to the pre-CASA6.4 terminology, as the version of python is now specified everywhere in the full path.
+##NB2: exception is pipeline6.5.3, which does not specify -py3.8 and thus has a different naming structure to that below.
+## (the %%-py* string removes the -py3.X part of the CASA_RELEASE variable name for the directory structure)
+RUN chown -R root:root /opt/${CASA_RELEASE%%-py*} && ln -s /opt/${CASA_RELEASE%%-py*} /opt/casa
+
+## add the admit enhancement (issue #25)
+RUN mkdir /opt/admit
+ADD admit /opt/admit
+RUN cd /opt/admit && \
+    autoupdate && autoconf && \
+    ./configure --with-casa-root=/opt/${CASA_RELEASE%%-py*}
+
+# 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/${CASA_RELEASE%%-py*}/data && \
+    ln -s /arc/projects/casa-data-repository/ /opt/${CASA_RELEASE%%-py*}/data && \
+    chmod 777 /opt/${CASA_RELEASE%%-py*} && \
+    cd /opt/${CASA_RELEASE%%-py*} && \
+    REPLACED_DATA=`find lib -name __data__` && \
+    chmod 777 ${REPLACED_DATA}/.. && \
+    rm -rf ${REPLACED_DATA} && \
+    ln -s /arc/projects/casa-data-repository/ /opt/${CASA_RELEASE%%-py*}/${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 $HOME)
+
+#NB: astropy & astroquery do not seem compatible with py3.6 & ubuntu20.04
+# At least some of the casa versions in this directory (6.4) do work with
+# py3.8 & ubuntu22.04, however, firefox does not currently work there,
+# and is helpful for some pipeline tasks
+###NEW for CASA6.*: explicitly add in astropy
+###Instructions here: https://casadocs.readthedocs.io/en/latest/notebooks/frequently-asked-questions.html
+#RUN /opt/casa/bin/python3 -m pip install --upgrade pip && \
+#    /opt/casa/bin/pip3 install astropy && \
+##also add astroquery (astroquery.readthedocs.io/en/latest/)
+#    /opt/casa/bin/python3 -m pip install --pre astroquery[all]
+
+RUN mkdir /skaha
+ADD init.sh /skaha/
+
+# generate missing dbus uuid (issue #47)
+RUN dbus-uuidgen --ensure
+
+ADD nsswitch.conf /etc/
+
+WORKDIR /opt
+COPY extract-casaviewer.sh .
+#below suggested by Seb to help with viewer script & variables, doesn't work
+# here for some reason, and generally hasn't been effective
+#ENV PYTHONPATH /opt/${CASA_RELEASE%%-py*}/lib/py/lib/python3.8/site-packages
+RUN bash extract-casaviewer.sh && rm extract-casaviewer.sh && \
+#
+    chmod 777 -R /opt/squashfs-root /opt/squashfs-root/usr /opt/squashfs-root/usr/*
+
+CMD [ "/skaha/init.sh" ]