Migrate ubuntu22.04 (#76)

* Fix GLIBC 2.10 deprecation of sys_siglist * Bump to latest casacore and python-casacore in 22.04 test, manually compiled until kern 9 release
ratt-ru · Feb 7, 2024 · 5651b2a · 5651b2a
1 parent 7e852f2
commit 5651b2a
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diff --git a/.ci/py3.docker → .ci/ubuntu20.04.docker b/.ci/py3.docker → .ci/ubuntu20.04.docker
diff --git a/.ci/ubuntu22.04.docker b/.ci/ubuntu22.04.docker
@@ -0,0 +1,122 @@
+FROM ubuntu:22.04
+ENV DEBIAN_FRONTEND noninteractive
+ENV DEBIAN_PRIORITY critical
+
+RUN apt update
+RUN apt install -y libblitz0-dev python3-dev libblas-dev liblapack-dev libqdbm-dev wcslib-dev \
+ libfftw3-dev python3-numpy libcfitsio-dev libboost-all-dev libboost-system-dev cmake g++ wget gfortran \
+ libncurses5-dev bison libbison-dev flex libreadline6-dev python3-pip rsync \
+ python3-virtualenv libgsl-dev
+
+#####################################################################
+## casa data from NRAO
+#####################################################################
+RUN mkdir -p /usr/share/casacore/data/
+WORKDIR /usr/share/casacore/data/
+RUN rsync -avz rsync://casa-rsync.nrao.edu/casa-data .
+
+#####################################################################
+## CASAcore from source
+#####################################################################
+RUN cd /opt && \
+    wget https://github.com/casacore/casacore/archive/v3.5.0.tar.gz && \
+    tar xvf v3.5.0.tar.gz && \
+    rm v3.5.0.tar.gz && \
+    mkdir casacore-3.5.0/build && \
+    cd /opt/casacore-3.5.0/build && \
+    cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release -DBUILD_DEPRECATED=OFF -DBUILD_PYTHON=OFF -DBUILD_PYTHON3=ON ../ && \
+    make -j 16 && \
+    make install && \
+    rm -r /opt/casacore-3.5.0 && \
+    ldconfig
+
+#####################################################################
+## CASArest from source
+#####################################################################
+RUN cd /opt && \
+    wget https://github.com/casacore/casarest/archive/v1.8.1.tar.gz && \
+    tar xvf v1.8.1.tar.gz && \
+    rm v1.8.1.tar.gz && \
+    cd /opt/casarest-1.8.1 && \
+    mkdir -p build && \
+    cd /opt/casarest-1.8.1/build && \
+    cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../ && \
+    make -j 16 && \
+    make install && \
+    rm -r /opt/casarest-1.8.1 && \
+    ldconfig
+
+#####################################################################
+## BUILD MAKEMS FROM SOURCE AND TEST
+#####################################################################
+WORKDIR /opt
+RUN wget https://github.com/ska-sa/makems/archive/v1.5.5.tar.gz && \
+    tar xvf v1.5.5.tar.gz && \
+    rm v1.5.5.tar.gz && \
+    mkdir -p /opt/makems-1.5.5/LOFAR/build/gnu_opt && \
+    cd /opt/makems-1.5.5/LOFAR/build/gnu_opt && \
+    cmake -DCMAKE_MODULE_PATH:PATH=/opt/makems-1.5.5/LOFAR/CMake \
+          -DUSE_LOG4CPLUS=OFF -DBUILD_TESTING=OFF -DCMAKE_BUILD_TYPE=Release \
+          -DCMAKE_INSTALL_PREFIX=/usr ../.. && \
+    make -j 16 && \
+    make install && \
+    cd /opt/makems-1.5.5/test && \
+    makems WSRT_makems.cfg && \
+    rm -r /opt/makems-1.5.5
+
+#####################################################################
+## BUILD MeqTrees from source
+#####################################################################
+WORKDIR /opt
+RUN virtualenv venv -p python3.10 --system-site-packages
+RUN . /opt/venv/bin/activate && pip install setuptools wheel pip -U
+# Get MeqTrees universe python packages
+RUN . /opt/venv/bin/activate && python3.10 -m pip install purr \
+                                                          owlcat \
+                                                          kittens \
+                                                          'meqtrees-cattery>=1.7.6' \
+                                                          astro-tigger-lsm \
+                                                          # possible ABI issues if this is not pinned to system version \
+                                                          python-casacore==3.5.2 \
+                                                          # possible ABI issues if this is not pinned to system version \
+                                                          numpy==1.21.5 \
+                                                          --no-binary 'python-casacore'
+
+
+ADD . /code
+RUN mkdir /code/build && \
+    cd /code/build && \
+    cmake -DCMAKE_INSTALL_PREFIX=/usr \
+          -DCMAKE_BUILD_TYPE=Release \
+          -DENABLE_PYTHON_3=ON \
+          .. && \
+    make -j8 && \
+    make install && \
+    rm -r /code/build && \
+    ldconfig
+
+#####################################################################
+## Run tests
+#####################################################################
+
+# basic install tests
+RUN . /opt/venv/bin/activate && flag-ms.py --help
+RUN . /opt/venv/bin/activate && meqtree-pipeliner.py --help
+RUN . /opt/venv/bin/activate && pyxis --help
+RUN . /opt/venv/bin/activate && python3 -c 'from Timba import mequtils'
+
+# run test when built
+WORKDIR /src
+RUN . /opt/venv/bin/activate && python3 -m pip install pynose
+RUN wget https://github.com/ska-sa/pyxis/archive/v1.7.4.3.tar.gz && \
+    tar -xvf v1.7.4.3.tar.gz && \
+    rm v1.7.4.3.tar.gz && \
+    . /opt/venv/bin/activate && \
+    python3.10 -m pip install /src/pyxis-1.7.4.3 && \
+    cd /src/pyxis-1.7.4.3/Pyxis/recipes/meqtrees-batch-test && \
+    pynose && \
+    rm -r /src/pyxis-1.7.4.3
+
+WORKDIR /
+ENTRYPOINT ["meqtree-pipeliner.py"]
+CMD ["--help"]
diff --git a/Jenkinsfile.sh b/Jenkinsfile.sh
@@ -21,4 +21,5 @@ cd $PROJECTS_DIR/meqtrees-timba
 IMAGENAME="mttimbapr"
 
 # build and test
-docker build -f .ci/py3.docker -t "${IMAGENAME}36:$BUILD_NUMBER" --no-cache=true .
+docker build -f .ci/ubuntu20.04.docker -t "${IMAGENAME}38:$BUILD_NUMBER" --no-cache=true .
+docker build -f .ci/ubuntu22.04.docker -t "${IMAGENAME}310:$BUILD_NUMBER" --no-cache=true .
diff --git a/OCTOPUSSY/src/Dispatcher.cc b/OCTOPUSSY/src/Dispatcher.cc
@@ -61,7 +61,11 @@ void Dispatcher::signalHandler (int signum,siginfo_t *,void *)
 #ifdef USE_THREADS
   if( DebugOctopussy::getDebugContext().check(2) )
   {
-    printf("thread %ld: received signal %d (%s)\n",(long)Thread::self().id(),signum,sys_siglist[signum]);
+    #if __GLIBC__ > 2 || (__GLIBC__ == 2 && __GLIBC_MINOR__ >= 10)
+      printf("thread %ld: received signal %d (%s)\n",(long)Thread::self().id(),signum,strsignal(signum));
+    #else
+      printf("thread %ld: received signal %d (%s)\n",(long)Thread::self().id(),signum,sys_siglist[signum]);  
+    #endif
   }
 #endif
   sigaddset(&raisedSignals,signum);

diff --git a/OCTOPUSSY/src/Dispatcher.h b/OCTOPUSSY/src/Dispatcher.h
@@ -41,6 +41,7 @@
 #include <OCTOPUSSY/WPInterface.h>
 #include <OCTOPUSSY/Message.h>
 #include <OCTOPUSSY/OctopussyDebugContext.h>
+#include <string.h>
 
 #pragma aid Argv
 

diff --git a/OCTOPUSSY/src/WPInterface.cc b/OCTOPUSSY/src/WPInterface.cc
@@ -1076,7 +1076,11 @@ int WPInterface::input (int fd, int flags)
 //##ModelId=3C7DFD240203
 int WPInterface::signal (int signum)
 {
-  dprintf(1)("unhandled signal(%s)\n",sys_siglist[signum]);
+  #if __GLIBC__ > 2 || (__GLIBC__ == 2 && __GLIBC_MINOR__ >= 10)
+    dprintf(1)("unhandled signal(%s)\n",strsignal(signum));
+  #else
+    dprintf(1)("unhandled signal(%s)\n",sys_siglist[signum]);
+  #endif
   return Message::ACCEPT;
 }
 

diff --git a/OCTOPUSSY/src/WPInterface.h b/OCTOPUSSY/src/WPInterface.h
@@ -37,6 +37,7 @@
 #include <list>
 #include <set>
 #include <queue>
+#include <string.h>
 
 namespace Octopussy
 {