From 8e1ba6478dbdd9ae5b8284af772bd09d76686560 Mon Sep 17 00:00:00 2001 From: Kalin Kiesling Date: Sat, 11 Apr 2020 15:36:19 -0500 Subject: [PATCH 01/15] starting docker image w/ visit --- pymoab-visit-py2-18.04 | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 pymoab-visit-py2-18.04 diff --git a/pymoab-visit-py2-18.04 b/pymoab-visit-py2-18.04 new file mode 100644 index 0000000..c1f4d23 --- /dev/null +++ b/pymoab-visit-py2-18.04 @@ -0,0 +1,16 @@ +FROM svalinn/pymoab-py2-18.04:latest + +ENV HOME /root + +RUN apt-get install -y --force-yes wget + +RUN cd $HOME/opt \ + && wget http://portal.nersc.gov/project/visit/releases/2.13.3/visit2_13_3.linux-x86_64-ubuntu18.tar.gz \ + && wget http://portal.nersc.gov/project/visit/releases/2.13.3/visit-install2_13_3 \ + && echo 1 > input \ + && bash visit-install2_13_3 2.13.3 linux-x86_64-ubuntu18 /usr/local/visit < input + +# set environment variables +ENV PATH /usr/local/visit/bin:$PATH +ENV LD_LIBRARY_PATH /usr/local/visit/2.13.3/linux-x86_64/lib/:$LD_LIBRARY_PATH +ENV PYTHONPATH /usr/local/visit/2.13.3/linux-x86_64/lib/site-packages:$PYTHONPATH From 14d931de3e7d1b2d66dcd9854287ddbff50f79f8 Mon Sep 17 00:00:00 2001 From: Kalin Kiesling Date: Sun, 12 Apr 2020 10:02:57 -0500 Subject: [PATCH 02/15] missing cpio --- pymoab-visit-py2-18.04 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pymoab-visit-py2-18.04 b/pymoab-visit-py2-18.04 index c1f4d23..21f0405 100644 --- a/pymoab-visit-py2-18.04 +++ b/pymoab-visit-py2-18.04 @@ -2,7 +2,7 @@ FROM svalinn/pymoab-py2-18.04:latest ENV HOME /root -RUN apt-get install -y --force-yes wget +RUN apt-get install -y --force-yes wget cpio RUN cd $HOME/opt \ && wget http://portal.nersc.gov/project/visit/releases/2.13.3/visit2_13_3.linux-x86_64-ubuntu18.tar.gz \ From 2b13c6d157e0b1baec130c45d06ead99a8d1e65e Mon Sep 17 00:00:00 2001 From: Kalin Kiesling Date: Sun, 12 Apr 2020 10:03:24 -0500 Subject: [PATCH 03/15] foolishly deleted installed moab folder :face_palm: --- pymoab-py2-18.04 | 4 +--- pymoab-py3-18.04 | 4 +--- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/pymoab-py2-18.04 b/pymoab-py2-18.04 index 90bd494..c033e9c 100644 --- a/pymoab-py2-18.04 +++ b/pymoab-py2-18.04 @@ -46,9 +46,7 @@ RUN cd $HOME/opt \ -DENABLE_HDF5=ON -DHDF5_ROOT=/usr/lib/x86_64-linux-gnu/hdf5/serial \ -DENABLE_NETCDF=OFF -DENABLE_METIS=OFF -DENABLE_IMESH=OFF -DENABLE_FBIGEOM=OFF \ -DENABLE_PYMOAB=ON -DPREFIX=$HOME/opt/moab \ - && make all -j 8 \ - && cd .. \ - && rm -rf build moab + && make all -j 8 # set environment variables ENV PATH $HOME/opt/moab/bin/:$PATH diff --git a/pymoab-py3-18.04 b/pymoab-py3-18.04 index 366eda9..4abc714 100644 --- a/pymoab-py3-18.04 +++ b/pymoab-py3-18.04 @@ -51,9 +51,7 @@ RUN cd $HOME/opt \ -DENABLE_HDF5=ON -DHDF5_ROOT=/usr/lib/x86_64-linux-gnu/hdf5/serial \ -DENABLE_NETCDF=OFF -DENABLE_METIS=OFF -DENABLE_IMESH=OFF -DENABLE_FBIGEOM=OFF \ -DENABLE_PYMOAB=ON -DPREFIX=$HOME/opt/moab \ - && make all -j 8 \ - && cd .. \ - && rm -rf build moab + && make all -j 8 # set environment variables ENV PATH $HOME/opt/moab/bin/:$PATH From 4126edd07be738480d0b7b5ff8f4f0da46eea8ca Mon Sep 17 00:00:00 2001 From: Kalin Kiesling Date: Sun, 12 Apr 2020 10:59:20 -0500 Subject: [PATCH 04/15] fixed prefix setting and actually install --- pymoab-py2-18.04 | 5 +++-- pymoab-py3-18.04 | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/pymoab-py2-18.04 b/pymoab-py2-18.04 index c033e9c..860ab99 100644 --- a/pymoab-py2-18.04 +++ b/pymoab-py2-18.04 @@ -45,8 +45,9 @@ RUN cd $HOME/opt \ -DCMAKE_SHARED_LINKER_FLAGS="-Wl,--no-undefined" -DENABLE_MPI=OFF \ -DENABLE_HDF5=ON -DHDF5_ROOT=/usr/lib/x86_64-linux-gnu/hdf5/serial \ -DENABLE_NETCDF=OFF -DENABLE_METIS=OFF -DENABLE_IMESH=OFF -DENABLE_FBIGEOM=OFF \ - -DENABLE_PYMOAB=ON -DPREFIX=$HOME/opt/moab \ - && make all -j 8 + -DENABLE_PYMOAB=ON -DCMAKE_INSTALL_PREFIX=$HOME/opt/moab \ + && make all -j 8 \ + && make install # set environment variables ENV PATH $HOME/opt/moab/bin/:$PATH diff --git a/pymoab-py3-18.04 b/pymoab-py3-18.04 index 4abc714..f50a402 100644 --- a/pymoab-py3-18.04 +++ b/pymoab-py3-18.04 @@ -50,8 +50,9 @@ RUN cd $HOME/opt \ -DCMAKE_SHARED_LINKER_FLAGS="-Wl,--no-undefined" -DENABLE_MPI=OFF \ -DENABLE_HDF5=ON -DHDF5_ROOT=/usr/lib/x86_64-linux-gnu/hdf5/serial \ -DENABLE_NETCDF=OFF -DENABLE_METIS=OFF -DENABLE_IMESH=OFF -DENABLE_FBIGEOM=OFF \ - -DENABLE_PYMOAB=ON -DPREFIX=$HOME/opt/moab \ - && make all -j 8 + -DENABLE_PYMOAB=ON -DCMAKE_INSTALL_PREFIX=$HOME/opt/moab \ + && make -j 8 \ + && make install # set environment variables ENV PATH $HOME/opt/moab/bin/:$PATH From 01f402123f51b6d09f308abbb2bcecce650396d7 Mon Sep 17 00:00:00 2001 From: Kalin Kiesling Date: Sun, 12 Apr 2020 15:54:24 -0500 Subject: [PATCH 05/15] install xmldiff --- pymoab-visit-py2-18.04 | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pymoab-visit-py2-18.04 b/pymoab-visit-py2-18.04 index 21f0405..c4ababd 100644 --- a/pymoab-visit-py2-18.04 +++ b/pymoab-visit-py2-18.04 @@ -10,6 +10,8 @@ RUN cd $HOME/opt \ && echo 1 > input \ && bash visit-install2_13_3 2.13.3 linux-x86_64-ubuntu18 /usr/local/visit < input +RUN pip install xmldiff + # set environment variables ENV PATH /usr/local/visit/bin:$PATH ENV LD_LIBRARY_PATH /usr/local/visit/2.13.3/linux-x86_64/lib/:$LD_LIBRARY_PATH From 6d97f4600d20a900f5a82c08e56e4ab53df4411a Mon Sep 17 00:00:00 2001 From: Kalin Kiesling Date: Mon, 13 Apr 2020 15:49:03 -0500 Subject: [PATCH 06/15] newer visit version with extra libraries --- pymoab-visit-py2-18.04 | 24 ++++++++++++++++-------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/pymoab-visit-py2-18.04 b/pymoab-visit-py2-18.04 index c4ababd..d4ee01e 100644 --- a/pymoab-visit-py2-18.04 +++ b/pymoab-visit-py2-18.04 @@ -2,17 +2,25 @@ FROM svalinn/pymoab-py2-18.04:latest ENV HOME /root -RUN apt-get install -y --force-yes wget cpio +RUN apt-get install -y --force-yes wget cpio libpcre3-dev + +RUN pip install xmldiff RUN cd $HOME/opt \ - && wget http://portal.nersc.gov/project/visit/releases/2.13.3/visit2_13_3.linux-x86_64-ubuntu18.tar.gz \ - && wget http://portal.nersc.gov/project/visit/releases/2.13.3/visit-install2_13_3 \ + && wget https://github.com/visit-dav/visit/releases/download/v3.1.1/visit3_1_1.linux-x86_64-ubuntu18.tar.gz \ + && wget https://github.com/visit-dav/visit/releases/download/v3.1.1/visit-install3_1_1 \ && echo 1 > input \ - && bash visit-install2_13_3 2.13.3 linux-x86_64-ubuntu18 /usr/local/visit < input - -RUN pip install xmldiff + && bash visit-install3_1_1 3.1.1 linux-x86_64-ubuntu18 /usr/local/visit < input \ + && rm -rf visit3_1_1.linux-x86_64-ubuntu18.tar.gz # set environment variables ENV PATH /usr/local/visit/bin:$PATH -ENV LD_LIBRARY_PATH /usr/local/visit/2.13.3/linux-x86_64/lib/:$LD_LIBRARY_PATH -ENV PYTHONPATH /usr/local/visit/2.13.3/linux-x86_64/lib/site-packages:$PYTHONPATH +ENV LD_LIBRARY_PATH /usr/local/visit/3.1.1/linux-x86_64/lib/:$LD_LIBRARY_PATH +ENV PYTHONPATH /usr/local/visit/3.1.1/linux-x86_64/lib/site-packages:$PYTHONPATH + +RUN apt-get install -y --fix-missing \ + libgl1-mesa-glx \ + libgl1-mesa-dev \ + libsm6 \ + libxt6 \ + libglu1-mesa From 3d07bd52631fc3532e2b39af7eb88e402685a8c5 Mon Sep 17 00:00:00 2001 From: Kalin Kiesling Date: Tue, 14 Apr 2020 09:50:31 -0500 Subject: [PATCH 07/15] move libraries before visit --- pymoab-visit-py2-18.04 | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/pymoab-visit-py2-18.04 b/pymoab-visit-py2-18.04 index d4ee01e..d19bec9 100644 --- a/pymoab-visit-py2-18.04 +++ b/pymoab-visit-py2-18.04 @@ -2,7 +2,15 @@ FROM svalinn/pymoab-py2-18.04:latest ENV HOME /root -RUN apt-get install -y --force-yes wget cpio libpcre3-dev +RUN apt-get install -y --fix-missing \ + wget \ + cpio \ + libpcre3-dev \ + libgl1-mesa-glx \ + libgl1-mesa-dev \ + libsm6 \ + libxt6 \ + libglu1-mesa RUN pip install xmldiff @@ -18,9 +26,3 @@ ENV PATH /usr/local/visit/bin:$PATH ENV LD_LIBRARY_PATH /usr/local/visit/3.1.1/linux-x86_64/lib/:$LD_LIBRARY_PATH ENV PYTHONPATH /usr/local/visit/3.1.1/linux-x86_64/lib/site-packages:$PYTHONPATH -RUN apt-get install -y --fix-missing \ - libgl1-mesa-glx \ - libgl1-mesa-dev \ - libsm6 \ - libxt6 \ - libglu1-mesa From ab8858f9a3818f0bf41332ccbd661c703c5b5c0f Mon Sep 17 00:00:00 2001 From: Kalin Kiesling Date: Tue, 14 Apr 2020 09:52:08 -0500 Subject: [PATCH 08/15] back to master branch version to avoid conflicts --- pymoab-py2-18.04 | 5 +++-- pymoab-py3-18.04 | 7 ++++--- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/pymoab-py2-18.04 b/pymoab-py2-18.04 index 860ab99..90bd494 100644 --- a/pymoab-py2-18.04 +++ b/pymoab-py2-18.04 @@ -45,9 +45,10 @@ RUN cd $HOME/opt \ -DCMAKE_SHARED_LINKER_FLAGS="-Wl,--no-undefined" -DENABLE_MPI=OFF \ -DENABLE_HDF5=ON -DHDF5_ROOT=/usr/lib/x86_64-linux-gnu/hdf5/serial \ -DENABLE_NETCDF=OFF -DENABLE_METIS=OFF -DENABLE_IMESH=OFF -DENABLE_FBIGEOM=OFF \ - -DENABLE_PYMOAB=ON -DCMAKE_INSTALL_PREFIX=$HOME/opt/moab \ + -DENABLE_PYMOAB=ON -DPREFIX=$HOME/opt/moab \ && make all -j 8 \ - && make install + && cd .. \ + && rm -rf build moab # set environment variables ENV PATH $HOME/opt/moab/bin/:$PATH diff --git a/pymoab-py3-18.04 b/pymoab-py3-18.04 index f50a402..366eda9 100644 --- a/pymoab-py3-18.04 +++ b/pymoab-py3-18.04 @@ -50,9 +50,10 @@ RUN cd $HOME/opt \ -DCMAKE_SHARED_LINKER_FLAGS="-Wl,--no-undefined" -DENABLE_MPI=OFF \ -DENABLE_HDF5=ON -DHDF5_ROOT=/usr/lib/x86_64-linux-gnu/hdf5/serial \ -DENABLE_NETCDF=OFF -DENABLE_METIS=OFF -DENABLE_IMESH=OFF -DENABLE_FBIGEOM=OFF \ - -DENABLE_PYMOAB=ON -DCMAKE_INSTALL_PREFIX=$HOME/opt/moab \ - && make -j 8 \ - && make install + -DENABLE_PYMOAB=ON -DPREFIX=$HOME/opt/moab \ + && make all -j 8 \ + && cd .. \ + && rm -rf build moab # set environment variables ENV PATH $HOME/opt/moab/bin/:$PATH From 36885ac7e6bab52f8451baee98bd325528642493 Mon Sep 17 00:00:00 2001 From: Kalin Kiesling Date: Tue, 14 Apr 2020 15:45:04 -0500 Subject: [PATCH 09/15] apt update --- pymoab-visit-py2-18.04 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pymoab-visit-py2-18.04 b/pymoab-visit-py2-18.04 index d19bec9..31cbd40 100644 --- a/pymoab-visit-py2-18.04 +++ b/pymoab-visit-py2-18.04 @@ -2,7 +2,8 @@ FROM svalinn/pymoab-py2-18.04:latest ENV HOME /root -RUN apt-get install -y --fix-missing \ +RUN apt-get -y --force-yes update \ + && apt-get install -y --fix-missing \ wget \ cpio \ libpcre3-dev \ From da770e75c265e41c77ce766f210e50e203a344e9 Mon Sep 17 00:00:00 2001 From: Kalin Kiesling Date: Tue, 14 Apr 2020 15:45:25 -0500 Subject: [PATCH 10/15] don't need to set environment variable --- pymoab-visit-py2-18.04 | 2 -- 1 file changed, 2 deletions(-) diff --git a/pymoab-visit-py2-18.04 b/pymoab-visit-py2-18.04 index 31cbd40..8accd0b 100644 --- a/pymoab-visit-py2-18.04 +++ b/pymoab-visit-py2-18.04 @@ -1,7 +1,5 @@ FROM svalinn/pymoab-py2-18.04:latest -ENV HOME /root - RUN apt-get -y --force-yes update \ && apt-get install -y --fix-missing \ wget \ From eb59af5c1df98939fb6dd3237daf67dafdf0baac Mon Sep 17 00:00:00 2001 From: Kalin Kiesling Date: Tue, 14 Apr 2020 16:21:09 -0500 Subject: [PATCH 11/15] remove install script --- pymoab-visit-py2-18.04 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pymoab-visit-py2-18.04 b/pymoab-visit-py2-18.04 index 8accd0b..16ad725 100644 --- a/pymoab-visit-py2-18.04 +++ b/pymoab-visit-py2-18.04 @@ -18,7 +18,7 @@ RUN cd $HOME/opt \ && wget https://github.com/visit-dav/visit/releases/download/v3.1.1/visit-install3_1_1 \ && echo 1 > input \ && bash visit-install3_1_1 3.1.1 linux-x86_64-ubuntu18 /usr/local/visit < input \ - && rm -rf visit3_1_1.linux-x86_64-ubuntu18.tar.gz + && rm -rf visit3_1_1.linux-x86_64-ubuntu18.tar.gz visit-install3_1_1 # set environment variables ENV PATH /usr/local/visit/bin:$PATH From 48442a92662adad4a52fb6bc1b2de1af7a0c041a Mon Sep 17 00:00:00 2001 From: Kalin Kiesling Date: Tue, 14 Apr 2020 18:55:05 -0500 Subject: [PATCH 12/15] python3 visit image --- pymoab-visit-py3-18.04 | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 pymoab-visit-py3-18.04 diff --git a/pymoab-visit-py3-18.04 b/pymoab-visit-py3-18.04 new file mode 100644 index 0000000..515aca2 --- /dev/null +++ b/pymoab-visit-py3-18.04 @@ -0,0 +1,27 @@ +FROM svalinn/pymoab-py3-18.04:latest + +RUN apt-get -y --force-yes update \ + && apt-get install -y --fix-missing \ + wget \ + cpio \ + libpcre3-dev \ + libgl1-mesa-glx \ + libgl1-mesa-dev \ + libsm6 \ + libxt6 \ + libglu1-mesa + +RUN pip install xmldiff + +RUN cd $HOME/opt \ + && wget https://github.com/visit-dav/visit/releases/download/v3.1.1/visit3_1_1.linux-x86_64-ubuntu18.tar.gz \ + && wget https://github.com/visit-dav/visit/releases/download/v3.1.1/visit-install3_1_1 \ + && echo 1 > input \ + && bash visit-install3_1_1 3.1.1 linux-x86_64-ubuntu18 /usr/local/visit < input \ + && rm -rf visit3_1_1.linux-x86_64-ubuntu18.tar.gz visit-install3_1_1 + +# set environment variables +ENV PATH /usr/local/visit/bin:$PATH +ENV LD_LIBRARY_PATH /usr/local/visit/3.1.1/linux-x86_64/lib/:$LD_LIBRARY_PATH +ENV PYTHONPATH /usr/local/visit/3.1.1/linux-x86_64/lib/site-packages:$PYTHONPATH + From acb6e92a518f661453322d616ed8a86c2a0c0c40 Mon Sep 17 00:00:00 2001 From: Kalin Kiesling Date: Tue, 14 Apr 2020 19:42:15 -0500 Subject: [PATCH 13/15] python 3 not working, so removing --- pymoab-visit-py3-18.04 | 27 --------------------------- 1 file changed, 27 deletions(-) delete mode 100644 pymoab-visit-py3-18.04 diff --git a/pymoab-visit-py3-18.04 b/pymoab-visit-py3-18.04 deleted file mode 100644 index 515aca2..0000000 --- a/pymoab-visit-py3-18.04 +++ /dev/null @@ -1,27 +0,0 @@ -FROM svalinn/pymoab-py3-18.04:latest - -RUN apt-get -y --force-yes update \ - && apt-get install -y --fix-missing \ - wget \ - cpio \ - libpcre3-dev \ - libgl1-mesa-glx \ - libgl1-mesa-dev \ - libsm6 \ - libxt6 \ - libglu1-mesa - -RUN pip install xmldiff - -RUN cd $HOME/opt \ - && wget https://github.com/visit-dav/visit/releases/download/v3.1.1/visit3_1_1.linux-x86_64-ubuntu18.tar.gz \ - && wget https://github.com/visit-dav/visit/releases/download/v3.1.1/visit-install3_1_1 \ - && echo 1 > input \ - && bash visit-install3_1_1 3.1.1 linux-x86_64-ubuntu18 /usr/local/visit < input \ - && rm -rf visit3_1_1.linux-x86_64-ubuntu18.tar.gz visit-install3_1_1 - -# set environment variables -ENV PATH /usr/local/visit/bin:$PATH -ENV LD_LIBRARY_PATH /usr/local/visit/3.1.1/linux-x86_64/lib/:$LD_LIBRARY_PATH -ENV PYTHONPATH /usr/local/visit/3.1.1/linux-x86_64/lib/site-packages:$PYTHONPATH - From 2fdfcf6a494cd97cbe3df57f43f9bb9c80aea104 Mon Sep 17 00:00:00 2001 From: Kalin Kiesling Date: Tue, 14 Apr 2020 19:42:55 -0500 Subject: [PATCH 14/15] moved to single run line --- pymoab-visit-py2-18.04 | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/pymoab-visit-py2-18.04 b/pymoab-visit-py2-18.04 index 16ad725..6962c48 100644 --- a/pymoab-visit-py2-18.04 +++ b/pymoab-visit-py2-18.04 @@ -9,9 +9,8 @@ RUN apt-get -y --force-yes update \ libgl1-mesa-dev \ libsm6 \ libxt6 \ - libglu1-mesa - -RUN pip install xmldiff + libglu1-mesa \ + && pip install xmldiff RUN cd $HOME/opt \ && wget https://github.com/visit-dav/visit/releases/download/v3.1.1/visit3_1_1.linux-x86_64-ubuntu18.tar.gz \ From 2e5e7dcd57af7fabca4890fa3ce175027a40bf45 Mon Sep 17 00:00:00 2001 From: Kalin Kiesling Date: Wed, 15 Apr 2020 09:49:06 -0500 Subject: [PATCH 15/15] separate again --- pymoab-visit-py2-18.04 | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pymoab-visit-py2-18.04 b/pymoab-visit-py2-18.04 index 6962c48..16ad725 100644 --- a/pymoab-visit-py2-18.04 +++ b/pymoab-visit-py2-18.04 @@ -9,8 +9,9 @@ RUN apt-get -y --force-yes update \ libgl1-mesa-dev \ libsm6 \ libxt6 \ - libglu1-mesa \ - && pip install xmldiff + libglu1-mesa + +RUN pip install xmldiff RUN cd $HOME/opt \ && wget https://github.com/visit-dav/visit/releases/download/v3.1.1/visit3_1_1.linux-x86_64-ubuntu18.tar.gz \