From 2bd47453b8e972bf2fe1befe9b50ac350372c8f6 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Thu, 22 Jul 2021 16:42:17 +0100 Subject: [PATCH 01/10] split up readmes --- README.md | 285 +++++++----------------------------------- README_dev.md | 208 ++++++++++++++++++++++++++++++ test_plugin/README.md | 19 +++ 3 files changed, 275 insertions(+), 237 deletions(-) create mode 100644 README_dev.md create mode 100644 test_plugin/README.md diff --git a/README.md b/README.md index fb8039a10..445069836 100644 --- a/README.md +++ b/README.md @@ -1,235 +1,56 @@ Svalinn plugins and command extensions for Cubit ================================================= -**Beta:** This software is currently under early development. It has been -demonstrated to work on a wide range of problems, but the build system is not -finalized. - -The plugin has been tested and is confirmed to work with various Cubit versions 17.1 up to 2020.2. - -Prerequisites -============= - -In order to build the plugin, you must have access to Cubit and the Cubit SDK. -Additionally, the following system packages must be present on -your computer: - -* EIGEN3 -* HDF5 - -On Ubuntu, these packages can be obtained by running - -``` -sudo apt install libeigen3-dev libhdf5-dev -``` - -The following packages are not available from the package manager and must be -built yourself: - -* MOAB 5.1.0 -* DAGMC +The plugin has been tested and is confirmed to work with various Corefoam Cubit +versions up to 2021.5 and versions of Cubit up to 15.8. Install Cubit ============== -Cubit can be installed by obtaining the Cubit `.deb` package and installing it -with the package manager; i.e. - -``` -sudo dpkg -i Cubit_DEB.deb -``` - -This installs Cubit to `/opt/Coreform-Cubit-VERSION` or `/opt/Trelis-VERSION` for older versions. - -For Cubit versions older than 2021, one needs to manually install the provided SDK - -### Note -There is also a bug (or some other unknown issue) in come Cubit SDK which requires a -file in the Cubit SDK to be modified. The following commands show how to make -this change. (This issue is not present in Cubit 17, so these commands do not -need to be run for Cubit 17.) - -``` -cd PATH_TO_CUBIT/bin -sudo cp -pv CubitExport.cmake CubitExport.cmake.orig -sudo sed -i "s/\"cubit_util\" \"showviz_base\"/\"cubit_util\"/" CubitExport.cmake -``` - -Notes on Build Instructions -=========================== - -A non-source directory build is recommended. These build instructions assume -that the plugin build will take place in the `${HOME}/plugin-build` directory, -and they assume that the Cubit-plugin repo has been cloned into -`${HOME}/plugin-build/Cubit-plugin`. - -**Before building anything, ensure that the `LD_LIBRARY_PATH` environment -variable is empty**. - -```bash -unset LD_LIBRARY_PATH -plugin, and if it is not empty it can only cause problems. Ensure that it -remains empty when running Cubit as well. -``` - -Build MOAB -========== - -MOAB must be built with HDF5 enabled. On Ubuntu 18.04, HDF5 is located in the -`/usr/lib/x86_64-linux-gnu/hdf5/serial` directory, but it may be located -somewhere else on other flavors or versions of Linux. MOAB should be built with -the Eigen matrix algebra library instead of LAPACK. The -`_GLIBCXX_USE_CXX11_ABI=0` flag is required for compatibility with Cubit. - -The following commands show how to correctly build the MOAB dependency. If HDF5 -is located somewhere other than `/usr/lib/x86_64-linux-gnu/hdf5/serial`, then -replace the directory with the correct one. - -``` -cd ${HOME}/plugin-build -mkdir -pv moab/bld -cd moab -git clone https://bitbucket.org/fathomteam/moab -b Version5.1.0 -cd moab -autoreconf -fi -cd ../bld -../moab/configure CXXFLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \ - --enable-shared \ - --enable-optimize \ - --disable-debug \ - --disable-blaslapack \ - --with-eigen3=/usr/include/eigen3 \ - --with-hdf5=/usr/lib/x86_64-linux-gnu/hdf5/serial \ - --prefix=${HOME}/plugin-build/moab -make -j`grep -c processor /proc/cpuinfo` -make install -``` - -Build DAGMC -=========== +Cubit or Corefoam Cubit can be installed by following the instructions on the +relevant website. Cubit is available for Sandia and US National labs users +while Coreform Cubit is available via comerical licenses or freeley available +for students and hobbyists as Cubit Learn. -The following commands show how to build the DAGMC dependency. The `uwuw` and -`make_watertight` features should be turned on, while other features should be -turned off. The `MOAB_DIR` variable should point to the location of the -previously-built MOAB library. The `_GLIBCXX_USE_CXX11_ABI=0` flag is once again -required. +- [Download Cubit](https://cubit.sandia.gov/downloads.html) from Sandia +- [Download Corefoam Cubit](https://coreform.com/products/downloads/) from Corefoam -The following commands show how to correctly build the DAGMC dependency. +
+ Expand - Ubuntu terminal commands for Corefoam Cubit + 

+    sudo apt update
+    sudo apt-get install wget
+    wget -O coreform-cubit-2021.5.deb https://f002.backblazeb2.com/file/cubit-downloads/Coreform-Cubit/Releases/Linux/Coreform-Cubit-2021.5%2B15962_5043ef39-Lin64.deb
+    sudo dpkg -i coreform-cubit-2021.5.deb 
+
+
-``` -cd ${HOME}/plugin-build -mkdir -pv DAGMC/bld -cd DAGMC -git clone https://github.com/svalinn/DAGMC -b develop -cd bld -cmake ../DAGMC -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \ - -DMOAB_DIR=${HOME}/plugin-build/moab \ - -DBUILD_UWUW=ON \ - -DBUILD_TALLY=OFF \ - -DBUILD_BUILD_OBB=OFF \ - -DBUILD_MAKE_WATERTIGHT=ON \ - -DBUILD_SHARED_LIBS=ON \ - -DBUILD_STATIC_LIBS=OFF \ - -DCMAKE_BUILD_TYPE=Release \ - -DCMAKE_INSTALL_PREFIX=${HOME}/plugin-build/DAGMC -make -j`grep -c processor /proc/cpuinfo` -make install -``` - -Build the Plugin -================ - -The following commands show how to build the plugin itself. The `CUBIT_ROOT` -variable should point to the location of Cubit. The `DAGMC_DIR` variable should -point to the location of the previously-built DAGMC library. - -``` -cd ${HOME}/plugin-build -mkdir -pv bld -cd bld -cmake ../Cubit-plugin -DCUBIT_ROOT=PATH_TO_CUBIT \ - -DDAGMC_DIR=${HOME}/plugin-build/DAGMC \ - -DCMAKE_BUILD_TYPE=Release \ - -DCMAKE_INSTALL_PREFIX=${HOME}/plugin-build -make -j`grep -c processor /proc/cpuinfo` -make install -``` - -### Submodules - -The plugin depends on another external repository called mcnp2cad. mcnp2cad is -available in this repo as a git submodule. It is pulled by default during the -`cmake` configuration step above. - -If a custom version of mcnp2cad is needed, this behavior pulling can be disabled -by adding `-DUPDATE_SUBMODULES=OFF` to the `cmake` configuration. mcnp2cad can -then be manually updated with the following commands: - -``` -cd ${HOME}/plugin-build/Cubit-plugin -git submodule update --init -``` - -Create the Tarball -================== - -The following commands show how to create the tarall for the plugin. Once again, -the location of HDF5 might be different than what is presented here depending on -what flavor or version of Linux is being used. -``` -# Set up the directory which will contain the libraries -cd ${HOME}/plugin-build -mkdir -p pack/bin/plugins/svalinn -cd pack/bin/plugins/svalinn - -# Copy all needed libraries into current directory -cp -pPv /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.100* . -cp -pPv ${HOME}/plugin-build/moab/lib/libMOAB.so* . -cp -pPv ${HOME}/plugin-build/DAGMC/lib/libdagmc.so* . -cp -pPv ${HOME}/plugin-build/DAGMC/lib/libmakeWatertight.so* . -cp -pPv ${HOME}/plugin-build/DAGMC/lib/libpyne_dagmc.so* . -cp -pPv ${HOME}/plugin-build/DAGMC/lib/libuwuw.so* . -cp -pPv ${HOME}/plugin-build/lib/* . -chmod 644 * - -# The resulting shared library objects require an update to their RPATH (runtime path) -# attribute to ensure that the correct set of libraries is discovered when starting -# Cubit and loading the plugin library. -patchelf --set-rpath PATH_TO_CUBIT/bin/plugins/svalinn libMOAB.so -patchelf --set-rpath PATH_TO_CUBIT/bin/plugins/svalinn libdagmc.so -patchelf --set-rpath PATH_TO_CUBIT/bin/plugins/svalinn libmakeWatertight.so -patchelf --set-rpath PATH_TO_CUBIT/bin/plugins/svalinn libpyne_dagmc.so -patchelf --set-rpath PATH_TO_CUBIT/bin/plugins/svalinn libuwuw.so - -# Create the Svalinn plugin tarball -cd .. -ln -sv svalinn/libsvalinn_plugin.so . -cd ../.. -tar --sort=name -czvf svalinn-plugin-17.1.tgz bin -mv -v svalinn-plugin-17.1.tgz .. -cd .. -rm -rf pack -``` +Install Plugin +============== -The Svalinn plugin tarball should now be located at -`${HOME}/plugin-build/svalinn-plugin-17.1.tgz`. +The Plugin can be downloaded from the [Release](https://github.com/svalinn/Cubit-plugin/releases) +section of this repository. Operating system specific assets are created with +each release and can be download for various Operating systems (Ubuntu 18, 20 +and MacOS 10.15). -Install the Plugin -================== +After downloading the compressed tgz file the contents should be uncompress to +your Cubit folder. +
+ Expand - Ubuntu terminal commands for Ubuntu 20.04 + 

+    wget https://github.com/svalinn/Cubit-plugin/releases/download/0.1.0/svalinn-plugin_ubuntu-20.04_cubit_2021.5.tgz
+    sudo tar -xzvf svalinn-plugin_ubuntu-20.04_cubit_2021.5.tgz -C /opt/Coreform-Cubit-2021.5
+
+
-To install the plugin, simply run - -``` -cd PATH_TO_CUBIT -sudo tar -xzvf ${HOME}/plugin-build/svalinn-plugin.tgz -``` Test the Plugin =============== -Run `coreform_cubit`. If the plugin was installed correctly, after the Cubit GUI -finishes loading, the following output should appear in the Cubit command line: +Run ```coreform_cubit``` from the command line. If the plugin was installed +correctly, after the Cubit GUI finishes loading, the following output should +appear in the Cubit command line: ``` Loaded Svalinn plugin. @@ -243,32 +64,22 @@ Cubit> If this output does not appear, then the plugin was not installed correctly. -To view the available command line options for the MCNP importer, type -`help mcnp` in the Cubit command line. Similarly for the DAGMC exporter, type -`help dagmc` in the Cubit command line. -Some sample files have been included in the `test_plugin` directory of this -repository. Navigate to that directory, then run `coreform_cubit`. In the Cubit command -line, type `import mcnp test.i`. This should result in the MCNP geometry and -material mapping contained within the MCNP input file `test.i` being imported -into Cubit. +Usage within Cubit +================== + +The DAGMC plugin commands should now be accessable via the Cubit command line. + +To view the available command line options for the MCNP importer, type +```help mcnp``` in the Cubit command line. -Next, run `export acis test.sat overwrite attributes_on`. This will save the -geometry in ACIS format to `test.sat`. +Similarly for the DAGMC exporter, type ```help dagmc``` in the Cubit command line. -Lastly, run -`export dagmc "test.h5m" faceting_tolerance 1e-3 make_watertight verbose`. This -will facet the geometry and save it in a format that can be used by DAGMC. +Some sample files have been included in the [test_plugin](https://github.com/svalinn/Cubit-plugin/tree/develop/test_plugin) +directory of this repository for testing the command line usage. -Test the Plugin (Command Line Mode) -=================================== -The plugin can also be run in command line mode, without needing to load the -Cubit GUI. The file `test.jou` in the `test_plugin` directory contains the five -commands mentioned in the previous section of this readme. To execute these -commands in command line mode, run -`coreform_cubit -batch -nographics -nojournal test.jou` from the regular command line. +Building the plugin +=================== -It is through this command line interface that one would replicate the workflows -of years past which involved the now-defunct `mcnp2cad` and `dagmc_preproc` -executables. +Building the plugin from source is also [possible](https://github.com/svalinn/Cubit-plugin/tree/develop/README_dev.md) but only recommended for developers. diff --git a/README_dev.md b/README_dev.md new file mode 100644 index 000000000..02da7783a --- /dev/null +++ b/README_dev.md @@ -0,0 +1,208 @@ +Svalinn plugins and command extensions for Cubit +================================================= + +**Beta:** This software is currently under early development. It has been +demonstrated to work on a wide range of problems, but the build system is not +finalized. + +The plugin has been tested and is confirmed to work with various Cubit versions 17.1 up to 2021.5. + +Prerequisites +============= + +In order to build the plugin, you must have access to Cubit and the Cubit SDK. +Additionally, the following system packages must be present on +your computer: + +* EIGEN3 +* HDF5 + +On Ubuntu, these packages can be obtained by running + +```bash +sudo apt install libeigen3-dev libhdf5-dev +``` + +The following packages are not available from the package manager and must be +built yourself: + +* [MOAB 5.3.0](https://bitbucket.org/fathomteam/moab/src/master/) +* [DAGMC 3.2](https://github.com/svalinn/DAGMC) + + +Notes on Build Instructions +=========================== + +A non-source directory build is recommended. These build instructions assume +that the plugin build will take place in the `${HOME}/plugin-build` directory, +and they assume that the Cubit-plugin repo has been cloned into +`${HOME}/plugin-build/Cubit-plugin`. + +**Before building anything, ensure that the `LD_LIBRARY_PATH` environment +variable is empty**. + +```bash +unset LD_LIBRARY_PATH +plugin, and if it is not empty it can only cause problems. Ensure that it +remains empty when running Cubit as well. +``` + +Build MOAB +========== + +MOAB must be built with HDF5 enabled. On Ubuntu 18.04, HDF5 is located in the +`/usr/lib/x86_64-linux-gnu/hdf5/serial` directory, but it may be located +somewhere else on other flavors or versions of Linux. MOAB should be built with +the Eigen matrix algebra library instead of LAPACK. The +`_GLIBCXX_USE_CXX11_ABI=0` flag is required for compatibility with Cubit. + +The following commands show how to correctly build the MOAB dependency. If HDF5 +is located somewhere other than `/usr/lib/x86_64-linux-gnu/hdf5/serial`, then +replace the directory with the correct one. + +```bash +cd ${HOME}/plugin-build +mkdir -pv moab/bld +cd moab +git clone https://bitbucket.org/fathomteam/moab -b Version5.1.0 +cd moab +autoreconf -fi +cd ../bld +../moab/configure CXXFLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \ + --enable-shared \ + --enable-optimize \ + --disable-debug \ + --disable-blaslapack \ + --with-eigen3=/usr/include/eigen3 \ + --with-hdf5=/usr/lib/x86_64-linux-gnu/hdf5/serial \ + --prefix=${HOME}/plugin-build/moab +make -j`grep -c processor /proc/cpuinfo` +make install +``` + +Build DAGMC +=========== + +The following commands show how to build the DAGMC dependency. The `uwuw` and +`make_watertight` features should be turned on, while other features should be +turned off. The `MOAB_DIR` variable should point to the location of the +previously-built MOAB library. The `_GLIBCXX_USE_CXX11_ABI=0` flag is once again +required. + +The following commands show how to correctly build the DAGMC dependency. + +```bash +cd ${HOME}/plugin-build +mkdir -pv DAGMC/bld +cd DAGMC +git clone https://github.com/svalinn/DAGMC -b develop +cd bld +cmake ../DAGMC -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \ + -DMOAB_DIR=${HOME}/plugin-build/moab \ + -DBUILD_UWUW=ON \ + -DBUILD_TALLY=OFF \ + -DBUILD_BUILD_OBB=OFF \ + -DBUILD_MAKE_WATERTIGHT=ON \ + -DBUILD_SHARED_LIBS=ON \ + -DBUILD_STATIC_LIBS=OFF \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX=${HOME}/plugin-build/DAGMC +make -j`grep -c processor /proc/cpuinfo` +make install +``` + +Build the Plugin +================ + +The following commands show how to build the plugin itself. The `CUBIT_ROOT` +variable should point to the location of Cubit. The `DAGMC_DIR` variable should +point to the location of the previously-built DAGMC library. + +```bash +cd ${HOME}/plugin-build +mkdir -pv bld +cd bld +cmake ../Cubit-plugin -DCUBIT_ROOT=PATH_TO_CUBIT \ + -DDAGMC_DIR=${HOME}/plugin-build/DAGMC \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX=${HOME}/plugin-build +make -j`grep -c processor /proc/cpuinfo` +make install +``` + +Submodules +========== + +The plugin depends on another external repository called mcnp2cad. mcnp2cad is +available in this repo as a git submodule. It is pulled by default during the +`cmake` configuration step above. + +If a custom version of mcnp2cad is needed, this behavior pulling can be disabled +by adding `-DUPDATE_SUBMODULES=OFF` to the `cmake` configuration. mcnp2cad can +then be manually updated with the following commands: + +```bash +cd ${HOME}/plugin-build/Cubit-plugin +git submodule update --init +``` + +Create the Tarball +================== + +The following commands show how to create the tarall for the plugin. Once again, +the location of HDF5 might be different than what is presented here depending on +what flavor or version of Linux is being used. + + +Set up the directory which will contain the libraries +```bash +cd ${HOME}/plugin-build +mkdir -p pack/bin/plugins/svalinn +cd pack/bin/plugins/svalinn +``` + +Copy all needed libraries into current directory +```bash +cp -pPv /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.100* . +cp -pPv ${HOME}/plugin-build/moab/lib/libMOAB.so* . +cp -pPv ${HOME}/plugin-build/DAGMC/lib/libdagmc.so* . +cp -pPv ${HOME}/plugin-build/DAGMC/lib/libmakeWatertight.so* . +cp -pPv ${HOME}/plugin-build/DAGMC/lib/libpyne_dagmc.so* . +cp -pPv ${HOME}/plugin-build/DAGMC/lib/libuwuw.so* . +cp -pPv ${HOME}/plugin-build/lib/* . +chmod 644 * +``` + +The resulting shared library objects require an update to their RPATH (runtime path) +attribute to ensure that the correct set of libraries is discovered when starting +Cubit and loading the plugin library. +```bash +patchelf --set-rpath PATH_TO_CUBIT/bin/plugins/svalinn libMOAB.so +patchelf --set-rpath PATH_TO_CUBIT/bin/plugins/svalinn libdagmc.so +patchelf --set-rpath PATH_TO_CUBIT/bin/plugins/svalinn libmakeWatertight.so +patchelf --set-rpath PATH_TO_CUBIT/bin/plugins/svalinn libpyne_dagmc.so +patchelf --set-rpath PATH_TO_CUBIT/bin/plugins/svalinn libuwuw.so +``` + +Create the Svalinn plugin tarball +```bash +cd .. +ln -sv svalinn/libsvalinn_plugin.so . +cd ../.. +tar --sort=name -czvf svalinn-plugin-17.1.tgz bin +mv -v svalinn-plugin-17.1.tgz .. +cd .. +rm -rf pack +``` + +The Svalinn plugin tarball should now be located at +`${HOME}/plugin-build/svalinn-plugin-17.1.tgz`. + +Install the Plugin +================== + +To install the plugin, simply run +```bash +cd PATH_TO_CUBIT +sudo tar -xzvf ${HOME}/plugin-build/svalinn-plugin.tgz +``` diff --git a/test_plugin/README.md b/test_plugin/README.md new file mode 100644 index 000000000..f0cb7e5b1 --- /dev/null +++ b/test_plugin/README.md @@ -0,0 +1,19 @@ +Test the Plugin (Command Line Mode) +=================================== + +Some sample files have been included in the ```test_plugin``` directory of this +repository. + +To test the loading of a sample MCNP geometry and materials: + +- Download or clone the repository +- Tthen navigate to the directory with ```cd Cubit-plugin/test_plugin``` +- Then run the ```coreform_cubit``` command +- In the Cubit command line, type ```import mcnp test.i``` +- Now save the geometry in ACIS format (.sat file) by entering ```export acis test.sat overwrite attributes_on``` in the Cubit command line. +- Finally enter ```export dagmc "test.h5m" faceting_tolerance 1e-3 make_watertight verbose``` into the cubit command line which will facet the geometry and save it in a format that can be used by DAGMC (.h5m file). + +The same test can also be carried out from the regular command line without +loading the Cubit GUI by running journals (.jou files). + +- In the regular commmand line enter ```coreform_cubit -batch -nographics -nojournal test.jou``` From 8aab8e4663cb1d1b6a5ef88e93341ccacb2d6448 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Thu, 22 Jul 2021 16:46:57 +0100 Subject: [PATCH 02/10] changed intro --- README_dev.md | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/README_dev.md b/README_dev.md index 02da7783a..e6212be18 100644 --- a/README_dev.md +++ b/README_dev.md @@ -1,11 +1,9 @@ -Svalinn plugins and command extensions for Cubit -================================================= +Building the DAGMC Cubit plugin from source +=========================================== -**Beta:** This software is currently under early development. It has been -demonstrated to work on a wide range of problems, but the build system is not -finalized. +This guide is intended for developers and maintainers of the Cubit plugin. +For installation instructions see the [installation guide](https://github.com/svalinn/Cubit-plugin/tree/develop/README_dev.md). -The plugin has been tested and is confirmed to work with various Cubit versions 17.1 up to 2021.5. Prerequisites ============= From 3e4eb7559b3df7bd670903f18ff3a4cfc81ac074 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Thu, 22 Jul 2021 16:52:53 +0100 Subject: [PATCH 03/10] typos fixed --- README.md | 4 ++-- README_dev.md | 4 +--- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 445069836..00ea79240 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,8 @@ Svalinn plugins and command extensions for Cubit ================================================= -The plugin has been tested and is confirmed to work with various Corefoam Cubit -versions up to 2021.5 and versions of Cubit up to 15.8. +The plugin has been tested and is confirmed to work with versions of Corefoam +Cubit up to 2021.5 and versions of Cubit up to 15.8. Install Cubit ============== diff --git a/README_dev.md b/README_dev.md index e6212be18..7c0cfb524 100644 --- a/README_dev.md +++ b/README_dev.md @@ -37,12 +37,10 @@ and they assume that the Cubit-plugin repo has been cloned into `${HOME}/plugin-build/Cubit-plugin`. **Before building anything, ensure that the `LD_LIBRARY_PATH` environment -variable is empty**. +variable is empty**. Ensure that it remains empty when running Cubit as well. ```bash unset LD_LIBRARY_PATH -plugin, and if it is not empty it can only cause problems. Ensure that it -remains empty when running Cubit as well. ``` Build MOAB From 30e8006d1962a9d176a23e9e7cc35816ea431fb6 Mon Sep 17 00:00:00 2001 From: Jonathan Shimwell Date: Thu, 22 Jul 2021 17:53:15 +0100 Subject: [PATCH 04/10] review suggestions --- README.md | 2 +- README_dev.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 00ea79240..b3f4f1266 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,7 @@ and MacOS 10.15). After downloading the compressed tgz file the contents should be uncompress to your Cubit folder.
- Expand - Ubuntu terminal commands for Ubuntu 20.04 + Expand - Terminal commands for Ubuntu 20.04 

     wget https://github.com/svalinn/Cubit-plugin/releases/download/0.1.0/svalinn-plugin_ubuntu-20.04_cubit_2021.5.tgz
     sudo tar -xzvf svalinn-plugin_ubuntu-20.04_cubit_2021.5.tgz -C /opt/Coreform-Cubit-2021.5
diff --git a/README_dev.md b/README_dev.md
index 7c0cfb524..235a03735 100644
--- a/README_dev.md
+++ b/README_dev.md
@@ -60,7 +60,7 @@ replace the directory with the correct one.
 cd ${HOME}/plugin-build
 mkdir -pv moab/bld
 cd moab
-git clone https://bitbucket.org/fathomteam/moab -b Version5.1.0
+git clone https://bitbucket.org/fathomteam/moab -b 5.3.0
 cd moab
 autoreconf -fi
 cd ../bld

From b4e961fc71b8f1bcd34d694f36c69a44a3e94a2c Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell 
Date: Thu, 22 Jul 2021 17:13:16 +0000
Subject: [PATCH 05/10] typo fix from review

Co-authored-by: Paul Wilson 
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 00ea79240..3cfb8d9f4 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 Svalinn plugins and command extensions for Cubit
 =================================================
 
-The plugin has been tested and is confirmed to work with versions of Corefoam
+The plugin has been tested and is confirmed to work with versions of Coreform 
 Cubit up to 2021.5 and versions of Cubit up to 15.8.
 
 Install Cubit

From 311ef92b17f94bae9cba58da9855e9d87230864b Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell 
Date: Fri, 23 Jul 2021 11:12:58 +0100
Subject: [PATCH 06/10] relative url instead of absolute

Co-authored-by: Paul Wilson 
---
 README.md     | 4 ++--
 README_dev.md | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 7fbd08bcc..6347f6176 100644
--- a/README.md
+++ b/README.md
@@ -75,11 +75,11 @@ To view the available command line options for the MCNP importer, type
 
 Similarly for the DAGMC exporter, type ```help dagmc``` in the Cubit command line.
 
-Some sample files have been included in the [test_plugin](https://github.com/svalinn/Cubit-plugin/tree/develop/test_plugin)
+Some sample files have been included in the [test_plugin](test_plugin)
 directory of this repository for testing the command line usage.
 
 
 Building the plugin
 ===================
 
-Building the plugin from source is also [possible](https://github.com/svalinn/Cubit-plugin/tree/develop/README_dev.md) but only recommended for developers.
+Building the plugin from source is also [possible](README_dev.md) but only recommended for developers.
diff --git a/README_dev.md b/README_dev.md
index 235a03735..2be8880e2 100644
--- a/README_dev.md
+++ b/README_dev.md
@@ -2,7 +2,7 @@ Building the DAGMC Cubit plugin from source
 ===========================================
 
 This guide is intended for developers and maintainers of the Cubit plugin.
-For installation instructions see the [installation guide](https://github.com/svalinn/Cubit-plugin/tree/develop/README_dev.md).
+For installation instructions see the [installation guide](README_dev.md).
 
 
 Prerequisites

From 5eded8aaeb2e24836dd829c96722483388f0b50a Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell 
Date: Fri, 23 Jul 2021 15:19:48 +0100
Subject: [PATCH 07/10] made readme match build scripts

---
 README_dev.md               | 26 +++++++++++++++-----------
 scripts/unix_share_build.sh |  2 +-
 2 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/README_dev.md b/README_dev.md
index 2be8880e2..e7b8fa863 100644
--- a/README_dev.md
+++ b/README_dev.md
@@ -62,18 +62,22 @@ mkdir -pv moab/bld
 cd moab
 git clone https://bitbucket.org/fathomteam/moab -b 5.3.0
 cd moab
-autoreconf -fi
-cd ../bld
-../moab/configure CXXFLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
-                  --enable-shared \
-                  --enable-optimize \
-                  --disable-debug \
-                  --disable-blaslapack \
-                  --with-eigen3=/usr/include/eigen3 \
-                  --with-hdf5=/usr/lib/x86_64-linux-gnu/hdf5/serial \
-                  --prefix=${HOME}/plugin-build/moab
-make -j`grep -c processor /proc/cpuinfo`
+# patching MOAB CMakeLists.txt to use default find(HDF5)
+$SED -i "s/HDF5_MOAB/HDF5/" CMakeLists.txt
+cd ..
+#end of patch
+cd bld
+cmake ../moab -DENABLE_HDF5=ON \
+        -DHDF5_ROOT=$HDF5_PATH \
+        -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS} \
+        -DENABLE_BLASLAPACK=OFF \
+        -DENABLE_FORTRAN=OFF \
+        $CMAKE_ADDITIONAL_FLAGS \
+        -DCMAKE_INSTALL_PREFIX=${PLUGIN_ABS_PATH}/moab
+make
 make install
+cd ../..
+rm -rf moab/moab moab/bld
 ```
 
 Build DAGMC
diff --git a/scripts/unix_share_build.sh b/scripts/unix_share_build.sh
index cb1981888..14cc75e03 100644
--- a/scripts/unix_share_build.sh
+++ b/scripts/unix_share_build.sh
@@ -110,7 +110,7 @@ function build_moab() {
     cd ${PLUGIN_ABS_PATH}
     mkdir -pv moab/bld
     cd moab
-    git clone https://bitbucket.org/fathomteam/moab -b Version5.1.0
+    git clone https://bitbucket.org/fathomteam/moab -b 5.3.0
     cd moab
     # patching MOAB CMakeLists.txt to use default find(HDF5)
     $SED -i "s/HDF5_MOAB/HDF5/" CMakeLists.txt

From 711607ab0e3a644c5f19f360889ff4eaff96b636 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell 
Date: Fri, 23 Jul 2021 15:21:05 +0100
Subject: [PATCH 08/10] corrected readme file link

Co-authored-by: Paul Wilson 
---
 README_dev.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README_dev.md b/README_dev.md
index e7b8fa863..42fac0eef 100644
--- a/README_dev.md
+++ b/README_dev.md
@@ -2,7 +2,7 @@ Building the DAGMC Cubit plugin from source
 ===========================================
 
 This guide is intended for developers and maintainers of the Cubit plugin.
-For installation instructions see the [installation guide](README_dev.md).
+For installation instructions see the [installation guide](README.md).
 
 
 Prerequisites

From 8802519a88d34975f3b60e609f8f1fb02e0479f0 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell 
Date: Mon, 26 Jul 2021 22:47:36 +0100
Subject: [PATCH 09/10] review fix from bam and gonuke

Co-authored-by: Baptiste Mouginot <15145274+bam241@users.noreply.github.com>
---
 README_dev.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README_dev.md b/README_dev.md
index 42fac0eef..b085a1322 100644
--- a/README_dev.md
+++ b/README_dev.md
@@ -125,6 +125,7 @@ cd bld
 cmake ../Cubit-plugin -DCUBIT_ROOT=PATH_TO_CUBIT \
                        -DDAGMC_DIR=${HOME}/plugin-build/DAGMC \
                        -DCMAKE_BUILD_TYPE=Release \
+                       -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
                        -DCMAKE_INSTALL_PREFIX=${HOME}/plugin-build
 make -j`grep -c processor /proc/cpuinfo`
 make install

From 50f501e52ea66e2a8eda5e5e66d7728269c41cb9 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell 
Date: Thu, 29 Jul 2021 15:26:12 +0100
Subject: [PATCH 10/10] correct testing text to use help dagmc

---
 README.md | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/README.md b/README.md
index 6347f6176..597ac83aa 100644
--- a/README.md
+++ b/README.md
@@ -48,22 +48,24 @@ your Cubit folder.
 Test the Plugin
 ===============
 
-Run ```coreform_cubit``` from the command line. If the plugin was installed
-correctly, after the Cubit GUI finishes loading, the following output should
-appear in the Cubit command line:
+Load Cubit by running ```coreform_cubit``` from the command line. After the
+Cubit GUI finishes loading, run the following command in the Cubit command line:
 
 ```
-Loaded Svalinn plugin.
--- DAGMC export command available.
--- iGeom_test command available.
--- MCNP import command available.
-Journaled Command: undo on
+help dagmc
+```
+
+If the plugin was installed correctly you should see the following text appear.
 
-Cubit>
 ```
+Help for words: dagmc.
 
-If this output does not appear, then the plugin was not installed correctly.
+export dagmc  [faceting_tolerance ] [length_tolerance ]
+     [normal_tolerance ] [make_watertight] [verbose]
+     [fatal_on_curves]
+```
 
+If this output does not appear, then the plugin was not installed correctly.
 
 Usage within Cubit
 ==================