From ec3effb97a0ba6973af287b0804b6bed74917373 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Tue, 6 Oct 2020 16:18:28 -0500
Subject: [PATCH 01/21] first try at proprocessing from plugin

---
 README.md                               |  2 +-
 export_dagmc_cmd/DAGMCExportCommand.cpp | 41 ++++++++++++++++++++++++-
 export_dagmc_cmd/DAGMCExportCommand.hpp |  5 ++-
 3 files changed, 45 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index d82a73b2c..712d021c5 100644
--- a/README.md
+++ b/README.md
@@ -108,7 +108,7 @@ cd DAGMC
 git clone https://github.com/svalinn/DAGMC -b develop
 cd bld
 cmake ../DAGMC -DMOAB_DIR=${HOME}/plugin-build/moab \
-               -DBUILD_UWUW=OFF \
+               -DBUILD_UWUW=ON \
                -DBUILD_TALLY=OFF \
                -DBUILD_BUILD_OBB=OFF \
                -DBUILD_MAKE_WATERTIGHT=ON \
diff --git a/export_dagmc_cmd/DAGMCExportCommand.cpp b/export_dagmc_cmd/DAGMCExportCommand.cpp
index 5907c6493..fd1ae405a 100644
--- a/export_dagmc_cmd/DAGMCExportCommand.cpp
+++ b/export_dagmc_cmd/DAGMCExportCommand.cpp
@@ -25,6 +25,9 @@
 #include "moab/Interface.hpp"
 #include "moab/GeomTopoTool.hpp"
 
+// DAGMC includes
+#include "uwuw_preprocessor.hpp"
+
 #define CHK_MB_ERR_RET(A,B)  if (moab::MB_SUCCESS != (B)) { \
   message << (A) << (B) << std::endl;                                   \
   CubitInterface::get_cubit_message_handler()->print_message(message.str().c_str()); \
@@ -46,6 +49,9 @@ DAGMCExportCommand::DAGMCExportCommand() :
   verbose_warnings = false;
   fatal_on_curves = false;
 
+  pyne_mat_lib = "";
+  hdf5_path = "/materials";
+
   CubitMessageHandler *console = CubitInterface::get_cubit_message_handler();
   if (console) {
     std::ostringstream load_message;
@@ -70,6 +76,8 @@ std::vector<std::string> DAGMCExportCommand::get_syntax()
       "[length_tolerance <value:label='length_tolerance',help='<length tolerance>'>] "
       "[normal_tolerance <value:label='normal_tolerance',help='<normal tolerance>'>] "
       "[make_watertight]"
+      "[pyne_mat_lib <string:label='pyne_mat_lib',help='<pyne_mat_lib>'>]"
+      "[hdf5_path <string:label='hdf5_path',help='<hdf5_path>'>]"
       "[verbose] [fatal_on_curves]";
 
   std::vector<std::string> syntax_list;
@@ -159,6 +167,24 @@ bool DAGMCExportCommand::execute(CubitCommandData &data)
   rval = teardown();
   CHK_MB_ERR_RET("Error tearing down export command.",rval);
   
+  // if a PyNE material library is provided then try to process the mats
+  if(pyne_mat_lib != "") {
+    bool fatal_errors = false;
+
+    uwuw_preprocessor* uwuw_preproc = new uwuw_preprocessor(pyne_mat_lib, filename, filename, hdf5_path, verbose_warnings, fatal_errors);
+    // process the materials
+    uwuw_preproc->process_materials();
+
+    // process the tallies
+    uwuw_preproc->process_tallies();
+
+    // write the material data
+    uwuw_preproc->write_uwuw_materials();
+
+    // write the tally data
+    uwuw_preproc->write_uwuw_tallies();
+  }
+
   return result;
 }
 
@@ -191,7 +217,20 @@ moab::ErrorCode DAGMCExportCommand::parse_options(CubitCommandData &data, moab::
   verbose_warnings = data.find_keyword("verbose");
   fatal_on_curves = data.find_keyword("fatal_on_curves");
   make_watertight = data.find_keyword("make_watertight");
-  
+
+  // read parsed command for normal tolerance
+  data.get_string("pyne_mat_lib", pyne_mat_lib);
+  if (pyne_mat_lib != "") {
+    message << "Looking for the PyNE material Lib in " << pyne_mat_lib << std::endl;
+    data.get_string("hdf5_path",hdf5_path);
+    message << "hdf5 path set to " << hdf5_path << std::endl;
+  }
+  else {
+    message
+        << "No Material Library set, material assignments will not be processed"
+        << std::endl;
+  }
+
   if (verbose_warnings && fatal_on_curves)
     message << "This export will fail if curves fail to facet" << std::endl;
 
diff --git a/export_dagmc_cmd/DAGMCExportCommand.hpp b/export_dagmc_cmd/DAGMCExportCommand.hpp
index 29ce1e636..ebbc625f7 100644
--- a/export_dagmc_cmd/DAGMCExportCommand.hpp
+++ b/export_dagmc_cmd/DAGMCExportCommand.hpp
@@ -70,7 +70,10 @@ class DAGMCExportCommand: public CubitCommand
   bool verbose_warnings;
   bool fatal_on_curves;
   bool make_watertight;
-  
+  std::string pyne_mat_lib;
+  std::string hdf5_path;
+
+
   int failed_curve_count;
   std::vector<int> failed_curves;
 

From 55a2f7c3264a75ec8a04b906a43a9d8741b6b5fc Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Tue, 6 Oct 2020 16:18:28 -0500
Subject: [PATCH 02/21] first try at proprocessing from plugin

---
 README.md                               |  2 +-
 export_dagmc_cmd/DAGMCExportCommand.cpp | 41 ++++++++++++++++++++++++-
 export_dagmc_cmd/DAGMCExportCommand.hpp |  5 ++-
 3 files changed, 45 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 23856306a..e12955017 100644
--- a/README.md
+++ b/README.md
@@ -108,7 +108,7 @@ cd DAGMC
 git clone https://github.com/svalinn/DAGMC -b develop
 cd bld
 cmake ../DAGMC -DMOAB_DIR=${HOME}/plugin-build/moab \
-               -DBUILD_UWUW=OFF \
+               -DBUILD_UWUW=ON \
                -DBUILD_TALLY=OFF \
                -DBUILD_BUILD_OBB=OFF \
                -DBUILD_MAKE_WATERTIGHT=ON \
diff --git a/export_dagmc_cmd/DAGMCExportCommand.cpp b/export_dagmc_cmd/DAGMCExportCommand.cpp
index 5907c6493..fd1ae405a 100644
--- a/export_dagmc_cmd/DAGMCExportCommand.cpp
+++ b/export_dagmc_cmd/DAGMCExportCommand.cpp
@@ -25,6 +25,9 @@
 #include "moab/Interface.hpp"
 #include "moab/GeomTopoTool.hpp"
 
+// DAGMC includes
+#include "uwuw_preprocessor.hpp"
+
 #define CHK_MB_ERR_RET(A,B)  if (moab::MB_SUCCESS != (B)) { \
   message << (A) << (B) << std::endl;                                   \
   CubitInterface::get_cubit_message_handler()->print_message(message.str().c_str()); \
@@ -46,6 +49,9 @@ DAGMCExportCommand::DAGMCExportCommand() :
   verbose_warnings = false;
   fatal_on_curves = false;
 
+  pyne_mat_lib = "";
+  hdf5_path = "/materials";
+
   CubitMessageHandler *console = CubitInterface::get_cubit_message_handler();
   if (console) {
     std::ostringstream load_message;
@@ -70,6 +76,8 @@ std::vector<std::string> DAGMCExportCommand::get_syntax()
       "[length_tolerance <value:label='length_tolerance',help='<length tolerance>'>] "
       "[normal_tolerance <value:label='normal_tolerance',help='<normal tolerance>'>] "
       "[make_watertight]"
+      "[pyne_mat_lib <string:label='pyne_mat_lib',help='<pyne_mat_lib>'>]"
+      "[hdf5_path <string:label='hdf5_path',help='<hdf5_path>'>]"
       "[verbose] [fatal_on_curves]";
 
   std::vector<std::string> syntax_list;
@@ -159,6 +167,24 @@ bool DAGMCExportCommand::execute(CubitCommandData &data)
   rval = teardown();
   CHK_MB_ERR_RET("Error tearing down export command.",rval);
   
+  // if a PyNE material library is provided then try to process the mats
+  if(pyne_mat_lib != "") {
+    bool fatal_errors = false;
+
+    uwuw_preprocessor* uwuw_preproc = new uwuw_preprocessor(pyne_mat_lib, filename, filename, hdf5_path, verbose_warnings, fatal_errors);
+    // process the materials
+    uwuw_preproc->process_materials();
+
+    // process the tallies
+    uwuw_preproc->process_tallies();
+
+    // write the material data
+    uwuw_preproc->write_uwuw_materials();
+
+    // write the tally data
+    uwuw_preproc->write_uwuw_tallies();
+  }
+
   return result;
 }
 
@@ -191,7 +217,20 @@ moab::ErrorCode DAGMCExportCommand::parse_options(CubitCommandData &data, moab::
   verbose_warnings = data.find_keyword("verbose");
   fatal_on_curves = data.find_keyword("fatal_on_curves");
   make_watertight = data.find_keyword("make_watertight");
-  
+
+  // read parsed command for normal tolerance
+  data.get_string("pyne_mat_lib", pyne_mat_lib);
+  if (pyne_mat_lib != "") {
+    message << "Looking for the PyNE material Lib in " << pyne_mat_lib << std::endl;
+    data.get_string("hdf5_path",hdf5_path);
+    message << "hdf5 path set to " << hdf5_path << std::endl;
+  }
+  else {
+    message
+        << "No Material Library set, material assignments will not be processed"
+        << std::endl;
+  }
+
   if (verbose_warnings && fatal_on_curves)
     message << "This export will fail if curves fail to facet" << std::endl;
 
diff --git a/export_dagmc_cmd/DAGMCExportCommand.hpp b/export_dagmc_cmd/DAGMCExportCommand.hpp
index 29ce1e636..ebbc625f7 100644
--- a/export_dagmc_cmd/DAGMCExportCommand.hpp
+++ b/export_dagmc_cmd/DAGMCExportCommand.hpp
@@ -70,7 +70,10 @@ class DAGMCExportCommand: public CubitCommand
   bool verbose_warnings;
   bool fatal_on_curves;
   bool make_watertight;
-  
+  std::string pyne_mat_lib;
+  std::string hdf5_path;
+
+
   int failed_curve_count;
   std::vector<int> failed_curves;
 

From ffcdfacb6c8f9ccec1f145da1d9cf30e8d30b6bd Mon Sep 17 00:00:00 2001
From: Lucas John Jacobson <ljacobson64@gmail.com>
Date: Wed, 7 Oct 2020 16:38:36 -0500
Subject: [PATCH 03/21] Add pyne_dagmc and uwuw to tarball

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index e12955017..f5618eeb5 100644
--- a/README.md
+++ b/README.md
@@ -174,6 +174,8 @@ cp -pPv ${HOME}/plugin-build/lib/* .
 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 /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.100* .
 chmod 644 *
 
@@ -181,6 +183,8 @@ chmod 644 *
 patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libMOAB.so
 patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libdagmc.so
 patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libmakeWatertight.so
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libpyne_dagmc.so
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libuwuw.so
 
 # Create the Svalinn plugin tarball
 cd ..

From 5e3632ed42f60d65b8e177ac5d8731ec947b0f13 Mon Sep 17 00:00:00 2001
From: Lucas John Jacobson <ljacobson64@gmail.com>
Date: Wed, 7 Oct 2020 16:39:01 -0500
Subject: [PATCH 04/21] Build moab and DAGMC with _GLIBCXX_USE_CXX11_ABI=0

---
 README.md | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index f5618eeb5..33abe583d 100644
--- a/README.md
+++ b/README.md
@@ -90,7 +90,8 @@ cd ../bld
                   --disable-blaslapack \
                   --with-eigen3=/usr/include/eigen3 \
                   --with-hdf5=/usr/lib/x86_64-linux-gnu/hdf5/serial \
-                  --prefix=${HOME}/plugin-build/moab
+                  --prefix=${HOME}/plugin-build/moab \
+                  CXXFLAGS=-D_GLIBCXX_USE_CXX11_ABI=0
 make -j`grep -c processor /proc/cpuinfo`
 make install
 ```
@@ -107,7 +108,8 @@ mkdir -pv DAGMC/bld
 cd DAGMC
 git clone https://github.com/svalinn/DAGMC -b develop
 cd bld
-cmake ../DAGMC -DMOAB_DIR=${HOME}/plugin-build/moab \
+cmake ../DAGMC -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
+               -DMOAB_DIR=${HOME}/plugin-build/moab \
                -DBUILD_UWUW=ON \
                -DBUILD_TALLY=OFF \
                -DBUILD_BUILD_OBB=OFF \

From 488273de60030d98a02e921a2857c7dabc2ae223 Mon Sep 17 00:00:00 2001
From: Lucas John Jacobson <ljacobson64@gmail.com>
Date: Thu, 8 Oct 2020 11:26:16 -0500
Subject: [PATCH 05/21] Add TRELIS_VERSION cmake variable

---
 CMakeLists.txt | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index ed46a5e13..609b2c4fb 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -24,15 +24,18 @@ endif ()
 set(CMAKE_CXX_STANDARD 11)
 
 # Adjust compiler setting for Linux using gcc version 5.0 and higher
-if (CMAKE_SYSTEM_NAME MATCHES Linux AND CMAKE_COMPILER_IS_GNUCXX)
-  if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER "5.0")
-    if (NOT CMAKE_CXX_FLAGS MATCHES _GLIBCXX_USE_CXX11_ABI)
-      set(CMAKE_CXX_FLAGS "-D_GLIBCXX_USE_CXX11_ABI=0 ${CMAKE_CXX_FLAGS}")
-    endif ()
-  endif ()
-endif ()
+#if (CMAKE_SYSTEM_NAME MATCHES Linux AND CMAKE_COMPILER_IS_GNUCXX)
+#  if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER "5.0")
+#    if (NOT CMAKE_CXX_FLAGS MATCHES _GLIBCXX_USE_CXX11_ABI)
+#      set(CMAKE_CXX_FLAGS "-D_GLIBCXX_USE_CXX11_ABI=0 ${CMAKE_CXX_FLAGS}")
+#    endif ()
+#  endif ()
+#endif ()
 
 # Find Cubit/Trelis
+if (NOT CUBIT_ROOT)
+  set(CUBIT_ROOT "/opt/Trelis-${TRELIS_VERSION}")
+endif ()
 list(APPEND CMAKE_PREFIX_PATH ${CUBIT_ROOT}/bin)
 find_package(Cubit REQUIRED CONFIG)
 include_directories(${CUBIT_INCLUDE_DIRS})

From 6b073d51f47201f62d56aacd86053d5cce5ea67b Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Fri, 9 Oct 2020 15:11:52 -0500
Subject: [PATCH 06/21] removing some unrelated change, rearanging
 CXXFLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 order for consistency

---
 CMakeLists.txt | 18 ++++++++----------
 README.md      |  6 +++---
 2 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 609b2c4fb..64a2d0770 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -24,18 +24,16 @@ endif ()
 set(CMAKE_CXX_STANDARD 11)
 
 # Adjust compiler setting for Linux using gcc version 5.0 and higher
-#if (CMAKE_SYSTEM_NAME MATCHES Linux AND CMAKE_COMPILER_IS_GNUCXX)
-#  if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER "5.0")
-#    if (NOT CMAKE_CXX_FLAGS MATCHES _GLIBCXX_USE_CXX11_ABI)
-#      set(CMAKE_CXX_FLAGS "-D_GLIBCXX_USE_CXX11_ABI=0 ${CMAKE_CXX_FLAGS}")
-#    endif ()
-#  endif ()
-#endif ()
+if (CMAKE_SYSTEM_NAME MATCHES Linux AND CMAKE_COMPILER_IS_GNUCXX)
+  if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER "5.0")
+    if (NOT CMAKE_CXX_FLAGS MATCHES _GLIBCXX_USE_CXX11_ABI)
+      set(CMAKE_CXX_FLAGS "-D_GLIBCXX_USE_CXX11_ABI=0 ${CMAKE_CXX_FLAGS}")
+    endif ()
+  endif ()
+endif ()
 
 # Find Cubit/Trelis
-if (NOT CUBIT_ROOT)
-  set(CUBIT_ROOT "/opt/Trelis-${TRELIS_VERSION}")
-endif ()
+
 list(APPEND CMAKE_PREFIX_PATH ${CUBIT_ROOT}/bin)
 find_package(Cubit REQUIRED CONFIG)
 include_directories(${CUBIT_INCLUDE_DIRS})
diff --git a/README.md b/README.md
index 33abe583d..d2c2b37a7 100644
--- a/README.md
+++ b/README.md
@@ -83,15 +83,15 @@ git clone https://bitbucket.org/fathomteam/moab -b Version5.1.0
 cd moab
 autoreconf -fi
 cd ../bld
-../moab/configure --disable-blaslapack \
+../moab/configure CXXFLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
+                  --disable-blaslapack \
                   --enable-shared \
                   --enable-optimize \
                   --disable-debug \
                   --disable-blaslapack \
                   --with-eigen3=/usr/include/eigen3 \
                   --with-hdf5=/usr/lib/x86_64-linux-gnu/hdf5/serial \
-                  --prefix=${HOME}/plugin-build/moab \
-                  CXXFLAGS=-D_GLIBCXX_USE_CXX11_ABI=0
+                  --prefix=${HOME}/plugin-build/moab
 make -j`grep -c processor /proc/cpuinfo`
 make install
 ```

From d41fe4de6cccc87e28074c6443f0da99e4b68f30 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Fri, 9 Oct 2020 15:31:52 -0500
Subject: [PATCH 07/21] One Script to link them all, one script to find them;
 one script to build them and in the plugin bind them.

---
 buid_plugin.sh | 97 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 97 insertions(+)
 create mode 100755 buid_plugin.sh

diff --git a/buid_plugin.sh b/buid_plugin.sh
new file mode 100755
index 000000000..aee76322a
--- /dev/null
+++ b/buid_plugin.sh
@@ -0,0 +1,97 @@
+#!/bin/bash
+
+# Setup
+CURRENT=$(pwd)
+SCRIPTPATH=`dirname $(realpath $0)`
+
+PLUGIN_DIR="plugin-build"
+
+mkdir ${PLUGIN_DIR}
+PLUGIN_ABS_PATH=${CURRENT}/${PLUGIN_DIR}
+
+echo "Building the Trelis plugin in ${CURRENT}\\${PLUGIN_DIR}"
+
+unset LD_LIBRARY_PATH
+
+cd ${PLUGIN_ABS_PATH}
+ln -s $SCRIPTPATH ./
+
+mkdir -pv moab/bld
+cd moab
+git clone https://bitbucket.org/fathomteam/moab -b Version5.1.0
+cd moab
+autoreconf -fi
+cd ../bld
+../moab/configure CXXFLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
+                  --disable-blaslapack \
+                  --enable-shared \
+                  --enable-optimize \
+                  --disable-debug \
+                  --disable-blaslapack \
+                  --with-eigen3=/usr/include/eigen3 \
+                  --with-hdf5=/usr/lib/x86_64-linux-gnu/hdf5/serial \
+                  --prefix=${PLUGIN_ABS_PATH}/moab
+make -j`grep -c processor /proc/cpuinfo`
+make install
+
+cd ${PLUGIN_ABS_PATH}
+mkdir -pv DAGMC/bld
+cd DAGMC
+git clone https://github.com/svalinn/DAGMC -b develop
+cd bld
+cmake ../DAGMC -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
+               -DMOAB_DIR=${PLUGIN_ABS_PATH}/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=${PLUGIN_ABS_PATH}/DAGMC
+make -j`grep -c processor /proc/cpuinfo`
+make install
+
+cd ${PLUGIN_ABS_PATH}
+mkdir -pv bld
+cd bld
+cmake ../Trelis-plugin -DCUBIT_ROOT=/opt/Trelis-16.5 \
+                       -DDAGMC_DIR=${PLUGIN_ABS_PATH}/DAGMC \
+                       -DCMAKE_BUILD_TYPE=Release \
+                       -DCMAKE_INSTALL_PREFIX=${PLUGIN_ABS_PATH}
+make -j`grep -c processor /proc/cpuinfo`
+make install
+
+cd ${PLUGIN_ABS_PATH}/Trelis-plugin
+git submodule update --init
+
+cd ${PLUGIN_ABS_PATH}
+mkdir -p pack/bin/plugins/svalinn
+cd pack/bin/plugins/svalinn
+
+# Copy all needed libraries into current directory
+cp -pPv ${PLUGIN_ABS_PATH}/lib/* .
+cp -pPv ${PLUGIN_ABS_PATH}/moab/lib/libMOAB.so* .
+cp -pPv ${PLUGIN_ABS_PATH}/DAGMC/lib/libdagmc.so* .
+cp -pPv ${PLUGIN_ABS_PATH}/DAGMC/lib/libmakeWatertight.so* .
+cp -pPv ${PLUGIN_ABS_PATH}/DAGMC/lib/libpyne_dagmc.so .
+cp -pPv ${PLUGIN_ABS_PATH}/DAGMC/lib/libuwuw.so .
+cp -pPv /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.100* .
+chmod 644 *
+
+# Set the RPATH to be the current directory for the DAGMC libraries
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libMOAB.so
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libdagmc.so
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libmakeWatertight.so
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libpyne_dagmc.so
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libuwuw.so
+
+# Create the Svalinn plugin tarball
+cd ..
+ln -sv svalinn/libsvalinn_plugin.so .
+cd ../..
+tar --sort=name -czvf svalinn-plugin.tgz bin
+mv -v svalinn-plugin.tgz ..
+cd ..
+rm -rf pack bld DAGMC lib moab
+rm Trelis-plugin
\ No newline at end of file

From d67a9a830c94facbeef766909dbda5a3e86cb675 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Thu, 15 Oct 2020 08:14:43 -0500
Subject: [PATCH 08/21] removing empty line

---
 CMakeLists.txt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index e094d55a5..1fd7d91f4 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -33,7 +33,6 @@ if (CMAKE_SYSTEM_NAME MATCHES Linux AND CMAKE_COMPILER_IS_GNUCXX)
 endif ()
 
 # Find Cubit/Trelis
-
 if (NOT CUBIT_ROOT)
   message(FATAL_ERROR "CUBIT_ROOT not specified")
 endif ()

From 51da7434561eb2fc4b33e4895055b2096c39b43b Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Fri, 16 Oct 2020 10:48:39 -0500
Subject: [PATCH 09/21] apt-get required package

---
 buid_plugin.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/buid_plugin.sh b/buid_plugin.sh
index aee76322a..85c0ae654 100755
--- a/buid_plugin.sh
+++ b/buid_plugin.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+sudo apt-gen install autogen autoconf libtool
+
 # Setup
 CURRENT=$(pwd)
 SCRIPTPATH=`dirname $(realpath $0)`

From d848f46195375a55c3a150ff2b71d2456fc790f8 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Fri, 16 Oct 2020 10:49:04 -0500
Subject: [PATCH 10/21] more apt-get

---
 buid_plugin.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/buid_plugin.sh b/buid_plugin.sh
index 85c0ae654..62dfcf6f0 100755
--- a/buid_plugin.sh
+++ b/buid_plugin.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-sudo apt-gen install autogen autoconf libtool
+sudo apt-gen install autogen autoconf libtool libeigen3-dev libhdf5-dev
 
 # Setup
 CURRENT=$(pwd)

From 22f453186c6279cb2c3c3032d8eb9b4d7307ef49 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Fri, 16 Oct 2020 11:29:40 -0500
Subject: [PATCH 11/21] fixing typo

---
 buid_plugin.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/buid_plugin.sh b/buid_plugin.sh
index 62dfcf6f0..c526c6b20 100755
--- a/buid_plugin.sh
+++ b/buid_plugin.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-sudo apt-gen install autogen autoconf libtool libeigen3-dev libhdf5-dev
+sudo apt-get install autogen autoconf libtool libeigen3-dev libhdf5-dev
 
 # Setup
 CURRENT=$(pwd)

From 5bf044f440efa200d8a2afcbab462cd8128916c9 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Fri, 16 Oct 2020 11:38:17 -0500
Subject: [PATCH 12/21] adding more package

---
 buid_plugin.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/buid_plugin.sh b/buid_plugin.sh
index c526c6b20..fae15c1c8 100755
--- a/buid_plugin.sh
+++ b/buid_plugin.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-sudo apt-get install autogen autoconf libtool libeigen3-dev libhdf5-dev
+sudo apt-get install autogen autoconf libtool libeigen3-dev libhdf5-dev patchelf gfortran
 
 # Setup
 CURRENT=$(pwd)

From e376152f6ab7a063212f8180e48770775d6d2bb0 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Fri, 16 Oct 2020 13:31:31 -0500
Subject: [PATCH 13/21] update script to 17.1

---
 buid_plugin.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/buid_plugin.sh b/buid_plugin.sh
index fae15c1c8..fbf41fe44 100755
--- a/buid_plugin.sh
+++ b/buid_plugin.sh
@@ -57,7 +57,7 @@ make install
 cd ${PLUGIN_ABS_PATH}
 mkdir -pv bld
 cd bld
-cmake ../Trelis-plugin -DCUBIT_ROOT=/opt/Trelis-16.5 \
+cmake ../Trelis-plugin -DCUBIT_ROOT=/opt/Trelis-17.1 \
                        -DDAGMC_DIR=${PLUGIN_ABS_PATH}/DAGMC \
                        -DCMAKE_BUILD_TYPE=Release \
                        -DCMAKE_INSTALL_PREFIX=${PLUGIN_ABS_PATH}

From 8f62d58d01dea64883dc9caefb1f4014435382f1 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Fri, 16 Oct 2020 14:20:56 -0500
Subject: [PATCH 14/21] no removeing

---
 buid_plugin.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/buid_plugin.sh b/buid_plugin.sh
index fbf41fe44..c4dafa501 100755
--- a/buid_plugin.sh
+++ b/buid_plugin.sh
@@ -95,5 +95,5 @@ cd ../..
 tar --sort=name -czvf svalinn-plugin.tgz bin
 mv -v svalinn-plugin.tgz ..
 cd ..
-rm -rf pack bld DAGMC lib moab
-rm Trelis-plugin
\ No newline at end of file
+#rm -rf pack bld DAGMC lib moab
+#rm Trelis-plugin
\ No newline at end of file

From 9d28f928be6d57df19cd5a61ccc5525222883b40 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Fri, 16 Oct 2020 14:21:45 -0500
Subject: [PATCH 15/21] reordering

---
 buid_plugin.sh | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/buid_plugin.sh b/buid_plugin.sh
index c4dafa501..55f645bb9 100755
--- a/buid_plugin.sh
+++ b/buid_plugin.sh
@@ -54,6 +54,10 @@ cmake ../DAGMC -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
 make -j`grep -c processor /proc/cpuinfo`
 make install
 
+
+cd ${PLUGIN_ABS_PATH}/Trelis-plugin
+git submodule update --init
+
 cd ${PLUGIN_ABS_PATH}
 mkdir -pv bld
 cd bld
@@ -64,8 +68,6 @@ cmake ../Trelis-plugin -DCUBIT_ROOT=/opt/Trelis-17.1 \
 make -j`grep -c processor /proc/cpuinfo`
 make install
 
-cd ${PLUGIN_ABS_PATH}/Trelis-plugin
-git submodule update --init
 
 cd ${PLUGIN_ABS_PATH}
 mkdir -p pack/bin/plugins/svalinn

From 06fa6cdda994afc861608d39563cc46fe66b301c Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Fri, 16 Oct 2020 14:35:58 -0500
Subject: [PATCH 16/21] restauring cleanup

---
 buid_plugin.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/buid_plugin.sh b/buid_plugin.sh
index 55f645bb9..98037a597 100755
--- a/buid_plugin.sh
+++ b/buid_plugin.sh
@@ -97,5 +97,5 @@ cd ../..
 tar --sort=name -czvf svalinn-plugin.tgz bin
 mv -v svalinn-plugin.tgz ..
 cd ..
-#rm -rf pack bld DAGMC lib moab
-#rm Trelis-plugin
\ No newline at end of file
+rm -rf pack bld DAGMC lib moab
+rm Trelis-plugin
\ No newline at end of file

From e8ee71cd6d4117c22a5bf744ed5a53e8505ca5cf Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Mon, 26 Oct 2020 11:01:13 -0500
Subject: [PATCH 17/21] some cleaning

---
 script/build_plug_linux.sh |   4 ++
 script/build_plugin.sh     | 110 +++++++++++++++++++++++++++++++++++++
 2 files changed, 114 insertions(+)
 create mode 100755 script/build_plug_linux.sh
 create mode 100755 script/build_plugin.sh

diff --git a/script/build_plug_linux.sh b/script/build_plug_linux.sh
new file mode 100755
index 000000000..b2aac02e2
--- /dev/null
+++ b/script/build_plug_linux.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+SCRIPTPATH=`dirname $(dirname $(realpath $0))`
+docker run -v "$SCRIPTPATH:/Trelis-plugin" -v "$2:/Trelis-sdk" -it $1 bash -c "/Trelis-plugin/script/build_plugin.sh $3"
\ No newline at end of file
diff --git a/script/build_plugin.sh b/script/build_plugin.sh
new file mode 100755
index 000000000..c4cc2a56c
--- /dev/null
+++ b/script/build_plugin.sh
@@ -0,0 +1,110 @@
+#!/bin/bash
+
+cd /Trelis-sdk 
+dpkg -i Trelis-$1-Lin64.deb
+
+cd /opt
+tar -xzvf /Trelis-sdk/Trelis-SDK-$1-Lin64.tar.gz
+
+apt-get update -y
+apt-get install -y autogen autoconf libtool libeigen3-dev libhdf5-dev patchelf gfortran git cmake
+
+cd 
+
+# Setup
+CURRENT=$(pwd)
+SCRIPTPATH=`dirname $(dirname $(realpath $0))`
+
+PLUGIN_DIR="plugin-build"
+
+mkdir ${PLUGIN_DIR}
+PLUGIN_ABS_PATH=${CURRENT}/${PLUGIN_DIR}
+
+echo "Building the Trelis plugin in ${CURRENT}\\${PLUGIN_DIR}"
+
+unset LD_LIBRARY_PATH
+
+cd ${PLUGIN_ABS_PATH}
+ln -s $SCRIPTPATH/ ./
+
+mkdir -pv moab/bld
+cd moab
+git clone https://bitbucket.org/fathomteam/moab -b Version5.1.0
+cd moab
+autoreconf -fi
+cd ../bld
+../moab/configure CXXFLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
+                  --disable-blaslapack \
+                  --enable-shared \
+                  --enable-optimize \
+                  --disable-debug \
+                  --disable-blaslapack \
+                  --with-eigen3=/usr/include/eigen3 \
+                  --with-hdf5=/usr/lib/x86_64-linux-gnu/hdf5/serial \
+                  --prefix=${PLUGIN_ABS_PATH}/moab
+make -j`grep -c processor /proc/cpuinfo`
+make install
+
+cd ${PLUGIN_ABS_PATH}
+mkdir -pv DAGMC/bld
+cd DAGMC
+git clone https://github.com/svalinn/DAGMC -b develop
+cd bld
+cmake ../DAGMC -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
+               -DMOAB_DIR=${PLUGIN_ABS_PATH}/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=${PLUGIN_ABS_PATH}/DAGMC
+make -j`grep -c processor /proc/cpuinfo`
+make install
+
+
+cd ${PLUGIN_ABS_PATH}/Trelis-plugin
+git submodule update --init
+
+cd ${PLUGIN_ABS_PATH}
+mkdir -pv bld
+cd bld
+cmake ../Trelis-plugin -DCUBIT_ROOT=/opt/Trelis-17.1 \
+                       -DDAGMC_DIR=${PLUGIN_ABS_PATH}/DAGMC \
+                       -DCMAKE_BUILD_TYPE=Release \
+                       -DCMAKE_INSTALL_PREFIX=${PLUGIN_ABS_PATH}
+make -j`grep -c processor /proc/cpuinfo`
+make install
+
+
+cd ${PLUGIN_ABS_PATH}
+mkdir -p pack/bin/plugins/svalinn
+cd pack/bin/plugins/svalinn
+
+# Copy all needed libraries into current directory
+cp -pPv ${PLUGIN_ABS_PATH}/lib/* .
+cp -pPv ${PLUGIN_ABS_PATH}/moab/lib/libMOAB.so* .
+cp -pPv ${PLUGIN_ABS_PATH}/DAGMC/lib/libdagmc.so* .
+cp -pPv ${PLUGIN_ABS_PATH}/DAGMC/lib/libmakeWatertight.so* .
+cp -pPv ${PLUGIN_ABS_PATH}/DAGMC/lib/libpyne_dagmc.so .
+cp -pPv ${PLUGIN_ABS_PATH}/DAGMC/lib/libuwuw.so .
+cp -pPv /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.100* .
+chmod 644 *
+
+# Set the RPATH to be the current directory for the DAGMC libraries
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libMOAB.so
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libdagmc.so
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libmakeWatertight.so
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libpyne_dagmc.so
+patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libuwuw.so
+
+# Create the Svalinn plugin tarball
+cd ..
+ln -sv svalinn/libsvalinn_plugin.so .
+cd ../..
+tar --sort=name -czvf svalinn-plugin_linux_$1.tgz bin
+mv -v svalinn-plugin_linux_$1.tgz /Trelis-sdk
+cd ..
+rm -rf pack bld DAGMC lib moab
+rm Trelis-plugin

From cfc769e2ca7a36c12c2085818d654106fe63c625 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Mon, 26 Oct 2020 11:01:38 -0500
Subject: [PATCH 18/21] cleaning again

---
 script/build_plugin.sh | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/script/build_plugin.sh b/script/build_plugin.sh
index c4cc2a56c..43ab86dd4 100755
--- a/script/build_plugin.sh
+++ b/script/build_plugin.sh
@@ -93,11 +93,12 @@ cp -pPv /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.100* .
 chmod 644 *
 
 # Set the RPATH to be the current directory for the DAGMC libraries
-patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libMOAB.so
-patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libdagmc.so
-patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libmakeWatertight.so
-patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libpyne_dagmc.so
-patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libuwuw.so
+patchelf --set-rpath /opt/Trelis-${1%.??}/bin/plugins/svalinn libMOAB.so
+patchelf --set-rpath /opt/Trelis-${1%.??}/bin/plugins/svalinn libdagmc.so
+patchelf --set-rpath /opt/Trelis-${1%.??}/bin/plugins/svalinn libmakeWatertight.so
+patchelf --set-rpath /opt/Trelis-${1%.??}/bin/plugins/svalinn libpyne_dagmc.so
+#patchelf --set-rpath /opt/Trelis-$1/bin/plugins libsvalinn_plugin.so
+patchelf --set-rpath /opt/Trelis-${1%.??}/bin/plugins/svalinn libuwuw.so
 
 # Create the Svalinn plugin tarball
 cd ..

From a13f40b47822f585f61ed7b983110c00e5f4987b Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Mon, 26 Oct 2020 11:01:53 -0500
Subject: [PATCH 19/21] cleaning

---
 buid_plugin.sh | 101 -------------------------------------------------
 1 file changed, 101 deletions(-)
 delete mode 100755 buid_plugin.sh

diff --git a/buid_plugin.sh b/buid_plugin.sh
deleted file mode 100755
index 98037a597..000000000
--- a/buid_plugin.sh
+++ /dev/null
@@ -1,101 +0,0 @@
-#!/bin/bash
-
-sudo apt-get install autogen autoconf libtool libeigen3-dev libhdf5-dev patchelf gfortran
-
-# Setup
-CURRENT=$(pwd)
-SCRIPTPATH=`dirname $(realpath $0)`
-
-PLUGIN_DIR="plugin-build"
-
-mkdir ${PLUGIN_DIR}
-PLUGIN_ABS_PATH=${CURRENT}/${PLUGIN_DIR}
-
-echo "Building the Trelis plugin in ${CURRENT}\\${PLUGIN_DIR}"
-
-unset LD_LIBRARY_PATH
-
-cd ${PLUGIN_ABS_PATH}
-ln -s $SCRIPTPATH ./
-
-mkdir -pv moab/bld
-cd moab
-git clone https://bitbucket.org/fathomteam/moab -b Version5.1.0
-cd moab
-autoreconf -fi
-cd ../bld
-../moab/configure CXXFLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
-                  --disable-blaslapack \
-                  --enable-shared \
-                  --enable-optimize \
-                  --disable-debug \
-                  --disable-blaslapack \
-                  --with-eigen3=/usr/include/eigen3 \
-                  --with-hdf5=/usr/lib/x86_64-linux-gnu/hdf5/serial \
-                  --prefix=${PLUGIN_ABS_PATH}/moab
-make -j`grep -c processor /proc/cpuinfo`
-make install
-
-cd ${PLUGIN_ABS_PATH}
-mkdir -pv DAGMC/bld
-cd DAGMC
-git clone https://github.com/svalinn/DAGMC -b develop
-cd bld
-cmake ../DAGMC -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
-               -DMOAB_DIR=${PLUGIN_ABS_PATH}/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=${PLUGIN_ABS_PATH}/DAGMC
-make -j`grep -c processor /proc/cpuinfo`
-make install
-
-
-cd ${PLUGIN_ABS_PATH}/Trelis-plugin
-git submodule update --init
-
-cd ${PLUGIN_ABS_PATH}
-mkdir -pv bld
-cd bld
-cmake ../Trelis-plugin -DCUBIT_ROOT=/opt/Trelis-17.1 \
-                       -DDAGMC_DIR=${PLUGIN_ABS_PATH}/DAGMC \
-                       -DCMAKE_BUILD_TYPE=Release \
-                       -DCMAKE_INSTALL_PREFIX=${PLUGIN_ABS_PATH}
-make -j`grep -c processor /proc/cpuinfo`
-make install
-
-
-cd ${PLUGIN_ABS_PATH}
-mkdir -p pack/bin/plugins/svalinn
-cd pack/bin/plugins/svalinn
-
-# Copy all needed libraries into current directory
-cp -pPv ${PLUGIN_ABS_PATH}/lib/* .
-cp -pPv ${PLUGIN_ABS_PATH}/moab/lib/libMOAB.so* .
-cp -pPv ${PLUGIN_ABS_PATH}/DAGMC/lib/libdagmc.so* .
-cp -pPv ${PLUGIN_ABS_PATH}/DAGMC/lib/libmakeWatertight.so* .
-cp -pPv ${PLUGIN_ABS_PATH}/DAGMC/lib/libpyne_dagmc.so .
-cp -pPv ${PLUGIN_ABS_PATH}/DAGMC/lib/libuwuw.so .
-cp -pPv /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.100* .
-chmod 644 *
-
-# Set the RPATH to be the current directory for the DAGMC libraries
-patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libMOAB.so
-patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libdagmc.so
-patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libmakeWatertight.so
-patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libpyne_dagmc.so
-patchelf --set-rpath /opt/Trelis-16.5/bin/plugins/svalinn libuwuw.so
-
-# Create the Svalinn plugin tarball
-cd ..
-ln -sv svalinn/libsvalinn_plugin.so .
-cd ../..
-tar --sort=name -czvf svalinn-plugin.tgz bin
-mv -v svalinn-plugin.tgz ..
-cd ..
-rm -rf pack bld DAGMC lib moab
-rm Trelis-plugin
\ No newline at end of file

From e23560b272e74cbb2e33cb476056821f8fd252e4 Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Wed, 28 Oct 2020 14:37:27 -0500
Subject: [PATCH 20/21] some update

---
 export_dagmc_cmd/DAGMCExportCommand.cpp | 26 +++++++++++++++++++------
 export_dagmc_cmd/DAGMCExportCommand.hpp |  1 +
 script/build_plugin.sh                  |  5 ++++-
 3 files changed, 25 insertions(+), 7 deletions(-)

diff --git a/export_dagmc_cmd/DAGMCExportCommand.cpp b/export_dagmc_cmd/DAGMCExportCommand.cpp
index fd1ae405a..99f89ddfb 100644
--- a/export_dagmc_cmd/DAGMCExportCommand.cpp
+++ b/export_dagmc_cmd/DAGMCExportCommand.cpp
@@ -164,27 +164,34 @@ bool DAGMCExportCommand::execute(CubitCommandData &data)
   rval = mdbImpl->write_file(filename.c_str());
   CHK_MB_ERR_RET("Error writing file: ",rval);
 
-  rval = teardown();
-  CHK_MB_ERR_RET("Error tearing down export command.",rval);
-  
+
   // if a PyNE material library is provided then try to process the mats
   if(pyne_mat_lib != "") {
     bool fatal_errors = false;
 
-    uwuw_preprocessor* uwuw_preproc = new uwuw_preprocessor(pyne_mat_lib, filename, filename, hdf5_path, verbose_warnings, fatal_errors);
+    uwuw_preprocessor* uwuw_preproc = new uwuw_preprocessor(pyne_mat_lib, mdbImpl, filename, hdf5_path, true, fatal_errors);
+    std::cout << __FILE__ << " : " << __LINE__ << std::endl;
     // process the materials
     uwuw_preproc->process_materials();
+    std::cout << __FILE__ << " : " << __LINE__ << std::endl;
 
     // process the tallies
     uwuw_preproc->process_tallies();
+    std::cout << __FILE__ << " : " << __LINE__ << std::endl;
 
     // write the material data
     uwuw_preproc->write_uwuw_materials();
+    std::cout << __FILE__ << " : " << __LINE__ << std::endl;
 
     // write the tally data
     uwuw_preproc->write_uwuw_tallies();
+    std::cout << __FILE__ << " : " << __LINE__ << std::endl;
+
   }
 
+  rval = teardown();
+  CHK_MB_ERR_RET("Error tearing down export command.",rval);
+  
   return result;
 }
 
@@ -222,8 +229,15 @@ moab::ErrorCode DAGMCExportCommand::parse_options(CubitCommandData &data, moab::
   data.get_string("pyne_mat_lib", pyne_mat_lib);
   if (pyne_mat_lib != "") {
     message << "Looking for the PyNE material Lib in " << pyne_mat_lib << std::endl;
-    data.get_string("hdf5_path",hdf5_path);
-    message << "hdf5 path set to " << hdf5_path << std::endl;
+    data.get_string("hdf5_path",hdf5);
+    if (hdf5 != "") {
+      hdf5_path = hdf5;
+    } else {
+      message << "hdf5 path not provided, falling back on default path"
+        << std::endl;
+    }
+
+    message << "hdf5 path set to " << hdf5 << std::endl;
   }
   else {
     message
diff --git a/export_dagmc_cmd/DAGMCExportCommand.hpp b/export_dagmc_cmd/DAGMCExportCommand.hpp
index ebbc625f7..966c19fc2 100644
--- a/export_dagmc_cmd/DAGMCExportCommand.hpp
+++ b/export_dagmc_cmd/DAGMCExportCommand.hpp
@@ -72,6 +72,7 @@ class DAGMCExportCommand: public CubitCommand
   bool make_watertight;
   std::string pyne_mat_lib;
   std::string hdf5_path;
+  std::string hdf5;
 
 
   int failed_curve_count;
diff --git a/script/build_plugin.sh b/script/build_plugin.sh
index 43ab86dd4..15bd3d7b5 100755
--- a/script/build_plugin.sh
+++ b/script/build_plugin.sh
@@ -48,7 +48,10 @@ make install
 cd ${PLUGIN_ABS_PATH}
 mkdir -pv DAGMC/bld
 cd DAGMC
-git clone https://github.com/svalinn/DAGMC -b develop
+git clone https://github.com/bam241/DAGMC -b preproc_plugin
+cd DAGMC
+git status
+cd ..
 cd bld
 cmake ../DAGMC -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
                -DMOAB_DIR=${PLUGIN_ABS_PATH}/moab \

From adca3fec371f78683a50fee3dcec904e6dc399ff Mon Sep 17 00:00:00 2001
From: Baptiste Mouginot <mouginot.baptiste@gmail.com>
Date: Wed, 28 Oct 2020 16:26:56 -0500
Subject: [PATCH 21/21] fixing verison of the script used

---
 script/build_plug_linux.sh |  2 +-
 script/build_plugin.sh     | 27 ++++++++++++++++-----------
 2 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/script/build_plug_linux.sh b/script/build_plug_linux.sh
index b2aac02e2..afd0dfd1d 100755
--- a/script/build_plug_linux.sh
+++ b/script/build_plug_linux.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 
 SCRIPTPATH=`dirname $(dirname $(realpath $0))`
-docker run -v "$SCRIPTPATH:/Trelis-plugin" -v "$2:/Trelis-sdk" -it $1 bash -c "/Trelis-plugin/script/build_plugin.sh $3"
\ No newline at end of file
+docker run -v "$SCRIPTPATH:/Trelis-plugin" -v "$2:/Trelis-sdk" -it $1 bash -c "/Trelis-plugin/script/build_plugin.sh $3; bash"
diff --git a/script/build_plugin.sh b/script/build_plugin.sh
index 15bd3d7b5..15bbddc20 100755
--- a/script/build_plugin.sh
+++ b/script/build_plugin.sh
@@ -5,6 +5,8 @@ dpkg -i Trelis-$1-Lin64.deb
 
 cd /opt
 tar -xzvf /Trelis-sdk/Trelis-SDK-$1-Lin64.tar.gz
+cd /opt/Trelis-16.5
+tar -xzvf /Trelis-sdk/Trelis-SDK-$1-Lin64.tar.gz
 
 apt-get update -y
 apt-get install -y autogen autoconf libtool libeigen3-dev libhdf5-dev patchelf gfortran git cmake
@@ -49,9 +51,6 @@ cd ${PLUGIN_ABS_PATH}
 mkdir -pv DAGMC/bld
 cd DAGMC
 git clone https://github.com/bam241/DAGMC -b preproc_plugin
-cd DAGMC
-git status
-cd ..
 cd bld
 cmake ../DAGMC -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
                -DMOAB_DIR=${PLUGIN_ABS_PATH}/moab \
@@ -73,13 +72,20 @@ git submodule update --init
 cd ${PLUGIN_ABS_PATH}
 mkdir -pv bld
 cd bld
-cmake ../Trelis-plugin -DCUBIT_ROOT=/opt/Trelis-17.1 \
+ls /opt/Trelis-${1::4}
+ls /opt/Trelis-*
+ls /opt
+cmake ../Trelis-plugin -DCUBIT_ROOT=/opt/Trelis-${1::4} \
                        -DDAGMC_DIR=${PLUGIN_ABS_PATH}/DAGMC \
                        -DCMAKE_BUILD_TYPE=Release \
                        -DCMAKE_INSTALL_PREFIX=${PLUGIN_ABS_PATH}
 make -j`grep -c processor /proc/cpuinfo`
 make install
-
+echo " cmake ../Trelis-plugin -DCubit_DIR=/opt/Trelis-${1::4} \
+                       -DCUBIT_ROOT=/opt/Trelis-${1::4} \
+                       -DDAGMC_DIR=${PLUGIN_ABS_PATH}/DAGMC \
+                       -DCMAKE_BUILD_TYPE=Release \
+                       -DCMAKE_INSTALL_PREFIX=${PLUGIN_ABS_PATH} "
 
 cd ${PLUGIN_ABS_PATH}
 mkdir -p pack/bin/plugins/svalinn
@@ -96,12 +102,11 @@ cp -pPv /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.100* .
 chmod 644 *
 
 # Set the RPATH to be the current directory for the DAGMC libraries
-patchelf --set-rpath /opt/Trelis-${1%.??}/bin/plugins/svalinn libMOAB.so
-patchelf --set-rpath /opt/Trelis-${1%.??}/bin/plugins/svalinn libdagmc.so
-patchelf --set-rpath /opt/Trelis-${1%.??}/bin/plugins/svalinn libmakeWatertight.so
-patchelf --set-rpath /opt/Trelis-${1%.??}/bin/plugins/svalinn libpyne_dagmc.so
-#patchelf --set-rpath /opt/Trelis-$1/bin/plugins libsvalinn_plugin.so
-patchelf --set-rpath /opt/Trelis-${1%.??}/bin/plugins/svalinn libuwuw.so
+patchelf --set-rpath /opt/Trelis-${1::4}/bin/plugins/svalinn libMOAB.so
+patchelf --set-rpath /opt/Trelis-${1::4}/bin/plugins/svalinn libdagmc.so
+patchelf --set-rpath /opt/Trelis-${1::4}/bin/plugins/svalinn libmakeWatertight.so
+patchelf --set-rpath /opt/Trelis-${1::4}/bin/plugins/svalinn libpyne_dagmc.so
+patchelf --set-rpath /opt/Trelis-${1::4}/bin/plugins/svalinn libuwuw.so
 
 # Create the Svalinn plugin tarball
 cd ..