First krino commit

PackagesList.cmake

@@ -112,6 +112,7 @@ TRIBITS_REPOSITORY_DEFINE_PACKAGES(
   Compadre              packages/compadre                 ST
   STK                   packages/stk                      PT # Depends on boost
   Percept               packages/percept                  PT # Depends on boost
+  Krino                 packages/krino                    PT # Depends on boost
   SCORECapf_zoltan      SCOREC/zoltan                     ST
   SCORECapf_stk         SCOREC/stk                        ST
   SCORECma              SCOREC/ma                         ST

packages/krino/CMakeLists.txt

@@ -0,0 +1,13 @@
+
+message("Building Krino as a Trilinos package")
+TRIBITS_PACKAGE(Krino)
+
+TRIBITS_ADD_DEBUG_OPTION()
+TRIBITS_ADD_SHOW_DEPRECATED_WARNINGS_OPTION()
+
+if (${Trilinos_ENABLE_Krino})
+  add_subdirectory(krino)
+  add_subdirectory(delete_small_elements)
+endif()
+
+TRIBITS_PACKAGE_POSTPROCESS()

packages/krino/LICENSE

@@ -0,0 +1,30 @@
+Copyright 2002 - 2008, 2010, 2011 National Technology & Engineering 
+Solutions of Sandia, LLC (NTESS). 
+
+Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
+retains certain rights in this software.
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, 
+   this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, 
+   this list of conditions and the following disclaimer in the documentation 
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors 
+   may be used to endorse or promote products derived from this software without 
+   specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

packages/krino/cmake/Dependencies.cmake

@@ -0,0 +1,8 @@
+SET(LIB_REQUIRED_DEP_PACKAGES SEACASIoss SEACASExodus STKBalance STKMath STKIO STKSearch STKTopology STKUtil STKTools STKEmend Percept Intrepid)
+SET(LIB_OPTIONAL_DEP_PACKAGES)
+SET(TEST_REQUIRED_DEP_PACKAGES Gtest STKUnit_test_utils)
+SET(TEST_OPTIONAL_DEP_PACKAGES)
+SET(LIB_REQUIRED_DEP_TPLS Boost)
+SET(LIB_OPTIONAL_DEP_TPLS MPI yaml-cpp)
+SET(TEST_REQUIRED_DEP_TPLS)
+SET(TEST_OPTIONAL_DEP_TPLS)

packages/krino/cmake_install_test/build_sierra_krino_as_Trilinos_package.sh

@@ -0,0 +1,108 @@
+#!/bin/sh
+
+function execute() {
+  stdbuf -o0 -e0 echo "% $@" ;
+  eval "$@" ;
+  if [ $? -ne 0 ] ; then
+    echo "'$@' failed.";
+    exit 1;
+  fi
+}
+
+function cd_to_new_dir()
+{
+    execute rm -rf $1
+    execute mkdir $1
+    execute cd $1
+}
+
+function exit_with_message()
+{
+    echo $1
+    exit 1
+}
+
+function make_and_install()
+{
+    make -j 16 || exit_with_message "Failed building $1"
+    make install || exit_with_message "Failed installing $1"
+}
+
+function build_yaml()
+{
+    productName=yaml
+
+    cd_to_new_dir ${output_dir}/${productName}
+    execute tar -xzf ${sierra_proj}/TPLs_src/spack/spack_tpls/yaml-cpp/*.tar.gz
+    cd_to_new_dir ${productName}_build
+
+    export CC=gcc
+    export CXX=g++
+    execute cmake -DCMAKE_BUILD_TYPE=${build_type^^} -DYAML_CPP_BUILD_TESTS=false -DCMAKE_INSTALL_PREFIX=../${productName}_install ../yaml-cpp
+    make_and_install $productName
+    unset CC
+    unset CXX
+}
+
+function build_trilinos_with_krino()
+{
+    productName=trilinos
+
+    trilinos_dir=${output_dir}/${productName}
+    if [ ! -d ${trilinos_dir} ] ; then
+      execute mkdir ${trilinos_dir}
+    fi
+    execute cd ${trilinos_dir}
+
+    if [ ! -d Trilinos ] ; then
+      execute git clone -b develop https://github.com/trilinos/Trilinos.git Trilinos
+    #else
+      #execute cd Trilinos
+      #execute git checkout develop
+      #execute git reset --hard origin/develop
+      #execute git pull
+      #execute cd ..
+    fi
+
+    if [ -d Trilinos/packages/krino ] ; then
+      execute rm -rf Trilinos/packages/krino;
+    fi
+    if [ ! -L Trilinos/packages/krino ] ; then
+      execute ln -s ${sierra_proj}/krino Trilinos/packages
+    fi
+
+    rm -rf ${productName}_install
+    cd_to_new_dir ${productName}_build
+
+    export TRILINOS_INSTALL_DIR=../${productName}_install
+    $sierra_proj/krino/cmake_install_test/run_cmake_krino
+    make_and_install $productName    
+}
+
+function runTests()
+{
+    cd $1
+    ctest -j 16 || exit_with_message "$2 tests failed"
+    cd ../..
+}
+
+sierra_proj=${SIERRA_PROJ:-${PWD}}
+output_dir=${OUTPUT_DIR:-${PWD}/../krino-cmake-testing}
+
+cuda_on_or_off=${CUDA:-OFF}
+build_type=${CMAKE_BUILD_TYPE:-release}
+date_suffix=`date +%F_%H-%M-%S`
+
+source $sierra_proj/krino/cmake_install_test/load_gcc_modules
+
+if [ ! -d ${output_dir} ] ; then
+  execute mkdir ${output_dir}
+fi
+
+build_yaml
+build_trilinos_with_krino
+
+#runTests morph/morph_build "Morph"
+#runTests morph_and_sgm/morph_and_sgm_build "Morph and SGM"
+#runTests morphWithExe/morphWithExe_build "MorphWithExe"
+

packages/krino/cmake_install_test/load_gcc_modules

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+module load cde/v2/cmake/3.19.2
+module load cde/v2/compiler/gcc/7.2.0
+module load cde/v2/gcc/7.2.0/openmpi/4.0.5
+module load cde/v2/gcc/7.2.0/netlib-lapack/3.8.0
+module load cde/v2/gcc/7.2.0/boost/1.73.0
+module load cde/v2/gcc/7.2.0/hdf5/1.10.6
+module load cde/v2/gcc/7.2.0/netcdf-c/4.7.3
+module load cde/v2/gcc/7.2.0/parallel-netcdf/1.12.1
+module load cde/v2/gcc/7.2.0/metis/5.1.0
+module load cde/v2/gcc/7.2.0/parmetis/4.0.3
+

packages/krino/cmake_install_test/run_cmake_krino

@@ -0,0 +1,52 @@
+#!/bin/bash
+
+trilinos_src_dir=${TRILINOS_DIR:-${PWD}/../Trilinos}
+build_dir=${BUILD_DIR:-${PWD}}
+build_type=${CMAKE_BUILD_TYPE:-release}
+trilinos_install_dir=${TRILINOS_INSTALL_DIR:-${PWD}/../trilinos_install_dir}
+
+yaml_install_dir=${YAML_INSTALL_DIR:-${build_dir}/../../yaml/yaml_install}
+
+printf "\nTRILINOS_DIR=${trilinos_src_dir}\n";
+printf "BUILD_DIR=${build_dir}\n";
+printf "CMAKE_BUILD_TYPE=${build_type}\n";
+printf "TRILINOS_INSTALL_DIR=${trilinos_install_dir}\n";
+printf "YAML_INSTALL_DIR=${yaml_install_dir}\n";
+printf "\nTo change these vars, set as env vars or pass to this script like 'VAR=value run_cmake_stk'\n\n";
+
+if [ ! -d ${trilinos_src_dir}/packages/seacas ] && [ ! -L ${trilinos_src_dir}/packages/seacas ] ; then
+  echo "Trilinos dir (${trilinos_src_dir}) doesn't have packages/seacas directory. If using a Sierra project, make a soft-link to Sierra's seacas directory.";
+  exit 1;
+fi
+if [ ! -d ${trilinos_src_dir}/packages/stk ] && [ ! -L ${trilinos_src_dir}/packages/stk ]; then
+  echo "Trilinos dir (${trilinos_src_dir}) doesn't have packages/stk directory. If using a Sierra project, make a soft-link to Sierra's stk directory.";
+  exit 1;
+fi
+if [ ! -d ${trilinos_src_dir}/packages/krino ] && [ ! -L ${trilinos_src_dir}/packages/krino ]; then
+  echo "Trilinos dir (${trilinos_src_dir}) doesn't have packages/krino directory. If using a Sierra project, make a soft-link to Sierra's krino directory.";
+  exit 1;
+fi
+
+mkdir -p $trilinos_install_dir
+mkdir -p $build_dir
+
+cd ${build_dir}
+
+# Cleanup old cache before we configure
+rm -rf CMakeFiles CMakeCache.txt
+
+cmake \
+-DCMAKE_INSTALL_PREFIX=$trilinos_install_dir \
+-DCMAKE_BUILD_TYPE=${build_type^^} \
+-DKrino_ENABLE_TESTS:BOOL=ON \
+-DTrilinos_ENABLE_Krino:BOOL=ON \
+-DTrilinos_ENABLE_Fortran:BOOL=ON \
+-DTPL_ENABLE_yaml-cpp=ON \
+-Dyaml-cpp_INCLUDE_DIRS=${yaml_install_dir}/include \
+-Dyaml-cpp_LIBRARY_DIRS=${yaml_install_dir}/lib \
+-DTPL_ENABLE_Boost:BOOL=ON \
+-DTPL_ENABLE_MPI=ON \
+-DTPL_ENABLE_Pnetcdf:BOOL=ON \
+-DTPL_ENABLE_HDF5:BOOL=ON \
+${trilinos_src_dir}/
+