Merge 'trilinos/Trilinos:develop' (b06bad0) into 'tcad-charon/Trilino…

…s:develop' (8380623).

* trilinos-develop: (81 commits)
  epetra: Fix for unguarded macro defined in SLU
  epetra: Fix for unguarded SuperLU macro
  MueLu: fixing an issue in the structured region driver data
  Xpetra: ETI conversion for Xpetra_TpetraExport.hpp
  Updates to handle when a non RK stepper observer is passed in. (trilinos#5324)
  Xpetra: add forced map writing to unit test
  MueLu: updating some tests/unit_tests, see issue trilinos#5310
  Xpetra: add option to force writing of all maps
  Fixes to make stk build when BoostLib is not enabled.
  Add Intel 18.0.5 compiler to ATDM environment.
  Tpetra: Fix trilinos#4627
  Xpetra: don't write maps unnecessarily
  Fix trilinos#5151.
  Fix stk cmake files to disable unit and doc tests that depend on STKNGP_TEST if STKNGP_TEST is not enabled.
  MueLu: removing the Epetra path tests for unit-tests-kokkos, see issue trilinos#4325
  Xpetra: fix MultiVector unit-test for Epetra=OFF configuration, see issue trilinos#5300
  fix another type of quoting error
  TrilinosCouplings: More updates for Avatar-as-external-package
  Correct shell quoting in the package file replacement for python
  SEACAS: bug fix for may snapshot
  ...

.gitignore

@@ -153,3 +153,6 @@ rsync.*
 # Eclipse IDE
 .project
 .settings/
+
+# pycharm ide
+.idea

PackagesList.cmake

@@ -76,6 +76,7 @@ TRIBITS_REPOSITORY_DEFINE_PACKAGES(
   SCORECmds             SCOREC/mds                        ST
   SCORECparma           SCOREC/parma                      ST
   SCORECspr             SCOREC/spr                        ST
+  AvatarT               packages/avatart                  EX
   Zoltan                packages/zoltan                   PT
   Shards                packages/shards                   PT
   GlobiPack             packages/globipack                PT
@@ -143,7 +144,7 @@ TRIBITS_REPOSITORY_DEFINE_PACKAGES(
   )
 
 # Allow builds even if some packages are missing
-
+TRIBITS_ALLOW_MISSING_EXTERNAL_PACKAGES(AvatarT)
 TRIBITS_ALLOW_MISSING_EXTERNAL_PACKAGES(SCOREC)
 TRIBITS_ALLOW_MISSING_EXTERNAL_PACKAGES(SCOREClion)
 TRIBITS_ALLOW_MISSING_EXTERNAL_PACKAGES(SCORECgmi)
@@ -158,6 +159,7 @@ TRIBITS_ALLOW_MISSING_EXTERNAL_PACKAGES(SCORECapf_stk)
 TRIBITS_ALLOW_MISSING_EXTERNAL_PACKAGES(SCORECapf_zoltan)
 TRIBITS_ALLOW_MISSING_EXTERNAL_PACKAGES(SCORECma)
 TRIBITS_ALLOW_MISSING_EXTERNAL_PACKAGES(SCORECpumi)
+TRIBITS_ALLOW_MISSING_EXTERNAL_PACKAGES(Avatar)
 TRIBITS_ALLOW_MISSING_EXTERNAL_PACKAGES(MOOCHO)
 TRIBITS_ALLOW_MISSING_EXTERNAL_PACKAGES(Sundance)
 TRIBITS_ALLOW_MISSING_EXTERNAL_PACKAGES(CTrilinos)

TPLsList.cmake

@@ -164,6 +164,7 @@ TRIBITS_REPOSITORY_DEFINE_TPLS(
   Avatar          "cmake/TPLs/"    EX
   pebbl           "cmake/TPLs/"    EX
   MAGMASparse     "cmake/TPLs/"    EX
+  Check           "cmake/TPLs/"    EX
   )
 
 # NOTES:

cmake/ExtraRepositoriesList.cmake

@@ -80,6 +80,7 @@ TRIBITS_PROJECT_DEFINE_EXTRA_REPOSITORIES(
   ForTrilinos_repo  packages/ForTrilinos  GIT  ${Trilinos_REPOS_URL_BASE}ForTrilinos  NOPACKAGES  EX
   Optika_repo  packages/optika  GIT  ${Trilinos_REPOS_URL_BASE}optika  NOPACKAGES  Nightly
   Mesquite_repo  packages/mesquite  GIT  ${Trilinos_REPOS_URL_BASE}mesquite  NOPACKAGES  Nightly
+  Avatar_repo packages/avatar GIT gitlab.sandia.gov/mhoemme/avatar.git NOPACKAGES EX 
   preCopyrightTrilinos  ""  GIT  software.sandia.gov:/space/git/preCopyrightTrilinos  ""  Continuous
   TerminalApplication  ""  GIT  software.sandia.gov:/space/git/TerminalApplication  ""   EX 
   )

cmake/TPLs/FindTPLCheck.cmake

@@ -0,0 +1,64 @@
+# @HEADER
+# ************************************************************************
+#
+#            Trilinos: An Object-Oriented Solver Framework
+#                 Copyright (2001) Sandia Corporation
+#
+#
+# Copyright (2001) Sandia Corporation. Under the terms of Contract
+# DE-AC04-94AL85000, there is a non-exclusive license for use of this
+# work by or on behalf of the U.S. Government.  Export of this program
+# may require a license from the United States Government.
+#
+# 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.
+#
+# 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 Corporation nor the names of the
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "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 SANDIA CORPORATION OR THE
+# 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.
+#
+# NOTICE:  The United States Government is granted for itself and others
+# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
+# license in this data to reproduce, prepare derivative works, and
+# perform publicly and display publicly.  Beginning five (5) years from
+# July 25, 2001, the United States Government is granted for itself and
+# others acting on its behalf a paid-up, nonexclusive, irrevocable
+# worldwide license in this data to reproduce, prepare derivative works,
+# distribute copies to the public, perform publicly and display
+# publicly, and to permit others to do so.
+#
+# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
+# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
+# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR
+# RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY
+# INFORMATION, APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS
+# THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS.
+#
+# ************************************************************************
+# @HEADER
+
+
+TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( Check
+  REQUIRED_HEADERS check.h check_stdint.h libcompat.h
+  REQUIRED_LIBS_NAMES check compat
+  )
+

cmake/ctest/drivers/geminga/cron_driver.sh

@@ -81,10 +81,8 @@ module load sems-boost/1.58.0/base
 module load sems-python/2.7.9
 module load sems-zlib/1.2.8/base
 module load kokkos-cuda/8.0.44
-module load kokkos-openmpi/1.8.7/cuda
+module load kokkos-openmpi/2.0.1/cuda
 module load sems-superlu/4.3
-module load sems-hdf5/1.8.12/parallel
-module load sems-netcdf/4.4.1/exo_parallel
 # See Trilinos github issue #2115.
 export OMPI_CXX=/home/jhu/code/trilinos-test/trilinos/packages/kokkos/bin/nvcc_wrapper
 
@@ -109,10 +107,8 @@ $SCRIPT_DIR/../cron_driver.py
 #module unload cuda
 #module unload gcc
 #module unload openmpi
-module load sems-netcdf/4.4.1/exo_parallel
-module unload sems-hdf5/1.8.12/parallel
 module load sems-superlu/4.3
-module unload kokkos-openmpi/1.8.7/cuda
+module unload kokkos-openmpi/2.0.1/cuda
 module unload kokkos-nvcc_wrapper/1
 module unload kokkos-cuda/8.0.44
 module unload sems-zlib/1.2.8/base

cmake/ctest/drivers/lightsaber/CMakeLists.txt

@@ -0,0 +1,11 @@
+TRILINOS_DRIVER_SETUP()
+
+TRILINOS_DRIVER_ADD_DASHBOARD(
+  SERIAL_RELEASE_DEFAULT
+  ctest_linux_experimental_mpi_release_avatar_lightsaber.cmake
+  CTEST_INSTALLER_TYPE release
+  RUN_SERIAL
+  TIMEOUT_MINUTES 330
+  )
+
+TRILINOS_ADD_REQUIRED_CMAKE_INSTALLS()

cmake/ctest/drivers/lightsaber/TrilinosCTestDriverCore.lightsaber.gcc.cmake

@@ -0,0 +1,129 @@
+# @HEADER
+# ************************************************************************
+#
+#            Trilinos: An Object-Oriented Solver Framework
+#                 Copyright (2001) Sandia Corporation
+#
+#
+# Copyright (2001) Sandia Corporation. Under the terms of Contract
+# DE-AC04-94AL85000, there is a non-exclusive license for use of this
+# work by or on behalf of the U.S. Government.  Export of this program
+# may require a license from the United States Government.
+#
+# 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 Corporation nor the names of the
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "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 SANDIA CORPORATION OR THE
+# 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.
+#
+# NOTICE:  The United States Government is granted for itself and others
+# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
+# license in this data to reproduce, prepare derivative works, and
+# perform publicly and display publicly.  Beginning five (5) years from
+# July 25, 2001, the United States Government is granted for itself and
+# others acting on its behalf a paid-up, nonexclusive, irrevocable
+# worldwide license in this data to reproduce, prepare derivative works,
+# distribute copies to the public, perform publicly and display
+# publicly, and to permit others to do so.
+#
+# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
+# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
+# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR
+# RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY
+# INFORMATION, APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS
+# THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS.
+#
+# ************************************************************************
+# @HEADER
+
+
+INCLUDE("${CTEST_SCRIPT_DIRECTORY}/../../TrilinosCTestDriverCore.cmake")
+
+#
+# Platform/compiler specific options for rocketman using gcc
+#
+
+MACRO(TRILINOS_SYSTEM_SPECIFIC_CTEST_DRIVER)
+
+  # Base of Trilinos/cmake/ctest then BUILD_DIR_NAME
+
+  IF(COMM_TYPE STREQUAL MPI)
+    string(TOUPPER $ENV{SEMS_MPI_NAME} UC_MPI_NAME)
+    SET(BUILD_DIR_NAME ${UC_MPI_NAME}-$ENV{SEMS_MPI_VERSION}_${BUILD_TYPE}_${BUILD_NAME_DETAILS})
+  ELSE()
+    SET(BUILD_DIR_NAME ${COMM_TYPE}-${BUILD_TYPE}_${BUILD_NAME_DETAILS})
+  ENDIF()
+
+
+  SET(CTEST_DASHBOARD_ROOT  "${TRILINOS_CMAKE_DIR}/../../${BUILD_DIR_NAME}" )
+  SET(CTEST_NOTES_FILES     "${CTEST_SCRIPT_DIRECTORY}/${CTEST_SCRIPT_NAME}" )
+  SET(CTEST_BUILD_FLAGS     "-j14 -i" )
+
+  SET_DEFAULT(CTEST_PARALLEL_LEVEL                  "14" )
+  SET_DEFAULT(Trilinos_ENABLE_SECONDARY_TESTED_CODE ON)
+  SET(Trilinos_CTEST_DO_ALL_AT_ONCE FALSE)
+  SET_DEFAULT(Trilinos_EXCLUDE_PACKAGES             ${EXTRA_EXCLUDE_PACKAGES} TriKota Optika)
+
+  SET(EXTRA_SYSTEM_CONFIGURE_OPTIONS
+    "-DBUILD_SHARED_LIBS=ON"
+    "-DCMAKE_BUILD_TYPE=${BUILD_TYPE}"
+    "-DCMAKE_VERBOSE_MAKEFILE=ON"
+
+    "-DTrilinos_ENABLE_COMPLEX:BOOL=OFF"
+    "-DTrilinos_ENABLE_Fortran=OFF"
+
+    "-DSuperLU_INCLUDE_DIRS=$ENV{SEMS_SUPERLU_INCLUDE_PATH}"
+    "-DSuperLU_LIBRARY_DIRS=$ENV{SEMS_SUPERLU_LIBRARY_PATH}"
+    "-DSuperLU_LIBRARY_NAMES=superlu"
+
+    ### PACKAGE CONFIGURATION ###
+
+    ### MISC ###
+    "-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON"
+    )
+
+  SET_DEFAULT(COMPILER_VERSION "$ENV{SEMS_COMPILER_NAME}-$ENV{SEMS_COMPILER_VERSION}")
+
+  # Ensure that MPI is on for all parallel builds that might be run.
+  IF(COMM_TYPE STREQUAL MPI)
+
+    SET(EXTRA_SYSTEM_CONFIGURE_OPTIONS
+        ${EXTRA_SYSTEM_CONFIGURE_OPTIONS}
+        "-DTPL_ENABLE_MPI=ON"
+            "-DMPI_BASE_DIR:PATH=$ENV{SEMS_OPENMPI_ROOT}"
+            "-DMPI_EXEC_POST_NUMPROCS_FLAGS:STRING=--bind-to\\\;socket\\\;--map-by\\\;socket"
+       )
+
+    SET(CTEST_MEMORYCHECK_COMMAND_OPTIONS
+        "--gen-suppressions=all --error-limit=no --log-file=nightly_suppressions.txt" ${CTEST_MEMORYCHECK_COMMAND_OPTIONS} )
+
+  ELSE()
+
+    SET( EXTRA_SYSTEM_CONFIGURE_OPTIONS
+      ${EXTRA_SYSTEM_CONFIGURE_OPTIONS}
+      "-DCMAKE_CXX_COMPILER=$ENV{SEMS_COMPILER_ROOT}/bin/g++"
+      "-DCMAKE_C_COMPILER=$ENV{SEMS_COMPILER_ROOT}/bin/gcc"
+      )
+
+  ENDIF()
+
+  TRILINOS_CTEST_DRIVER()
+
+ENDMACRO()

cmake/ctest/drivers/lightsaber/cron_driver.csh

@@ -0,0 +1,71 @@
+#!/bin/csh
+
+echo
+echo "Starting nightly Trilinos development testing on dorksaber: `date`"
+echo
+
+#
+# TrilinosDriver settings:
+#
+
+setenv TDD_PARALLEL_LEVEL 2
+
+# Trilinos settings:
+#
+
+# Submission mode for the *TrilinosDriver* dashboard
+setenv TDD_CTEST_TEST_TYPE Nightly
+
+
+# Machine specific environment
+#
+
+setenv TDD_HTTP_PROXY "http://wwwproxy.sandia.gov:80"
+setenv TDD_HTTPS_PROXY "https://wwwproxy.sandia.gov:80"
+setenv http_proxy "http://wwwproxy.sandia.gov:80"
+setenv https_proxy "https://wwwproxy.sandia.gov:80"
+setenv TDD_FORCE_CMAKE_INSTALL 1
+setenv TDD_DEBUG_VERBOSE 1
+
+source ~/.cshrc
+
+
+# If you update the list of modules, go to ~/code/trilinos-test/trilinos/ and
+# do "git pull". Otherwise, the tests could fail on the first night, as we
+# would first run old cron_driver.sh and only then pull
+
+# ===========================================================================
+setenv CTEST_CONFIGURATION "default"
+module purge
+module load sems-env
+module load sems-cmake/3.10.3
+module load sems-gcc/5.3.0
+module load sems-openmpi/1.10.1
+module load sems-superlu/4.3/base
+
+# Remove colors (-fdiagnostics-color) from OMPI flags
+# It may result in non-XML characters on the Dashboard
+#setenv OMPI_CFLAGS="`echo $OMPI_CFLAGS | sed 's/-fdiagnostics-color//'`"
+#setenv OMPI_CXXFLAGS="`echo $OMPI_CXXFLAGS | sed 's/-fdiagnostics-color//'`"
+
+echo "Configuration = $CTEST_CONFIGURATION"
+env
+
+setenv OMP_NUM_THREADS 2
+
+
+
+# Machine independent cron_driver:
+setenv SCRIPT_DIR `dirname "$0"`
+echo "SCRIPT_DIR = " $SCRIPT_DIR
+$SCRIPT_DIR/../cron_driver.py
+
+module unload sems-superlu/4.3/base
+module unload sems-openmpi/1.10.1
+module unload sems-gcc/5.3.0
+module unload sems-cmake/3.10.3
+# ===========================================================================
+
+echo
+echo "Ending nightly Trilinos development testing on dorksaber: `date`"
+echo

cmake/ctest/drivers/lightsaber/crontab

@@ -0,0 +1,31 @@
+SHELL=/bin/bash
+# * * * * *  command to execute
+# │ │ │ │ │
+# │ │ │ │ │
+# │ │ │ │ └───── day of week (0 - 6) (0 to 6 are Sunday to Saturday, or use names; 7 is Sunday, the same as 0)
+# │ │ │ └────────── month (1 - 12)
+# │ │ └─────────────── day of month (1 - 31)
+# │ └──────────────────── hour (0 - 23)
+# └───────────────────────── min (0 - 59)
+
+# MIN HOUR DAY MONTH
+
+# nightly tests
+
+0  22 * * * cd /home/nightlyTesting/Trilinos/cmake/ctest/drivers/lightsaber; git pull ; ./cron_driver.csh >&! /home/nightlyTesting/cron_driver.log; cd /home/nightlyTesting; /home/nightlyTesting/Trilinos/cmake/ctest/drivers/rocketman/sendTestSummary.sh cron_driver.log 
+
+#
+#@reboot /home/jhu/bin/send-reboot-email.sh
+
+
+#description of fields
+#minute This controls what minute of the hour the command will run on,
+#         and is between '0' and '59'
+#hour   This controls what hour the command will run on, and is specified in
+#         the 24 hour clock, values must be between 0 and 23 (0 is midnight)
+#dom    This is the Day of Month, that you want the command run on, e.g. to
+#         run a command on the 19th of each month, the dom would be 19.
+#month  This is the month a specified command will run on, it may be specified
+#         numerically (0-12), or as the name of the month (e.g. May)
+#dow    This is the Day of Week that you want a command to be run on, it can
+#         also be numeric (0-7) or as the name of the day (e.g. sun).