sandialabs · gsjaardema · Mar 14, 2025 · Mar 14, 2025 · Mar 14, 2025 · Mar 14, 2025
diff --git a/packages/seacas/libraries/aprepro_lib/strings.cc b/packages/seacas/libraries/aprepro_lib/strings.cc
@@ -62,8 +62,10 @@ std::vector<std::string> build_strings()
   strings.emplace_back(R"({cd = tand(180/4)}	{180-4*atand(cd)}	$ tan(180/4))");
   strings.emplace_back(R"()");
   strings.emplace_back(R"(Test max, min, sign, dim, abs)");
-  strings.emplace_back(R"({pmin = min(0.5, 1.0)}	{nmin = min(-0.5, -1.0)} $ Should be 0.5, -1)");
-  strings.emplace_back(R"({pmax = max(0.5, 1.0)}	{nmax = max(-0.5, -1.0)} $ Should be 1.0, -0.5)");
+  strings.emplace_back(
+      R"({pmin = min(0.5, 1.0)}	{nmin = min(-0.5, -1.0)} $ Should be 0.5, -1)");
+  strings.emplace_back(
+      R"({pmax = max(0.5, 1.0)}	{nmax = max(-0.5, -1.0)} $ Should be 1.0, -0.5)");
   strings.emplace_back(R"({zero = 0} {sign(0.5, zero) + sign(0.5, -zero)}	$ Should be 0 1)");
   strings.emplace_back(
       R"({nonzero = 1} {sign(0.5, nonzero) + sign(0.5, -nonzero)} $ Should be 1 0)");

diff --git a/packages/seacas/libraries/exodus/CMakeLists.txt b/packages/seacas/libraries/exodus/CMakeLists.txt
@@ -7,8 +7,6 @@ endif()
 TRIBITS_INCLUDE_DIRECTORIES(
   "${CMAKE_CURRENT_SOURCE_DIR}/include"
 )
-message("installing shared exodus to: ${CMAKE_INSTALL_LIBDIR}")
-
 FILE(GLOB SOURCES src/ex_*.c)
 
 if (NOT ${PACKAGE_NAME}_HIDE_DEPRECATED_CODE)
@@ -51,7 +49,6 @@ if (SEACASExodus_ENABLE_SHARED)
       # This keeps the library out of the `all_libs` targets...
       set_target_properties(exodus_shared PROPERTIES TRIBITS_TESTONLY_LIB TRUE)
       set_target_properties(exodus_shared PROPERTIES OUTPUT_NAME exodus)
-      message("installing shared exodus to: ${CMAKE_INSTALL_LIBDIR}")
       INSTALL(TARGETS exodus_shared DESTINATION ${CMAKE_INSTALL_LIBDIR})
    endif()
 endif()
@@ -76,7 +73,6 @@ if (SEACASExodus_ENABLE_STATIC)
    # Create a symbolic link from libexodus.a to libexoIIv2c.a -- do only for static lib
    InstallSymLink(libexodus.a ${CMAKE_INSTALL_PREFIX}/lib/libexoIIv2c.a)
 endif()
-message("installing shared exodus to: ${CMAKE_INSTALL_LIBDIR}")
 
 if (${CMAKE_PROJECT_NAME} STREQUAL "Seacas")
    # add a target to generate API documentation with Doxygen
@@ -91,7 +87,6 @@ if (${CMAKE_PROJECT_NAME} STREQUAL "Seacas")
      endif(DOXYGEN_FOUND)
    endif()
 endif()
-message("installing shared exodus to: ${CMAKE_INSTALL_LIBDIR}")
 
 TRIBITS_ADD_TEST_DIRECTORIES(test)
 

diff --git a/packages/seacas/libraries/ioss/src/Ioss_DatabaseIO.h b/packages/seacas/libraries/ioss/src/Ioss_DatabaseIO.h
@@ -289,7 +289,7 @@ namespace Ioss {
     /** \brief If a database type supports internal change sets, open the change set
      *         specified [zero-based] index
      *
-     *  \param[in] child_index The [zero-based] index of the internal change set to open.
+     *  \param[in] set_index The [zero-based] index of the internal change set to open.
      *  \returns True if successful.
      */
     bool open_internal_change_set(int set_index)

diff --git a/packages/seacas/libraries/ioss/src/Ioss_Utils.h b/packages/seacas/libraries/ioss/src/Ioss_Utils.h
@@ -506,11 +506,11 @@ namespace Ioss {
      *  \param[in] sb Compute the offset for element sides in this SideBlock
      *  \returns The offset.
      */
+    IOSS_NODISCARD static int64_t get_side_offset(const Ioss::SideBlock *sb);
+
     IOSS_NODISCARD static int64_t get_side_offset(const Ioss::ElementTopology *parent_topo,
                                                   const Ioss::ElementTopology *side_topo);
 
-    IOSS_NODISCARD static int64_t get_side_offset(const Ioss::SideBlock *sb);
-
     IOSS_NODISCARD static unsigned int hash(const std::string &name);
 
     IOSS_NODISCARD static double timer();

diff --git a/packages/seacas/libraries/ioss/src/heartbeat/Iohb_Layout.C b/packages/seacas/libraries/ioss/src/heartbeat/Iohb_Layout.C
@@ -1,4 +1,4 @@
-// Copyright(C) 1999-2022, 2024 National Technology & Engineering Solutions
+// Copyright(C) 1999-2022, 2024, 2025 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.
 //
@@ -36,10 +36,12 @@ namespace Iohb {
     }
   }
 
+#ifndef DOXYGEN_SKIP_THIS
   template void Layout::add(const std::string &name, const std::string &value);
   template void Layout::add(const std::string &name, const int &value);
   template void Layout::add(const std::string &name, const int64_t &value);
   template void Layout::add(const std::string &name, const size_t &value);
+#endif
 
   // Ideally, this would be in the include file, but when building in Sierra, we
   // need to keep all `fmt` includes out of the include file due to some TPLs
@@ -71,9 +73,11 @@ namespace Iohb {
     }
   }
 
+#ifndef DOXYGEN_SKIP_THIS
   template void Layout::add(const std::string &name, const std::vector<int> &value);
   template void Layout::add(const std::string &name, const std::vector<int64_t> &value);
   template void Layout::add(const std::string &name, const std::vector<size_t> &value);
+#endif
 
   template <typename T> void Layout::add(const std::string &name, const std::vector<T> &value)
   {

diff --git a/packages/zoltan/CMakeLists.txt b/packages/zoltan/CMakeLists.txt
@@ -49,7 +49,7 @@ OPTION(${PACKAGE_NAME}_ENABLE_CPPDRIVER
   "Enable C++ driver for ${PACKAGE_NAME}."
   ${${PROJECT_NAME}_ENABLE_CXX} )
 
-IF (${PROJECT_NAME}_ENABLE_CXX)
+IF (${PROJECT_NAME}_ENABLE_CXX) 
   SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DMPICH_IGNORE_CXX_SEEK")
 ENDIF()
 

diff --git a/packages/zoltan/COPYRIGHT b/packages/zoltan/COPYRIGHT
@@ -0,0 +1,9 @@
+
+Zoltan Toolkit for Load-balancing, Partitioning, Ordering and Coloring
+                    Copyright (c) 2012 NTESS
+
+Copyright 2012 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.
+
+Copyright the Zoltan contributors.
diff --git a/packages/zoltan/COPYRIGHT_AND_LICENSE b/packages/zoltan/COPYRIGHT_AND_LICENSE
diff --git a/packages/zoltan/LICENSE b/packages/zoltan/LICENSE
@@ -0,0 +1,31 @@
+SPDX-License-Identifier: BSD-3-Clause
+
+Copyright (c) 2012 NTESS and the Zoltan contributors.
+
+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.
diff --git a/packages/zoltan/Makefile.am b/packages/zoltan/Makefile.am
@@ -1,47 +1,3 @@
-# @HEADER
-#
-########################################################################
-#
-#  Zoltan Toolkit for Load-balancing, Partitioning, Ordering and Coloring
-#                  Copyright 2012 Sandia Corporation
-#
-# Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
-# 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 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.
-#
-# Questions? Contact Karen Devine	kddevin@sandia.gov
-#                    Erik Boman	        egboman@sandia.gov
-#
-########################################################################
-#
-# @HEADER
-
 
 ## #######################################################################
 ## Options to automake (rarely used - don't worry about it)

diff --git a/packages/zoltan/Makefile.export.zoltan.in b/packages/zoltan/Makefile.export.zoltan.in
@@ -10,7 +10,7 @@ ZOLTAN_INCLUDES = -I@abs_top_builddir@/src/include -I@abs_top_srcdir@/src/includ
 #@BUILD_FORTRAN90DRIVER_FALSE@ZFORLIBS = $(ZFLIBS)
 ZFORLIBS = $(ZFLIBS)
 
-ZOLTAN_LIBS = @LDFLAGS@ -L@abs_top_builddir@/src -lzoltan @LIBS@ $(ZFORLIBS) $(SIMPI_LIBS)
+ZOLTAN_LIBS = @LDFLAGS@ -L@abs_top_builddir@/src -lzoltan @LIBS@ $(ZFORLIBS) $(SIMPI_LIBS) 
 
 ZOLTAN_LIBRARY_INCLUDES = -I@abs_top_builddir@/src/include -I@abs_top_srcdir@/src/include -I@abs_top_srcdir@/src/all -I@abs_top_srcdir@/src/coloring -I@abs_top_srcdir@/src/ha -I@abs_top_srcdir@/src/hier -I@abs_top_srcdir@/src/hsfc -I@abs_top_srcdir@/src/lb -I@abs_top_srcdir@/src/oct -I@abs_top_srcdir@/src/order -I@abs_top_srcdir@/src/par -I@abs_top_srcdir@/src/params -I@abs_top_srcdir@/src/tpls -I@abs_top_srcdir@/src/ccolamd -I@abs_top_srcdir@/src/phg -I@abs_top_srcdir@/src/rcb -I@abs_top_srcdir@/src/reftree -I@abs_top_srcdir@/src/timer -I@abs_top_srcdir@/src/Utilities/Communication -I@abs_top_srcdir@/src/Utilities/Timer -I@abs_top_srcdir@/src/Utilities/DDirectory -I@abs_top_srcdir@/src/Utilities/Memory -I@abs_top_srcdir@/src/Utilities/shared -I@abs_top_srcdir@/src/zz -I@abs_top_srcdir@/src/graph -I@abs_top_srcdir@/src/matrix -I@abs_top_srcdir@/src/simple $(SIMPI_INCDIR)
 
@@ -59,7 +59,7 @@ ZOLTAN_DEFS = @DEFS@
 # Fortran compilation flags
 @BUILD_FORTRAN90DRIVER_TRUE@ZOLTAN_FCFLAGS = @FCFLAGS@
 @USE_FORTRAN_TRUE@ZOLTAN_FFLAGS = @FFLAGS@
-
+ 
 # C compilation flags
 ZOLTAN_CFLAGS = @CFLAGS@
 
@@ -77,3 +77,4 @@ ZOLTAN_LDFLAGS = @LDFLAGS@
 ############################################################################
 
 ZOLTAN_RANLIB = @RANLIB@
+
diff --git a/packages/zoltan/Makefile.in b/packages/zoltan/Makefile.in
@@ -15,49 +15,6 @@
 
 @SET_MAKE@
 
-# @HEADER
-#
-########################################################################
-#
-#  Zoltan Toolkit for Load-balancing, Partitioning, Ordering and Coloring
-#                  Copyright 2012 Sandia Corporation
-#
-# Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
-# 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 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.
-#
-# Questions? Contact Karen Devine	kddevin@sandia.gov
-#                    Erik Boman	        egboman@sandia.gov
-#
-########################################################################
-#
-# @HEADER
 VPATH = @srcdir@
 pkgdatadir = $(datadir)/@PACKAGE@
 pkgincludedir = $(includedir)/@PACKAGE@
@@ -300,7 +257,7 @@ ZOLTAN_TESTS = \
     test/runtests \
     test/ctest_zoltan.pl \
     test/ch_simple \
-    test/hg_simple
+    test/hg_simple 
 
 ZOLTAN_DOCS = \
     doc/Zoltan_html/Zoltan.html \
@@ -416,7 +373,7 @@ ZOLTAN_DOCS = \
     doc/Zoltan_html/ug_html/ug_util.html \
     doc/Zoltan_html/ug_html/ug_util_comm.html \
     doc/Zoltan_html/ug_html/ug_util_dd.html \
-    doc/Zoltan_html/ug_html/ug_util_mem.html
+    doc/Zoltan_html/ug_html/ug_util_mem.html 
 
 ZOLTAN_SAMPLE = \
        SampleConfigurationScripts/mac_osX_no_fortran \
@@ -446,11 +403,11 @@ EXTRA_DIST = config/generate-makeoptions.pl \
        Disclaimer GNU_Lesser_GPL.txt Known_Problems VERSION \
        $(ZOLTAN_DOCS) $(ZOLTAN_SAMPLE) $(ZOLTAN_TESTS)
 
-AUX_DIST = config/install-sh config/missing config/mkinstalldirs
+AUX_DIST = config/install-sh config/missing config/mkinstalldirs 
 MAINTAINERCLEANFILES = Makefile.in aclocal.m4 autom4te.cache/* \
 	configure config.status config.log \
 	src/common/config-h.in src/common/stamp-h.in \
-	$(AUX_DIST)
+	$(AUX_DIST) 
 
 
 #We now build tests and examples through separate make targets, rather than
@@ -460,11 +417,11 @@ MAINTAINERCLEANFILES = Makefile.in aclocal.m4 autom4te.cache/* \
 #tarball.
 
 #Add this later
-@SUB_TEST_TRUE@TEST_SUBDIR =
+@SUB_TEST_TRUE@TEST_SUBDIR = 
 @SUB_EXAMPLE_TRUE@EXAMPLE_SUBDIR = example
 @HAVE_MPI_FALSE@SIMPI_SUBDIR = siMPI
-@HAVE_MPI_TRUE@SIMPI_SUBDIR =
-SUBDIRS = $(SIMPI_SUBDIR) src $(EXAMPLE_SUBDIR) $(TEST_SUBDIR)
+@HAVE_MPI_TRUE@SIMPI_SUBDIR = 
+SUBDIRS = $(SIMPI_SUBDIR) src $(EXAMPLE_SUBDIR) $(TEST_SUBDIR) 
 TRILINOS_HOME_DIR = @abs_top_srcdir@/../..
 TRILINOS_BUILD_DIR = @abs_top_builddir@/../..
 TRILINOS_MPI_MAX_PROC = 4
@@ -514,7 +471,7 @@ src/include/Zoltan_config.h: src/include/stamp-h1
 src/include/stamp-h1: $(top_srcdir)/src/include/Zoltan_config.h.in $(top_builddir)/config.status
 	@rm -f src/include/stamp-h1
 	cd $(top_builddir) && $(SHELL) ./config.status src/include/Zoltan_config.h
-$(top_srcdir)/src/include/Zoltan_config.h.in: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)
+$(top_srcdir)/src/include/Zoltan_config.h.in: @MAINTAINER_MODE_TRUE@ $(am__configure_deps) 
 	($(am__cd) $(top_srcdir) && $(AUTOHEADER))
 	rm -f src/include/stamp-h1
 	touch $@
@@ -1049,7 +1006,7 @@ runtests-mpi :
   --verbosity=1 \
   --packages=zoltan
 
-@USING_EXPORT_MAKEFILES_TRUE@install-exec-hook:
+@USING_EXPORT_MAKEFILES_TRUE@install-exec-hook:	
 @USING_EXPORT_MAKEFILES_TRUE@	mkdir -p $(DESTDIR)$(includedir)
 @USING_EXPORT_MAKEFILES_TRUE@	cp $(top_builddir)/Makefile.export.zoltan $(DESTDIR)$(includedir)/.
 @USING_EXPORT_MAKEFILES_TRUE@	$(PERL_EXE) $(top_srcdir)/config/replace-install-prefix.pl \