Pull request #513: update version numbers

Merge in SUNDIALS/sunrepo from release/6.1.0 to develop Squashed commit of the following: commit 57838f0 Author: David J. Gardner <[email protected]> Date: Tue Jan 11 22:42:29 2022 -0800 reorder recent changes commit 885c3e4 Author: David J. Gardner <[email protected]> Date: Tue Jan 11 16:29:37 2022 -0800 add comments, move openmp offload up commit c97ea12 Author: Balos, Cody Joe <[email protected]> Date: Tue Jan 11 12:34:58 2022 -0800 find MPI and OpenMP first commit 60e9ad0 Author: David J. Gardner <[email protected]> Date: Sat Jan 8 10:20:10 2022 -0800 replace CLOCK_MONOTONIC_RAW with CLOCK_MONOTONIC commit 5047ac0 Author: David J. Gardner <[email protected]> Date: Fri Jan 7 17:06:58 2022 -0800 update UG year in bib file commit 723116f Author: David J. Gardner <[email protected]> Date: Fri Jan 7 17:00:47 2022 -0800 udpate CHANGELOG/recent changes versions commit d5ec1a2 Author: Balos, Cody Joe <[email protected]> Date: Fri Jan 7 14:53:27 2022 -0800 update version numbers
LLNL · Jan 12, 2022 · 840fc4d · 840fc4d
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,12 +1,6 @@
 # SUNDIALS Changelog
 
-## Changes to SUNDIALS in release x.x.x
-
-Additionally export `SUNDIALS::<lib>` targets with no static/shared suffix for
-use within the build directory (this mirrors how the targets are exported upon
-installation).
-
-Fixed memory leaks in the SUNLINSOL_SUPERLUMT linear solver.
+## Changes to SUNDIALS in release 6.1.0
 
 Added new reduction implementations for the CUDA and HIP NVECTORs that use
 shared memory (local data storage) instead of atomics. These new implementations
@@ -16,11 +10,16 @@ these by default, but the `N_VSetKernelExecPolicy_Cuda` and
 `N_VSetKernelExecPolicy_Hip` functions can be used to choose between
 different reduction implementations.
 
+`SUNDIALS::<lib>` targets with no static/shared suffix have been added for use
+within the build directory (this mirrors the targets exported on installation).
+
 ``CMAKE_C_STANDARD`` is now set to 99 by default.
 
+Fixed exported `SUNDIALSConfig.cmake` when profiling is enabled without Caliper.
+
 Fixed `sundials_export.h` include in `sundials_config.h`.
 
-Fixed exported `SUNDIALSConfig.cmake` when profiling is enabled without Caliper.
+Fixed memory leaks in the SUNLINSOL_SUPERLUMT linear solver.
 
 ## Changes to SUNDIALS in release 6.0.0
 

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -36,52 +36,52 @@ rather than the combined SUNDIALS online guide:
 @Misc{arkodeDocumentation,
   author = {Daniel R. Reynolds and David J. Gardner and Carol S. Woodward and Cody J. Balos},
   title  = {User Documentation for ARKODE},
-  year   = {2021},
-  note   = {v5.0.0}
+  year   = {2022},
+  note   = {v5.1.0}
 }
 ```
 
 ```bibtex
 @Misc{cvodeDocumentation,
   author = {Alan C. Hindmarsh and Radu Serban and Cody J. Balos and David J. Gardner and Daniel R. Reynolds and Carol S. Woodward},
   title  = {User Documentation for CVODE},
-  year   = {2021},
-  note   = {v6.0.0}
+  year   = {2022},
+  note   = {v6.1.0}
 }
 ```
 
 ```bibtex
 @Misc{cvodesDocumentation,
   author = {Alan C. Hindmarsh and Radu Serban and Cody J. Balos and David J. Gardner and Daniel R. Reynolds and Carol S. Woodward},
   title  = {User Documentation for CVODES},
-  year   = {2021},
-  note   = {v6.0.0}
+  year   = {2022},
+  note   = {v6.1.0}
 }
 ```
 
 ```bibtex
 @Misc{idaDocumentation,
   author = {Alan C. Hindmarsh and Radu Serban and Cody J. Balos and David J. Gardner and Daniel R. Reynolds and Carol S. Woodward},
   title  = {User Documentation for IDA},
-  year   = {2021},
-  note   = {v6.0.0}
+  year   = {2022},
+  note   = {v6.1.0}
 }
 ```
 
 ```bibtex
 @Misc{idasDocumentation,
   author = {Radu Serban and Cosmin Petra and Alan C. Hindmarsh and Cody J. Balos and David J. Gardner and Daniel R. Reynolds and Carol S. Woodward},
   title  = {User Documentation for IDAS},
-  year   = {2021},
-  note   = {v5.0.0}
+  year   = {2022},
+  note   = {v5.1.0}
 }
 ```
 
 ```bibtex
 @Misc{kinsolDocumentation,
   author = {Alan C. Hindmarsh and Radu Serban and Cody J. Balos and David J. Gardner and Daniel R. Reynolds and Carol S. Woodward},
   title  = {User Documentation for KINSOL},
-  year   = {2021},
-  note   = {v6.0.0}
+  year   = {2022},
+  note   = {v6.1.0}
 }
 ```
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -42,7 +42,7 @@ include(FindPackageHandleStandardArgs)
 # Set some variables with info on the SUNDIALS project
 set(PACKAGE_BUGREPORT "[email protected]")
 set(PACKAGE_NAME "SUNDIALS")
-set(PACKAGE_STRING "SUNDIALS 6.0.0")
+set(PACKAGE_STRING "SUNDIALS 6.1.0")
 set(PACKAGE_TARNAME "sundials")
 
 # Set SUNDIALS version numbers
@@ -51,7 +51,7 @@ message(STATUS "SUNDIALS_GIT_VERSION: ${SUNDIALS_GIT_VERSION}")
 
 # (use "" for the version label if none is needed)
 set(PACKAGE_VERSION_MAJOR "6")
-set(PACKAGE_VERSION_MINOR "0")
+set(PACKAGE_VERSION_MINOR "1")
 set(PACKAGE_VERSION_PATCH "0")
 set(PACKAGE_VERSION_LABEL "")
 
@@ -67,37 +67,37 @@ endif()
 
 # Specify the VERSION and SOVERSION for shared libraries
 
-set(arkodelib_VERSION "5.0.0")
+set(arkodelib_VERSION "5.1.0")
 set(arkodelib_SOVERSION "5")
 
-set(cvodelib_VERSION "6.0.0")
+set(cvodelib_VERSION "6.1.0")
 set(cvodelib_SOVERSION "6")
 
-set(cvodeslib_VERSION "6.0.0")
+set(cvodeslib_VERSION "6.1.0")
 set(cvodeslib_SOVERSION "6")
 
-set(idalib_VERSION "6.0.0")
+set(idalib_VERSION "6.1.0")
 set(idalib_SOVERSION "6")
 
-set(idaslib_VERSION "5.0.0")
+set(idaslib_VERSION "5.1.0")
 set(idaslib_SOVERSION "5")
 
-set(kinsollib_VERSION "6.0.0")
+set(kinsollib_VERSION "6.1.0")
 set(kinsollib_SOVERSION "6")
 
 set(cpodeslib_VERSION "0.0.0")
 set(cpodeslib_SOVERSION "0")
 
-set(nveclib_VERSION "6.0.0")
+set(nveclib_VERSION "6.1.0")
 set(nveclib_SOVERSION "6")
 
-set(sunmatrixlib_VERSION "4.0.0")
+set(sunmatrixlib_VERSION "4.1.0")
 set(sunmatrixlib_SOVERSION "4")
 
-set(sunlinsollib_VERSION "4.0.0")
+set(sunlinsollib_VERSION "4.1.0")
 set(sunlinsollib_SOVERSION "4")
 
-set(sunnonlinsollib_VERSION "3.0.0")
+set(sunnonlinsollib_VERSION "3.1.0")
 set(sunnonlinsollib_SOVERSION "3")
 
 set(sundialslib_VERSION

diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 # SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic equation Solvers #
-### Version 6.0.0 (Dec 2021) ###
+### Version 6.1.0 (Jan 2022) ###
 
 **Center for Applied Scientific Computing, Lawrence Livermore National Laboratory**
 

diff --git a/benchmarks/nvector/test_nvector_performance.c b/benchmarks/nvector/test_nvector_performance.c
@@ -2589,10 +2589,10 @@ void SetTiming(int onoff, int myid)
 {
 #if defined(SUNDIALS_HAVE_POSIX_TIMERS) && defined(_POSIX_TIMERS)
   struct timespec spec;
-  clock_gettime( CLOCK_MONOTONIC_RAW, &spec );
+  clock_gettime( CLOCK_MONOTONIC, &spec );
   base_time_tv_sec = spec.tv_sec;
 
-  clock_getres( CLOCK_MONOTONIC_RAW, &spec);
+  clock_getres( CLOCK_MONOTONIC, &spec);
   if (myid == 0)
     printf("Timer resolution: %ld ns = %g s\n", spec.tv_nsec, ((double)(spec.tv_nsec) / 1E9));
 #endif
@@ -2677,7 +2677,7 @@ static double get_time()
   double time;
 #if defined(SUNDIALS_HAVE_POSIX_TIMERS) && defined(_POSIX_TIMERS)
   struct timespec spec;
-  clock_gettime( CLOCK_MONOTONIC_RAW, &spec );
+  clock_gettime( CLOCK_MONOTONIC, &spec );
   time = (double)(spec.tv_sec - base_time_tv_sec) + ((double)(spec.tv_nsec) / 1E9);
 #else
   time = 0;

diff --git a/cmake/SundialsSetupTPLs.cmake b/cmake/SundialsSetupTPLs.cmake
@@ -14,6 +14,42 @@
 # Setup third-party libraries
 # ---------------------------------------------------------------
 
+# ---------------------------------------------------------------
+# Setup MPI, OpenMP, and OpenMP offload first as other TPLs may
+# need targets or variables corresponding to these TPLs.
+# ---------------------------------------------------------------
+
+# ---------------------------------------------------------------
+# Find MPI
+# ---------------------------------------------------------------
+
+if(ENABLE_MPI)
+  include(SundialsMPI)
+  list(APPEND SUNDIALS_TPL_LIST "MPI")
+endif()
+
+# ---------------------------------------------------------------
+# Find OpenMP
+# ---------------------------------------------------------------
+
+if(ENABLE_OPENMP)
+  include(SundialsOpenMP)
+  list(APPEND SUNDIALS_TPL_LIST "OPENMP")
+endif()
+
+# ---------------------------------------------------------------
+# Find OpenMP with device offloading
+# --------------------------------------------------------------
+
+if(ENABLE_OPENMP_DEVICE)
+  include(SundialsOpenMP)
+  list(APPEND SUNDIALS_TPL_LIST "OPENMP_DEVICE")
+endif()
+
+# ---------------------------------------------------------------
+# Setup other TPLs (listed in alphabetical order)
+# ---------------------------------------------------------------
+
 # ---------------------------------------------------------------
 # Find (and test) the Caliper libraries
 # ---------------------------------------------------------------
@@ -59,15 +95,6 @@ if(ENABLE_MAGMA)
   list(APPEND SUNDIALS_TPL_LIST "MAGMA")
 endif()
 
-# ---------------------------------------------------------------
-# Find MPI.
-# ---------------------------------------------------------------
-
-if(ENABLE_MPI)
-  include(SundialsMPI)
-  list(APPEND SUNDIALS_TPL_LIST "MPI")
-endif()
-
 # ---------------------------------------------------------------
 # Find (and test) the oneMKL libraries
 # ---------------------------------------------------------------
@@ -77,24 +104,6 @@ if(ENABLE_ONEMKL)
   list(APPEND SUNDIALS_TPL_LIST "ONEMKL")
 endif()
 
-# ---------------------------------------------------------------
-# Find OpenMP
-# ---------------------------------------------------------------
-
-if(ENABLE_OPENMP)
-  include(SundialsOpenMP)
-  list(APPEND SUNDIALS_TPL_LIST "OPENMP")
-endif()
-
-# ---------------------------------------------------------------
-# Find OpenMP with device offloading
-# --------------------------------------------------------------
-
-if(ENABLE_OPENMP_DEVICE)
-  include(SundialsOpenMP)
-  list(APPEND SUNDIALS_TPL_LIST "OPENMP_DEVICE")
-endif()
-
 # ---------------------------------------------------------------
 # Find (and test) the PETSc libraries
 # ---------------------------------------------------------------
@@ -156,4 +165,4 @@ endif()
 if(ENABLE_XBRAID)
   include(SundialsXBRAID)
   list(APPEND SUNDIALS_TPL_LIST "XBRAID")
-endif()
+endif()
diff --git a/cmake/tpl/SundialsPOSIXTimers.cmake b/cmake/tpl/SundialsPOSIXTimers.cmake
@@ -56,8 +56,8 @@ macro(posix_timers_test)
     "#include <unistd.h>\n"
     "int main(){\n"
     "struct timespec spec;\n"
-    "clock_gettime(CLOCK_MONOTONIC_RAW, &spec);\n"
-    "clock_getres(CLOCK_MONOTONIC_RAW, &spec);\n"
+    "clock_gettime(CLOCK_MONOTONIC, &spec);\n"
+    "clock_getres(CLOCK_MONOTONIC, &spec);\n"
     "return(0);\n"
     "}\n")
 

diff --git a/doc/arkode/guide/source/Introduction.rst b/doc/arkode/guide/source/Introduction.rst
@@ -118,15 +118,9 @@ provided with SUNDIALS, or again may utilize a user-supplied module.
 Changes from previous versions
 ==============================
 
-Changes in vx.x.x
+Changes in v5.1.0
 -----------------
 
-Additionally export ``SUNDIALS::<lib>`` targets with no static/shared suffix for
-use within the build directory (this mirrors how the targets are exported upon
-installation).
-
-Fixed memory leaks in the SUNLINSOL_SUPERLUMT linear solver.
-
 Added new reduction implementations for the CUDA and HIP NVECTORs that use
 shared memory (local data storage) instead of atomics. These new implementations
 are recommended when the target hardware does not provide atomic support for the
@@ -135,11 +129,16 @@ these by default, but the :c:func:`N_VSetKernelExecPolicy_Cuda` and
 :c:func:`N_VSetKernelExecPolicy_Hip` functions can be used to choose between
 different reduction implementations.
 
+``SUNDIALS::<lib>`` targets with no static/shared suffix have been added for use
+within the build directory (this mirrors the targets exported on installation).
+
 :cmakeop:`CMAKE_C_STANDARD` is now set to 99 by default.
 
+Fixed exported ``SUNDIALSConfig.cmake`` when profiling is enabled without Caliper.
+
 Fixed ``sundials_export.h`` include in ``sundials_config.h``.
 
-Fixed exported ``SUNDIALSConfig.cmake`` when profiling is enabled without Caliper.
+Fixed memory leaks in the SUNLINSOL_SUPERLUMT linear solver.
 
 Changes in v5.0.0
 -----------------

diff --git a/doc/cvode/guide/source/Introduction.rst b/doc/cvode/guide/source/Introduction.rst
@@ -111,15 +111,9 @@ implementations.
 Changes from previous versions
 ==============================
 
-Changes in vx.x.x
+Changes in v6.1.0
 -----------------
 
-Additionally export ``SUNDIALS::<lib>`` targets with no static/shared suffix for
-use within the build directory (this mirrors how the targets are exported upon
-installation).
-
-Fixed memory leaks in the SUNLINSOL_SUPERLUMT linear solver.
-
 Added new reduction implementations for the CUDA and HIP NVECTORs that use
 shared memory (local data storage) instead of atomics. These new implementations
 are recommended when the target hardware does not provide atomic support for the
@@ -128,11 +122,16 @@ these by default, but the :c:func:`N_VSetKernelExecPolicy_Cuda` and
 :c:func:`N_VSetKernelExecPolicy_Hip` functions can be used to choose between
 different reduction implementations.
 
+``SUNDIALS::<lib>`` targets with no static/shared suffix have been added for use
+within the build directory (this mirrors the targets exported on installation).
+
 :cmakeop:`CMAKE_C_STANDARD` is now set to 99 by default.
 
+Fixed exported ``SUNDIALSConfig.cmake`` when profiling is enabled without Caliper.
+
 Fixed ``sundials_export.h`` include in ``sundials_config.h``.
 
-Fixed exported ``SUNDIALSConfig.cmake`` when profiling is enabled without Caliper.
+Fixed memory leaks in the SUNLINSOL_SUPERLUMT linear solver.
 
 Changes in v6.0.0
 -----------------

diff --git a/doc/cvodes/guide/source/Introduction.rst b/doc/cvodes/guide/source/Introduction.rst
@@ -111,15 +111,9 @@ Fortran.
 Changes from previous versions
 ==============================
 
-Changes in vx.x.x
+Changes in v6.1.0
 -----------------
 
-Additionally export ``SUNDIALS::<lib>`` targets with no static/shared suffix for
-use within the build directory (this mirrors how the targets are exported upon
-installation).
-
-Fixed memory leaks in the SUNLINSOL_SUPERLUMT linear solver.
-
 Added new reduction implementations for the CUDA and HIP NVECTORs that use
 shared memory (local data storage) instead of atomics. These new implementations
 are recommended when the target hardware does not provide atomic support for the
@@ -128,10 +122,17 @@ these by default, but the :c:func:`N_VSetKernelExecPolicy_Cuda` and
 :c:func:`N_VSetKernelExecPolicy_Hip` functions can be used to choose between
 different reduction implementations.
 
+``SUNDIALS::<lib>`` targets with no static/shared suffix have been added for use
+within the build directory (this mirrors the targets exported on installation).
+
 :cmakeop:`CMAKE_C_STANDARD` is now set to 99 by default.
 
+Fixed exported ``SUNDIALSConfig.cmake`` when profiling is enabled without Caliper.
+
 Fixed ``sundials_export.h`` include in ``sundials_config.h``.
 
+Fixed memory leaks in the SUNLINSOL_SUPERLUMT linear solver.
+
 Changes in v6.0.0
 -----------------