Merge branch 'develop' into feature/wrtobin/memspace-aware-packing

.gitlab-ci.yml

@@ -15,11 +15,11 @@ stages:
 .build_script:
   script:
     # Change submodule paths to absolute github paths (default is relative to GEOSX gitlab path)
-    - git submodule set-url src/coreComponents/LvArray https://github.com/GEOSX/LvArray.git
+    - git submodule set-url src/coreComponents/LvArray https://github.com/GEOS-DEV/LvArray.git
     - git submodule set-url src/cmake/blt https://github.com/LLNL/blt.git
-    - git submodule set-url src/coreComponents/constitutive/PVTPackage https://github.com/GEOSX/PVTPackage.git
+    - git submodule set-url src/coreComponents/constitutive/PVTPackage https://github.com/GEOS-DEV/PVTPackage.git
     - git submodule set-url integratedTests [email protected]:GEOSX/integratedTests.git
-    - git submodule set-url src/coreComponents/fileIO/coupling/hdf5_interface https://github.com/GEOSX/hdf5_interface.git
+    - git submodule set-url src/coreComponents/fileIO/coupling/hdf5_interface https://github.com/GEOS-DEV/hdf5_interface.git
 
     # Update submodules
     - git submodule update --init --recursive src/cmake/blt
@@ -30,6 +30,9 @@ stages:
 
     - mkdir ${SYSTEM}
 
+    # geosxats needs python2 to run
+    - module load python/2
+
     # CONFIGURE
     - echo "~~~~~~~~~~ START - configure ~~~~~~~~~~~"
     - config_code=0
@@ -117,9 +120,9 @@ stages:
 
 ####
 # quartz job
-quartz_clang_10_0_0_build:
+quartz_clang_14_build:
   variables:
-    HOST_CONFIG: "quartz-clang@10.0.0.cmake"
+    HOST_CONFIG: "quartz-clang@14.cmake"
   extends: [.build_on_quartz]
 
 ####

.gitmodules

@@ -1,15 +1,15 @@
 [submodule "src/coreComponents/LvArray"]
 	path = src/coreComponents/LvArray
-	url = ../../GEOSX/LvArray.git
+	url = ../../GEOS-DEV/LvArray.git
 [submodule "src/cmake/blt"]
 	path = src/cmake/blt
 	url = ../../LLNL/blt.git
 [submodule "src/coreComponents/constitutive/PVTPackage"]
 	path = src/coreComponents/constitutive/PVTPackage
-	url = ../../GEOSX/PVTPackage.git
+	url = ../../GEOS-DEV/PVTPackage.git
 [submodule "integratedTests"]
 	path = integratedTests
-	url = ../../GEOSX/integratedTests.git
+	url = ../../GEOS-DEV/integratedTests.git
 [submodule "src/coreComponents/fileIO/coupling/hdf5_interface"]
 	path = src/coreComponents/fileIO/coupling/hdf5_interface
-	url = ../../GEOSX/hdf5_interface.git
+	url = ../../GEOS-DEV/hdf5_interface.git

.travis.yml

@@ -7,7 +7,7 @@ vm:
 
 env:
   global:
-  - GEOSX_TPL_TAG=203-915
+  - GEOSX_TPL_TAG=215-929
   - secure: CGs2uH6efq1Me6xJWRr0BnwtwxoujzlowC4FHXHdWbNOkPsXf7nCgdaW5vthfD3bhnOeEUQSrfxdhTRtyU/NfcKLmKgGBnZOdUG4/JJK4gDSJ2Wp8LZ/mB0QEoODKVxbh+YtoAiHe3y4M9PGCs+wkNDw/3eEU00cK12DZ6gad0RbLjI3xkhEr/ZEZDZkcYg9yHAhl5bmpqoh/6QGnIg8mxIqdAtGDw+6tT0EgUqjeqc5bG5WwsamKzJItHSXD5zx8IJAlgDk4EzEGjZe0m56YnNfb9iwqqUsmL3Cuwgs7ByVDYw78JC5Kv42YqoxA5BxMT2mFsEe37TpYNXlzofU7ma2Duw9DGXWQd4IkTCcBxlyR0I0bfo0TmgO+y7PYG9lIyHPUkENemdozsZcWamqqkqegiEdRhDVYlSRo3mu7iCwTS6ZTALliVyEYjYxYb7oAnR3cNywXjblTCI8oKfgLSY+8WijM9SRl57JruIHLkLMCjmRI+cZBfv5tS2tYQTBPkygGrigrrN77ZiC7/TGyfggSN0+y0oYtOAgqEnBcKcreiibMW7tKcV2Z1RFD9ZvIkSc1EXLUPDP8FX1oyhmqBMqVo8LksrYLDJHQ05+F3YNgl2taSt7uMjQ4e8iZ3/IjFeMnbylDw+cj/RbS520HXsFPbWFm2Pb9pceA9n6GnY=
 
 # The integrated test repository contains large data (using git lfs) and we do not use them here.

CITATION.cff

@@ -92,4 +92,4 @@ title: "GEOSX"
 version: 0.2.1
 doi: 10.5281/zenodo.7151032
 date-released: 2022-10-06
-url: "https://github.com/GEOSX/GEOSX"
+url: "https://github.com/GEOS-DEV/GEOS"

CONTRIBUTORS

@@ -3,4 +3,4 @@ CONTRIBUTORS
 A current list of individuals who have contributed source code to the 
 GEOSX project is available at:
 
-https://github.com/GEOSX/GEOSX/graphs/contributors
+https://github.com/GEOS-DEV/GEOS/graphs/contributors

RELEASE_NOTES.md

@@ -9,12 +9,12 @@
 [comment]: # (All right reserved)
 [comment]: # 
 [comment]: # (For more details see:)
-[comment]: # (  https://github.com/GEOSX/GEOSX/LICENSE)
-[comment]: # (  https://github.com/GEOSX/GEOSX/COPYRIGHT)
-[comment]: # (  https://github.com/GEOSX/GEOSX/CONTRIBUTORS)
-[comment]: # (  https://github.com/GEOSX/GEOSX/NOTICE)
-[comment]: # (  https://github.com/GEOSX/GEOSX/ACKNOWLEDGEMENTS)
-[comment]: # (  https://github.com/GEOSX/GEOSX/RELEASE)
+[comment]: # (  https://github.com/GEOS-DEV/GEOS/LICENSE)
+[comment]: # (  https://github.com/GEOS-DEV/GEOS/COPYRIGHT)
+[comment]: # (  https://github.com/GEOS-DEV/GEOS/CONTRIBUTORS)
+[comment]: # (  https://github.com/GEOS-DEV/GEOS/NOTICE)
+[comment]: # (  https://github.com/GEOS-DEV/GEOS/ACKNOWLEDGEMENTS)
+[comment]: # (  https://github.com/GEOS-DEV/GEOS/RELEASE)
 
 
 Version v0.2.0 -- Release date 2020-06-20

examples/ObjectCatalog/Base.hpp

@@ -26,14 +26,14 @@ class Parameter
   Parameter( Parameter const & source ):
     member( source.member )
   {
-    GEOSX_LOG( "called copy constructor for Parameter" );
+    GEOS_LOG( "called copy constructor for Parameter" );
   }
 
 #if ( __cplusplus >= 201103L )
   Parameter( Parameter && source ):
     member( std::move( source.member ))
   {
-    GEOSX_LOG( "called move constructor for Parameter" );
+    GEOS_LOG( "called move constructor for Parameter" );
   }
 #endif
 
@@ -47,12 +47,12 @@ class Base
 public:
   Base( int junk, double const & junk2, Parameter& pbv )
   {
-    GEOSX_LOG( "calling Base constructor with arguments (" << junk << " " << junk2 << ")" );
+    GEOS_LOG( "calling Base constructor with arguments (" << junk << " " << junk2 << ")" );
   }
 
   ~Base()
   {
-    GEOSX_LOG( "calling Base destructor" );
+    GEOS_LOG( "calling Base destructor" );
   }
 
   using CatalogInterface = dataRepository::CatalogInterface< Base, int, double const &, Parameter& >;

examples/ObjectCatalog/Derived1.cpp

@@ -18,12 +18,12 @@
 Derived1::Derived1( int junk, double const & junk2, Parameter& param ):
   Base( junk, junk2, param )
 {
-  GEOSX_LOG( "calling Derived1 constructor with arguments ("<<junk<<" "<<junk2<<")" );
+  GEOS_LOG( "calling Derived1 constructor with arguments ("<<junk<<" "<<junk2<<")" );
 }
 
 Derived1::~Derived1()
 {
-  GEOSX_LOG( "calling Derived1 destructor" );
+  GEOS_LOG( "calling Derived1 destructor" );
 }
 
 REGISTER_CATALOG_ENTRY( Base, Derived1, int, double const &, Parameter& )

examples/ObjectCatalog/Derived2.cpp

@@ -17,12 +17,12 @@
 Derived2::Derived2( int junk, double const & junk2, Parameter& param ):
   Base( junk, junk2, param )
 {
-  GEOSX_LOG( "calling Derived2 constructor with arguments ("<<junk<<" "<<junk2<<")" );
+  GEOS_LOG( "calling Derived2 constructor with arguments ("<<junk<<" "<<junk2<<")" );
 }
 
 Derived2::~Derived2()
 {
-  GEOSX_LOG( "calling Derived2 destructor" );
+  GEOS_LOG( "calling Derived2 destructor" );
 }
 
 REGISTER_CATALOG_ENTRY( Base, Derived2, int, double const &, Parameter& )

examples/ObjectCatalog/main.cpp

@@ -22,18 +22,18 @@
 
 int main( int argc, char *argv[] )
 {
-  GEOSX_LOG( "EXECUTING MAIN" );
+  GEOS_LOG( "EXECUTING MAIN" );
   int junk = 1;
   double junk2 = 3.14;
   double junk3 = 2*3.14;
   Parameter param;
 
 
-  GEOSX_LOG( "Attempting to create a Derived1 object" );
+  GEOS_LOG( "Attempting to create a Derived1 object" );
   std::unique_ptr<Base> derived1 = Base::CatalogInterface::Factory( "derived1", junk, junk2, param );
-  GEOSX_LOG( "Attempting to create a Derived2 object" );
+  GEOS_LOG( "Attempting to create a Derived2 object" );
   std::unique_ptr<Base> derived2 = Base::CatalogInterface::Factory( "derived2", junk, junk3, param );
 
   Base::CatalogInterface::catalog_cast<Derived1>( *(derived2.get()));
-  GEOSX_LOG( "EXITING MAIN" );
+  GEOS_LOG( "EXITING MAIN" );
 }

host-configs/LLNL/lassen-base.cmake

@@ -42,6 +42,7 @@ set(ESSL_LIBRARIES /usr/tcetmp/packages/essl/essl-6.2.1/lib64/libesslsmpcuda.so
 # TPL
 set(ENABLE_PAPI OFF CACHE BOOL "")
 set(SILO_BUILD_TYPE powerpc64-unknown-linux-gnu CACHE STRING "")
+set(ENABLE_FESAPI OFF CACHE BOOL "" FORCE)
 
 # GEOSX specific options
 set(ENABLE_PVTPackage ON CACHE BOOL "")

host-configs/LLNL/lassen-clang@upstream.cmake

@@ -1,15 +1,15 @@
 include(${CMAKE_CURRENT_LIST_DIR}/../../src/coreComponents/LvArray/host-configs/LLNL/[email protected])
 
 # Fortran
-set(CMAKE_Fortran_COMPILER /usr/tce/packages/xl/xl-beta-2019.06.20/bin/xlf_r CACHE PATH "")
+set(CMAKE_Fortran_COMPILER /usr/tce/packages/xl/xl-2020.11.12/bin/xlf_r CACHE PATH "")
 set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -qarch=pwr9 -qtune=pwr9" CACHE STRING "")
 set(FORTRAN_MANGLE_NO_UNDERSCORE ON CACHE BOOL "")
 set(OpenMP_Fortran_FLAGS "-qsmp=omp" CACHE STRING "")
 set(OpenMP_Fortran_LIB_NAMES "" CACHE STRING "")
 
 # MPI
 set(MPI_HOME /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-clang-upstream-2019.03.26 CACHE PATH "")
-set(MPI_Fortran_COMPILER /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-xl-beta-2019.06.20/bin/mpifort CACHE PATH "")
+set(MPI_Fortran_COMPILER /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-xl-2020.11.12/bin/mpifort CACHE PATH "")
 
 include(${CMAKE_CURRENT_LIST_DIR}/lassen-base.cmake)
 

host-configs/LLNL/quartz-base.cmake

@@ -29,10 +29,28 @@ set(ENABLE_OPENMP ON CACHE BOOL "")
 set(ENABLE_PVTPackage ON CACHE BOOL "")
 set(ENABLE_PETSC OFF CACHE BOOL "Enables PETSc." FORCE)
 
+# PYGEOSX
+set(ENABLE_PYGEOSX ON CACHE BOOL "")
+set(Python3_ROOT_DIR /usr/gapps/GEOSX/thirdPartyLibs/python/quartz-gcc-python/python CACHE PATH "")
+set(Python3_EXECUTABLE ${Python3_ROOT_DIR}/bin/python3 CACHE PATH "")
+
 # YAPF python formatting
-set(YAPF_EXECUTABLE /usr/gapps/GEOSX/thirdPartyLibs/python/linux-rhel7-x86_64-gcc@8.1.0/python@3.8.5/bin/yapf CACHE PATH "" FORCE)
+set(YAPF_EXECUTABLE /usr/gapps/GEOSX/thirdPartyLibs/python/quartz-gcc-python/python/bin/yapf CACHE PATH "" FORCE)
 
 # Sphinx
-set(SPHINX_EXECUTABLE /usr/gapps/GEOSX/thirdPartyLibs/python/documentation/documentation/bin/sphinx-build CACHE PATH "" FORCE)
+set(SPHINX_EXECUTABLE /usr/gapps/GEOSX/thirdPartyLibs/python/quartz-gcc-python/python/bin/sphinx-build CACHE PATH "" FORCE)
+
+
+set(ENABLE_FESAPI OFF CACHE BOOL "" FORCE)
+
+# MKL
+set(ENABLE_MKL ON CACHE BOOL "")
+set(MKL_ROOT /usr/tce/packages/mkl/mkl-2022.1.0)
+set(MKL_INCLUDE_DIRS ${MKL_ROOT}/include CACHE STRING "")
+set(MKL_LIBRARIES ${MKL_ROOT}/lib/intel64/libmkl_intel_lp64.so
+                  ${MKL_ROOT}/lib/intel64/libmkl_gnu_thread.so
+                  ${MKL_ROOT}/lib/intel64/libmkl_core.so
+                  CACHE STRING "")
+
 
 include(${CMAKE_CURRENT_LIST_DIR}/../tpls.cmake)

host-configs/LLNL/quartz-clang@14.cmake

@@ -0,0 +1,11 @@
+include(${CMAKE_CURRENT_LIST_DIR}/../../src/coreComponents/LvArray/host-configs/LLNL/[email protected])
+
+# Fortran
+set(CMAKE_Fortran_COMPILER /usr/tce/packages/gcc/gcc-12.1.1-magic/bin/gfortran CACHE PATH "")
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -march=native -mtune=native" CACHE STRING "")
+
+# MPI
+set(MPI_HOME /usr/tce/packages/mvapich2/mvapich2-2.3.6-clang-14.0.6-magic CACHE PATH "")
+
+
+include(${CMAKE_CURRENT_LIST_DIR}/quartz-base.cmake)