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Pull request #295: Plp/feature/hector3
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Merge in JGCRI/gcam-core from plp/feature/hector3 to master

Squashed commit of the following:

commit 4564b491b9fde9d7740737ff2cceb878b924a6e8
Merge: 327084b3c 2b55555
Author: Pralit Patel <[email protected]>
Date:   Sat Jun 3 23:09:11 2023 -0400

    Merge remote-tracking branch 'origin/master' into plp/feature/hector3

commit 327084b3c422144de964f1ba0690a05defdde1ca
Author: Pralit Patel <[email protected]>
Date:   Fri Jun 2 23:21:26 2023 -0400

    Address PR comments

commit 9b710946309e9713b1b1b9d23d93ea32047f797f
Merge: a6f3c13f9 bdfb2c8
Author: Pralit Patel <[email protected]>
Date:   Thu Jun 1 14:13:03 2023 -0400

    Merge remote-tracking branch 'origin/master' into plp/feature/hector3

commit a6f3c13f99d8ec9d59cbb4f02cd96e83b8cb2e6f
Author: Pralit Patel <[email protected]>
Date:   Thu Jun 1 14:10:44 2023 -0400

    Update the Core policy configuration to include a small partial-UCT to
    ensure some protection on the land side in deep mitigation scenarios

commit 3ded5ee78a9e04f8b321736279864580c297d27d
Author: Pralit Patel <[email protected]>
Date:   Wed May 31 21:35:30 2023 -0400

    Include all combinations of GMAT, GMST x Relative to climate model
    native or 1850-1900 mean in the XMLDB output.

    Update the query to get GMST - 1850-1990 mean by default but also lost
    of comments detailing the others including how to query them

commit b45c8d461a4e4c30b6213ee0b96fee886a991c83
Author: Pralit Patel <[email protected]>
Date:   Sun May 28 12:38:08 2023 -0400

    Add a flag to let users get GMAT or GMST in "native" temperature
    anomaly or relative to 1850-1900 mean

commit 3a008934d9a9e7389a3d26c9c4a4b31ae5599c61
Author: kdorheim <[email protected]>
Date:   Thu May 25 16:44:40 2023 -0400

    update to hector v3.1.1

commit 7cdf491700d685a324c6181df8f97563e684ce79
Author: kdorheim <[email protected]>
Date:   Mon May 22 21:32:30 2023 -0400

    Update version

commit 6923be4180496ec5456b1c937fdc8de3ad91260f
Author: Pralit Patel <[email protected]>
Date:   Mon May 22 10:07:10 2023 -0400

    Avoid error messages from Hector about extrapolating emissinos when an
    early stop year/period is configured in GCAM.

commit 1305f97625df6cef40d819b4cbeabecf557ae1d9
Merge: ceddb0fb9 47dc17eff
Author: Dorheim, Kalyn R <[email protected]>
Date:   Fri May 19 19:22:27 2023 +0000

    Pull request #303: Plp/feature/hector3 gmst

    Merge in JGCRI/gcam-core from plp/feature/hector3_gmst to plp/feature/hector3

    * commit '47dc17eff3cf98bfce5f93f197184631c284f9b2':
      Update gcam-integrationv3 branch
      Add global mean surface temperature (GMST) as output saved from Hector
      Update Hector to V3.1 that produces gmst output

commit 47dc17eff3cf98bfce5f93f197184631c284f9b2
Author: kdorheim <[email protected]>
Date:   Fri May 19 14:53:04 2023 -0400

    Update gcam-integrationv3 branch

commit dac9cd6e8c8a18c39cbde084bc43ead124f2583d
Author: kdorheim <[email protected]>
Date:   Fri May 19 14:38:08 2023 -0400

    Add global mean surface temperature (GMST) as output saved from Hector

commit 96048a7cd58bfa9746b7bd95e83c14de45ddb77f
Author: kdorheim <[email protected]>
Date:   Fri May 19 12:46:02 2023 -0400

    Update Hector to V3.1 that produces gmst output

commit ceddb0fb95afb4b897ae2c9a002570afdb020622
Author: Pralit Patel <[email protected]>
Date:   Tue May 16 13:32:06 2023 -0400

    A couple more minor cleanup

commit a72e1af96df2575c4d6b32682c21413ffe1476ac
Author: Pralit Patel <[email protected]>
Date:   Tue May 16 12:44:17 2023 -0400

    Address remaining tasks:
    * "land flux" should be pulling from D_NBP
    * Set some default filters that will strip LUC emissions details from
      the XMLDB by default.  But could be easily re-configured to be added
    back if a user wanted to pull emissions from the DB to run through a
    standalone Hector, for instance.

commit f4434f0f74b5f5d03b75dc7e6bd72b4dcc89997a
Author: Pralit Patel <[email protected]>
Date:   Tue May 16 10:46:12 2023 -0400

    Some clean up and comments

commit 872a7c462bf62cefa14dd93325df5901f8601b5b
Author: Pralit Patel <[email protected]>
Date:   Wed May 10 16:51:59 2023 -0400

    Update Xcode project file to use C++ 17 and ensure it still finds /
    links Hector.  In addition some tweaks to the build location and
    "install" location of the GCAM exe to ensure we can still "Clean Build"
    with the latest Xcode

commit 445978773f3a1b9abac01ad6098504c1cef1aede
Author: Pralit Patel <[email protected]>
Date:   Wed May 10 12:24:08 2023 -0700

    Some clean up related to std::unary / binary function being removed in
    the C++ 17 standard (had been deprecated since C++ 11)

commit d5e7da073a71be2c24141eb0c967d8efaf7c8c7b
Merge: b58f4ba77 3fd6edd
Author: Pralit Patel <[email protected]>
Date:   Mon May 8 04:25:38 2023 -0400

    Merge remote-tracking branch 'origin/master' into plp/feature/hector3

commit b58f4ba775638f5c99d876982e53c0ddcf95333f
Author: Pralit Patel <[email protected]>
Date:   Thu Apr 13 15:51:29 2023 -0400

    Fix to clear out above positive LUC emissions during eReverseCalc

... and 16 more commits
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@kdorheim @pralitp
kdorheim authored and pralitp committed Jun 4, 2023
1 parent 2b55555 commit 2039103
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Showing 103 changed files with 2,363 additions and 2,507 deletions.
2 changes: 1 addition & 1 deletion .gitmodules
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
[submodule "cvs/objects/climate/source/hector"]
path = cvs/objects/climate/source/hector
url = https://github.com/JGCRI/hector.git
branch = gcam-integration
branch = gcam-integrationv3
[submodule "output/modelinterface/modelinterface"]
path = output/modelinterface/modelinterface
url = https://github.com/JGCRI/modelinterface.git
Expand Down
1 change: 1 addition & 0 deletions cvs/objects/build/linux/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -77,6 +77,7 @@ varchk:

clean :
-$(RM) libgcam.a
-$(RM) libhector.a
-$(RM) objs/*.o
-$(MAKE) -C ../../containers/source clean
-$(MAKE) -C ../../demographics/source clean
Expand Down
29 changes: 22 additions & 7 deletions cvs/objects/build/linux/configure.gcam
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,16 @@ CXXBASEOPTS = $(CXXDEBUG)
ARCH_FLAGS =
ENVLIBS =

# only hector is using C++ 17 features and even then only to replace
# the need to link the Boost system and filesystem libraries
# however we can easily fall back to C++ 14 if needed (but then will need
# to link those Boost libraries)
ifeq ($(strip $(NO_CXX17)),)
CXXSTD = c++17
else
CXXSTD = c++14
endif

## sets if we have Java which is required to GCAM output into a BaseX database
## should a user not be able to use Java they could concievably turn this off
## and set DEBUG_XML_DB in xml_db_outputter.ccp to just have the data written
Expand Down Expand Up @@ -52,17 +62,22 @@ ifeq ($(USE_HECTOR),1)

# hector Makefile is looking for slightly different names for BOOST
# include and lib
BOOSTROOT=$(BOOST_INCLUDE)
BOOSTINC=$(BOOST_INCLUDE)
BOOSTLIB=$(BOOST_LIB)
export BOOSTROOT BOOSTLIB
export BOOSTINC BOOSTLIB

HECTOR_INCLUDE = -I../../climate/source/hector/headers

ifeq ($(strip $(BOOST_LIB)),)
$(error Unable to detect Boost lib path, please set env variable BOOST_LIB)
# hector allows us to fall back to the C++ 14 standard if we do not have it
# however, we then need to link the Boost system and filesystem libraries
ifeq ($(strip $(NO_CXX17)),)
HECTOR_LIB = -lhector
else
ifeq ($(strip $(BOOST_LIB)),)
$(error Unable to detect Boost lib path, please set env variable BOOST_LIB)
endif
HECTOR_LIB = -L$(BOOST_LIB) -Wl,-rpath,$(BOOST_LIB) -lhector -lboost_system -lboost_filesystem
endif

HECTOR_LIB = -L$(BOOST_LIB) -Wl,-rpath,$(BOOST_LIB) -lhector -lboost_system -lboost_filesystem
endif # if(USE_HECTOR==1)

# we may want to not use TBB in which case we have guard against empty -I or -L directives
Expand Down Expand Up @@ -143,7 +158,7 @@ LIBDIR = -L/usr/local/lib -L$(BUILDPATH) $(JAVALIB) $(TBB_LIBRARY)
### The rest should be mostly compiler independent
## Note $(PROF) will be set as needed if we are building the gcam-prof target
CPPFLAGS = $(INCLUDE) $(ARCH_FLAGS) $(JARSLIB) -DGCAM_PARALLEL_ENABLED=$(USE_GCAM_PARALLEL) -DUSE_HECTOR=$(USE_HECTOR) $(MKL_CFLAGS)
CXXFLAGS = $(CXXOPTIM) $(CXXBASEOPTS) $(PROF) -MMD -std=c++14 -Wno-deprecated
CXXFLAGS = $(CXXOPTIM) $(CXXBASEOPTS) $(PROF) -MMD -std=$(CXXSTD) -Wno-deprecated
FCFLAGS = $(FCOPTIM) $(FCBASEOPTS) $(PROF)
LD = $(CXX) $(PROF)
LDFLAGS = $(CXXFLAGS) $(JAVA_RPATH) $(TBB_RPATH) $(MKL_LDFLAGS)
Expand Down
2 changes: 2 additions & 0 deletions cvs/objects/build/vc10/objects.vcxproj
View file
Original file line number Diff line number Diff line change
Expand Up @@ -240,6 +240,7 @@
<WarningLevel>Level3</WarningLevel>
<DebugInformationFormat>
</DebugInformationFormat>
<LanguageStandard>stdcpp17</LanguageStandard>
</ClCompile>
<Link>
<AdditionalDependencies>jvm.lib;%(AdditionalDependencies)</AdditionalDependencies>
Expand Down Expand Up @@ -381,6 +382,7 @@
<WarningLevel>Level3</WarningLevel>
<DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
<ShowIncludes>false</ShowIncludes>
<LanguageStandard>stdcpp17</LanguageStandard>
</ClCompile>
<Link>
<SuppressStartupBanner>true</SuppressStartupBanner>
Expand Down
2 changes: 1 addition & 1 deletion cvs/objects/build/vc10/objects.vcxproj.filters
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1898,4 +1898,4 @@
<Filter>Header Files\technologies</Filter>
</ClInclude>
</ItemGroup>
</Project>
</Project>
116 changes: 63 additions & 53 deletions cvs/objects/build/xcode3/objects.xcodeproj/project.pbxproj
View file
Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@
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Expand Down Expand Up @@ -235,7 +236,6 @@
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Expand Down Expand Up @@ -273,41 +273,36 @@
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remoteInfo = hector;
remoteGlobalIDString = CDD51F4529CB9695001E23D6;
remoteInfo = "hector-lib";
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isa = PBXContainerItemProxy;
containerPortal = CD966E671D92F1BB00A93938 /* hector.xcodeproj */;
proxyType = 2;
remoteGlobalIDString = CD97CE321BFBBF2E005689AD;
remoteInfo = "hector-lib";
remoteGlobalIDString = 27A02A882615CBB800AF9BFA;
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remoteInfo = hector;
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isa = PBXContainerItemProxy;
containerPortal = CD966E671D92F1BB00A93938 /* hector.xcodeproj */;
proxyType = 1;
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remoteGlobalIDString = CDD51F4429CB9695001E23D6;
remoteInfo = "hector-lib";
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0E05C9001E435B3600C73D94 /* gcam_fusion.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = gcam_fusion.cpp; sourceTree = "<group>"; };
Expand Down Expand Up @@ -910,7 +905,7 @@
isa = PBXFrameworksBuildPhase;
buildActionMask = 2147483647;
files = (
CD966E751D92F1CD00A93938 /* libhector-lib.a in Frameworks */,
CD3379E129CB9838005DD5D9 /* libhector-lib.a in Frameworks */,
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runOnlyForDeploymentPostprocessing = 0;
};
Expand All @@ -923,6 +918,7 @@
CD966E671D92F1BB00A93938 /* hector.xcodeproj */,
CD488409122873C000F5A88A /* objects */,
CD299E9711B9C11800E6D196 /* Products */,
CD3379DB29CB9838005DD5D9 /* Frameworks */,
);
name = objects;
sourceTree = "<group>";
Expand All @@ -935,6 +931,13 @@
name = Products;
sourceTree = "<group>";
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CD3379DB29CB9838005DD5D9 /* Frameworks */ = {
isa = PBXGroup;
children = (
);
name = Frameworks;
sourceTree = "<group>";
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CD488409122873C000F5A88A /* objects */ = {
isa = PBXGroup;
children = (
Expand Down Expand Up @@ -2067,7 +2070,8 @@
isa = PBXGroup;
children = (
CD966E6E1D92F1BB00A93938 /* hector */,
CD966E721D92F1BB00A93938 /* libhector-lib.a */,
CD605E452886FFBA0093079B /* hector-tests */,
CD3379E029CB9838005DD5D9 /* libhector-lib.a */,
);
name = Products;
sourceTree = "<group>";
Expand Down Expand Up @@ -2113,12 +2117,11 @@
buildPhases = (
8DD76F640486A84900D96B5E /* Sources */,
8DD76F660486A84900D96B5E /* Frameworks */,
8DD76F690486A84900D96B5E /* CopyFiles */,
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CD966E741D92F1C500A93938 /* PBXTargetDependency */,
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name = objects;
productInstallPath = "$(HOME)/bin";
Expand Down Expand Up @@ -2161,18 +2164,25 @@
/* End PBXProject section */

/* Begin PBXReferenceProxy section */
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CD3379E029CB9838005DD5D9 /* libhector-lib.a */ = {
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remoteRef = CD605E442886FFBA0093079B /* PBXContainerItemProxy */;
sourceTree = BUILT_PRODUCTS_DIR;
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Expand Down Expand Up @@ -2450,10 +2460,10 @@
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/* End PBXTargetDependency section */

Expand All @@ -2462,15 +2472,14 @@
isa = XCBuildConfiguration;
buildSettings = {
ALWAYS_SEARCH_USER_PATHS = NO;
CLANG_CXX_LANGUAGE_STANDARD = "c++14";
CLANG_CXX_LIBRARY = "libc++";
COPY_PHASE_STRIP = NO;
GCC_DYNAMIC_NO_PIC = NO;
GCC_ENABLE_FIX_AND_CONTINUE = YES;
GCC_MODEL_TUNING = G5;
GCC_OPTIMIZATION_LEVEL = 0;
INSTALL_PATH = /usr/local/bin;
MACOSX_DEPLOYMENT_TARGET = 10.15;
INSTALL_PATH = ./;
MACOSX_DEPLOYMENT_TARGET = 12.4;
PRODUCT_NAME = gcam;
};
name = Debug;
Expand All @@ -2479,19 +2488,21 @@
isa = XCBuildConfiguration;
buildSettings = {
ALWAYS_SEARCH_USER_PATHS = NO;
CLANG_CXX_LANGUAGE_STANDARD = "c++14";
CLANG_CXX_LIBRARY = "libc++";
DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
GCC_MODEL_TUNING = G5;
INSTALL_PATH = /usr/local/bin;
MACOSX_DEPLOYMENT_TARGET = 10.15;
INSTALL_PATH = ./;
MACOSX_DEPLOYMENT_TARGET = 12.4;
PRODUCT_NAME = gcam;
};
name = Release;
};
1DEB923608733DC60010E9CD /* Debug */ = {
isa = XCBuildConfiguration;
buildSettings = {
CLANG_CXX_LANGUAGE_STANDARD = "c++17";
DEPLOYMENT_LOCATION = YES;
DSTROOT = ../../../../exe;
ENABLE_TESTABILITY = YES;
GCC_AUTO_VECTORIZATION = NO;
GCC_C_LANGUAGE_STANDARD = gnu99;
Expand All @@ -2513,28 +2524,28 @@
../../../../libs/java/include/darwin,
../../../../libs/tbb/include,
);
LD_RUNPATH_SEARCH_PATHS = "../libs/java/lib ../libs/boost-lib/stage/lib ../libs ../libs/tbb/lib";
INSTALL_PATH = "";
LD_RUNPATH_SEARCH_PATHS = "../libs/java/lib ../libs ../libs/tbb/lib";
LIBRARY_SEARCH_PATHS = (
../../../../libs/java/lib,
"../../../../libs/boost-lib/stage/lib",
../../../../libs/tbb/lib,
);
MACOSX_DEPLOYMENT_TARGET = 12.4;
ONLY_ACTIVE_ARCH = YES;
OTHER_LDFLAGS = (
"-ljvm",
"-lboost_system",
"-lboost_filesystem",
);
OTHER_LDFLAGS = "-ljvm";
PREBINDING = NO;
SDKROOT = "";
SYMROOT = ../../../../exe;
SYMROOT = ../../../../exe/build;
USER_HEADER_SEARCH_PATHS = "../.. ../../climate/source/hector/headers";
};
name = Debug;
};
1DEB923708733DC60010E9CD /* Release */ = {
isa = XCBuildConfiguration;
buildSettings = {
CLANG_CXX_LANGUAGE_STANDARD = "c++17";
DEPLOYMENT_LOCATION = YES;
DSTROOT = ../../../../exe;
GCC_AUTO_VECTORIZATION = YES;
GCC_C_LANGUAGE_STANDARD = gnu99;
GCC_ENABLE_SSE3_EXTENSIONS = YES;
Expand All @@ -2559,24 +2570,23 @@
../../../../libs/eigen,
../../../../libs/tbb/include,
);
LD_RUNPATH_SEARCH_PATHS = "../libs/java/lib ../libs/boost-lib/stage/lib ../libs ../libs/tbb/lib";
INSTALL_PATH = "";
LD_RUNPATH_SEARCH_PATHS = "../libs/java/lib ../libs ../libs/tbb/lib";
LIBRARY_SEARCH_PATHS = (
../../../../libs/java/lib,
"../../../../libs/boost-lib/stage/lib",
../../../../libs/tbb/lib,
);
MACOSX_DEPLOYMENT_TARGET = 12.4;
ONLY_ACTIVE_ARCH = YES;
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"-lboost_system",
"-lboost_filesystem",
"-ltbb",
"-ltbbmalloc",
"-ltbbmalloc_proxy",
);
PREBINDING = NO;
SDKROOT = "";
SYMROOT = ../../../../exe;
SYMROOT = ../../../../exe/build;
USER_HEADER_SEARCH_PATHS = "../.. ../../climate/source/hector/headers";
};
name = Release;
Expand Down
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