New3rd party libraries

.circleci/config.yml

@@ -104,15 +104,16 @@ jobs:
       - run:
           name: Get libomp
           command: |
-            sudo /opt/local/bin/port selfupdate
-            (sudo yes || true) | sudo /opt/local/bin/port install libomp
+            #sudo /opt/local/bin/port selfupdate
+            #(sudo yes || true) | sudo /opt/local/bin/port install libomp
           no_output_timeout: 30m
 
       - run:
-          name: Get clang12
+          name: Get clang13
           command: |
-            (sudo yes || true) | sudo /opt/local/bin/port install clang-12
-            sudo /opt/local/bin/port select --set clang mp-clang-12
+            sudo /opt/local/bin/port selfupdate
+            (sudo yes || true) | sudo /opt/local/bin/port install clang-13
+            sudo /opt/local/bin/port select --set clang mp-clang-13
             /opt/local/bin/clang++ -v > clangVersion.txt
           no_output_timeout: 30m
 
@@ -130,7 +131,7 @@ jobs:
             cd build
             git checkout $CIRCLE_BRANCH
             export PATH=/opt/local/bin:$PATH
-            sudo port select --set clang mp-clang-12
+            sudo port select --set clang mp-clang-13
             cmake -DCPACK_BINARY_DRAGNDROP=ON -DCMAKE_BUILD_TYPE:String=Release -DDIST_INSTALLER:string=ON -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang -DUSE_OMP=ON ..
             make -j2
             make installer -j2
@@ -349,6 +350,15 @@ jobs:
             pip3 install scikit-build command
 
       - run:
+          name: update 3rd party libraries
+          command: |
+            rm -rf /usr/local/VAPOR-Deps/2019-Aug
+            pip3 install gdown --upgrade
+            gdown https://drive.google.com/uc?id=1elB8v-UNMzkNmnsJPtxk3cI1zBelJ3Hd
+            filename="/root/project/2019-Aug-Ubuntu.tar.xz"
+            tar -xf ${filename} -C /usr/local/VAPOR-Deps
+
+      - run: 
           name: update cmake
           command: |
             apt remove -y --purge --auto-remove cmake
@@ -640,7 +650,6 @@ workflows:
       #- clang-tidy
       - build_ubuntu18
       - build_centos7
-      #- foo
       #- test_clang_format
       #- build_win10_installer
       #- build_osx_installer

CMakeLists.txt

@@ -143,6 +143,7 @@ find_library(UDUNITS2 udunits2)
 find_library(FREETYPE freetype)
 find_library(GEOTIFF geotiff)
 find_library(JPEG jpeg)
+find_library(HDF5_LIB hdf5)
 
 # find_package(Python)
 #   Output
@@ -342,6 +343,11 @@ if (WIN32)
 			${QTDIR}/plugins/platforms/qwindows.dll
 			DESTINATION platforms
 		)
+		install (
+			DIRECTORY ${THIRD_PARTY_DIR}/share/plugins
+			DESTINATION ${INSTALL_LIB_DIR}/share
+			COMPONENT Dependencies
+		)
 	endif (GENERATE_FULL_INSTALLER)
 
 	set (CPACK_NSIS_MODIFY_PATH OFF)
@@ -415,6 +421,12 @@ if (APPLE)
                 COMPONENT Dependencies
                 )
         endif ()
+        file (GLOB_RECURSE HDF5_PLUGINS "${THIRD_PARTY_DIR}/share/plugins/*.so")
+		install (
+			FILES ${HDF5_PLUGINS}
+			DESTINATION "${INSTALL_SHARE_DIR}/plugins"
+			COMPONENT Dependencies
+			)
 
     endif ()
 endif (APPLE)
@@ -434,6 +446,9 @@ if (UNIX AND NOT APPLE)
         if (BUILD_PYTHON)
             set (PARSE_BINARY "${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/libvapi.so")
         endif()
+        message( STATUS "${CMAKE_SOURCE_DIR}/buildutils/gen_linux_shared_libs.pl
+            ${PARSE_BINARY} ${EXTRA_LIBS_SEARCH} >
+            ${CMAKE_BINARY_DIR}/LinuxInstallLibs.txt")
 		add_custom_target (
 			linuxpreinstall
 			COMMAND ${CMAKE_SOURCE_DIR}/buildutils/gen_linux_shared_libs.pl
@@ -490,6 +505,13 @@ if (UNIX AND NOT APPLE)
 				)
 		endif ()
 
+		file (GLOB HDF5_PLUGINS "${THIRD_PARTY_DIR}/share/plugins/*.so")
+		message(STATUS "HDF5_PLUGINS ${HDF5_PLUGINS}")
+			install (
+				FILES ${HDF5_PLUGINS}
+				DESTINATION "${INSTALL_SHARE_DIR}/plugins"
+				COMPONENT Dependencies
+				)
 
 	endif (DIST_INSTALLER AND GENERATE_FULL_INSTALLER)
 endif (UNIX AND NOT APPLE)

apps/cf2vdc/cf2vdc.cpp

@@ -9,6 +9,7 @@
 #include <vapor/VDCNetCDF.h>
 #include <vapor/DCCF.h>
 #include <vapor/FileUtils.h>
+#include <vapor/SetHDF5PluginPath.h>
 
 using namespace Wasp;
 using namespace VAPoR;
@@ -223,6 +224,8 @@ vector<string> remove_vector(vector<string> v1, vector<string> v2)
 
 int main(int argc, char **argv)
 {
+    VAPoR::SetHDF5PluginPath();
+
     OptionParser op;
 
     MyBase::SetErrMsgFilePtr(stderr);

apps/cfvdccreate/cfvdccreate.cpp

@@ -9,6 +9,7 @@
 #include <vapor/VDCNetCDF.h>
 #include <vapor/DCCF.h>
 #include <vapor/FileUtils.h>
+#include <vapor/SetHDF5PluginPath.h>
 
 using namespace Wasp;
 using namespace VAPoR;
@@ -144,6 +145,8 @@ void defineMapProjection(const DCCF &dc, VDCNetCDF &vdc) { vdc.SetMapProjection(
 
 int main(int argc, char **argv)
 {
+    VAPoR::SetHDF5PluginPath();
+
     OptionParser op;
 
     MyBase::SetErrMsgFilePtr(stderr);

apps/ncdf2wasp/ncdf2wasp.cpp

@@ -8,6 +8,7 @@
 #include <vapor/OptionParser.h>
 #include <vapor/WASP.h>
 #include <vapor/FileUtils.h>
+#include <vapor/SetHDF5PluginPath.h>
 
 using namespace Wasp;
 using namespace VAPoR;
@@ -394,6 +395,8 @@ void Process(string ncdffile, string waspfile)
 
 int main(int argc, char **argv)
 {
+    VAPoR::SetHDF5PluginPath();
+
     OptionParser op;
 
     MyBase::SetErrMsgFilePtr(stderr);

apps/vaporgui/main.cpp

@@ -31,9 +31,11 @@
 #include <vapor/OptionParser.h>
 #include <vapor/FileUtils.h>
 #include <vapor/OSPRay.h>
+#include <vapor/SetHDF5PluginPath.h>
 #ifdef WIN32
     #include "Windows.h"
 #endif
+
 using namespace std;
 using namespace VAPoR;
 using namespace Wasp;
@@ -151,7 +153,6 @@ int           main(int argc, char **argv)
 // For Mac and Linux, set the PYTHONHOME in this app
 #if PRE_PYTHON_API_REFACTOR
 #ifndef WIN32
-
     const char *s = getenv("PYTHONHOME");
     string      phome = s ? s : "";
     if (!phome.empty()) {
@@ -172,10 +173,11 @@ int           main(int argc, char **argv)
         setenv("PYTHONHOME", phome.c_str(), 1);
     }
     MyBase::SetDiagMsg("PYTHONHOME = %s", phome.c_str());
-
 #endif
 #endif
 
+    VAPoR::SetHDF5PluginPath();
+
     app = &a;
 
     vector<QString> files;

apps/wrf2vdc/wrf2vdc.cpp

@@ -9,6 +9,7 @@
 #include <vapor/VDCNetCDF.h>
 #include <vapor/DCWRF.h>
 #include <vapor/FileUtils.h>
+#include <vapor/SetHDF5PluginPath.h>
 
 using namespace Wasp;
 using namespace VAPoR;
@@ -54,6 +55,8 @@ string ProgName;
 
 int main(int argc, char **argv)
 {
+    VAPoR::SetHDF5PluginPath();
+
     OptionParser op;
 
     MyBase::SetErrMsgFilePtr(stderr);

apps/wrfvdccreate/wrfvdccreate.cpp

@@ -9,6 +9,7 @@
 #include <vapor/VDCNetCDF.h>
 #include <vapor/DCWRF.h>
 #include <vapor/FileUtils.h>
+#include <vapor/SetHDF5PluginPath.h>
 
 using namespace Wasp;
 using namespace VAPoR;
@@ -58,6 +59,8 @@ void defineMapProjection(const DCWRF &dcwrf, VDCNetCDF &vdc) { vdc.SetMapProject
 
 int main(int argc, char **argv)
 {
+    VAPoR::SetHDF5PluginPath();
+
     OptionParser op;
 
     MyBase::SetErrMsgFilePtr(stderr);

include/vapor/SetHDF5PluginPath.h

@@ -0,0 +1,21 @@
+#pragma once
+
+#include "vapor/ResourcePath.h"
+
+#ifndef WIN32
+    #include <H5PLpublic.h>
+#endif
+
+namespace VAPoR {
+VDF_API void SetHDF5PluginPath() {
+    string plugins = Wasp::GetSharePath("plugins");
+
+    #ifndef WIN32
+        H5PLreplace(plugins.c_str(), 0);
+    #else
+        plugins = "HDF5_PLUGIN_PATH=" + plugins;
+        int rc=_putenv(plugins.c_str());
+        if (rc != 0) MyBase::SetErrMsg("Unable to set environtment variable %s", plugins.c_str());
+    #endif
+}
+};    // namespace VAPoR

lib/common/CMakeLists.txt

@@ -55,7 +55,7 @@ if (CONDA_BUILD AND UNIX AND NOT APPLE)
 endif()
 
 if (NOT WIN32)
-	target_link_libraries (common pthread)
+	target_link_libraries (common pthread ${HDF5_LIB})
 	add_definitions (-DENABLE_THREADS)
 endif()
 

lib/vdc/CMakeLists.txt

@@ -92,6 +92,7 @@ set (HEADERS
 	${PROJECT_SOURCE_DIR}/include/vapor/OpenMPSupport.h
 	${PROJECT_SOURCE_DIR}/include/vapor/DCUGRID.h
 	${PROJECT_SOURCE_DIR}/include/vapor/UnstructuredGridCoordless.h
+	${PROJECT_SOURCE_DIR}/include/vapor/SetHDF5PluginPath.h
 )
 
 add_library (vdc SHARED ${SRC} ${HEADERS})