Merge pull request #1 from jedwards4b/GDAL_jpe2

Gdal jpe2

Author: msl3v

CMakeLists.txt

@@ -95,6 +95,7 @@ option (PIO_USE_MPIIO        "Enable support for MPI-IO auto detect"        ON)
 option (PIO_USE_MPISERIAL    "Enable mpi-serial support (instead of MPI)"   OFF)
 option (PIO_USE_PNETCDF_VARD       "Use pnetcdf put_vard "  OFF)
 option (WITH_PNETCDF         "Require the use of PnetCDF"                   ON)
+option (PIO_USE_GDAL         "Enable support for Geospatial Data Abstraction Library ON")
 option (BUILD_SHARED_LIBS    "Build shared libraries"                       OFF)
 
 if(APPLE)
@@ -110,6 +111,14 @@ else()
   set(USE_VARD 0)
 endif()
 
+# Set a variable that appears in the config.h.in file.
+if(PIO_USE_GDAL)
+  set(USE_GDAL 1)
+else()
+  set(USE_GDAL 0)
+endif()
+
+
 # Set a variable that appears in the config.h.in file.
 if(PIO_ENABLE_LOGGING)
   set(ENABLE_LOGGING 1)

cmake_config.h.in

@@ -46,4 +46,6 @@
 /* Does PIO support using pnetcdf for I/O? */
 #cmakedefine _PNETCDF
 
+#cmakedefine USE_GDAL
+
 #endif /* _PIO_CONFIG_ */

src/clib/CMakeLists.txt

@@ -29,7 +29,9 @@ if (NETCDF_INTEGRATION)
   set (src ${src} ../ncint/nc_get_vard.c ../ncint/ncintdispatch.c ../ncint/ncint_pio.c ../ncint/nc_put_vard.c)
 endif ()
 # This needs to be in an IF statement. using GDAL_INTEGRATION. But haven't figured that out yet.
-set (src ${src} pio_gdal.c)
+if (USE_GDAL)
+  set (src ${src} pio_gdal.c)
+endif()
 
 add_library (pioc ${src})
 
@@ -176,12 +178,12 @@ if (PIO_USE_MPISERIAL)
 endif ()
 
 #===== GDAL ===== <M.Long>
-#if (GDAL_Found)
+if (USE_GDAL)
   target_include_directories (pioc
     PUBLIC ${GDAL_INCLUDE_DIR})
   target_link_libraries (pioc
-    PUBLIC ${GDAL_LIBRARY})
-#endif ()
+    PUBLIC "-L${GDAL_LIBRARY_PATH} -lgdal")
+endif ()
 
 include(CheckTypeSize)
 check_type_size("size_t" SIZEOF_SIZE_T)

src/clib/pio_darray.c

@@ -949,10 +949,12 @@ PIOc_read_darray(int ncid, int varid, int ioid, PIO_Offset arraylen,
         if ((ierr = pio_read_darray_nc(file, iodesc, varid, iobuf)))
             return pio_err(ios, file, ierr, __FILE__, __LINE__);
         break;
+#ifdef USE_GDAL
     case PIO_IOTYPE_GDAL:
         if ((ierr = pio_read_darray_shp(file, iodesc, varid, iobuf)))
             return pio_err(ios, file, ierr, __FILE__, __LINE__);
         break;
+#endif
     default:
         return pio_err(NULL, NULL, PIO_EBADIOTYPE, __FILE__, __LINE__);
     }

src/clib/pio_gdal.c

@@ -1,6 +1,7 @@
 #include <config.h>
 #include <pio.h>
 #include <pio_internal.h>
+#ifdef USE_GDAL
 #include <ogr_api.h>
 
 /**
@@ -457,11 +458,6 @@ int GDALc_inq_timeid(int fileid, int *timeid) { // Is there a field of type OFTD
     for (int i=0;i<(file->nvars)-1;i++) {
       OGRFieldDefnH hFlD = OGR_FD_GetFieldDefn(hFD,i);
       OGRFieldType Fld = OGR_Fld_GetType(hFlD);
-      if (Fld == NULL)
-        return pio_err(NULL, NULL, ierr, __FILE__, __LINE__);
-
-//      const char* FldTyp = OGR_GetFieldTypeName(Fld);
-//      PRINTMSG("Field type: " << FldTyp);
     }
 
 //    OGR_FD_Destroy(hFD);
@@ -816,3 +812,4 @@ GDALc_shp_get_float_field(int fileid, int varid, const size_t *startp,
 /**
  * @}
  */
+#endif

src/clib/pio_internal.h

@@ -91,6 +91,11 @@
 
 #define PIO_DATATYPE_NULL MPI_CHAR
 
+#ifdef USE_GDAL
+int
+pio_read_darray_shp(file_desc_t *file, io_desc_t *iodesc, int vid,
+		    void *iobuf);
+#endif
 
 #if PIO_ENABLE_LOGGING
 void pio_log(int severity, const char *fmt, ...);

tests/cunit/CMakeLists.txt

@@ -22,6 +22,11 @@ endif()
 set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g -O0")
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -O0")
 
+
+set(CMAKE_MACOSX_RPATH 1)
+if(USE_GDAL)  
+  set(CMAKE_BUILD_RPATH ${GDAL_LIBRARY_PATH})
+endif()
 #==============================================================================
 #  PREPARE FOR TESTING
 #==============================================================================
@@ -344,9 +349,16 @@ else ()
   #   EXECUTABLE ${CMAKE_CURRENT_BINARY_DIR}/test_async_perf
   #   NUMPROCS ${EXACTLY_FOUR_TASKS}
   #   TIMEOUT ${DEFAULT_TEST_TIMEOUT})
-  add_mpi_test(test_gdal
-    EXECUTABLE ${CMAKE_CURRENT_BINARY_DIR}/test_gdal
-    NUMPROCS ${EXACTLY_FOUR_TASKS}
-    TIMEOUT ${DEFAULT_TEST_TIMEOUT})
+  if(USE_GDAL)  
+    add_custom_target(link_target ALL
+                      COMMAND ${CMAKE_COMMAND} -E create_symlink
+                      ${CMAKE_CURRENT_SOURCE_DIR}/data ${CMAKE_CURRENT_BINARY_DIR}/data)
+    add_mpi_test(test_gdal
+      EXECUTABLE ${CMAKE_CURRENT_BINARY_DIR}/test_gdal
+      NUMPROCS ${EXACTLY_FOUR_TASKS}
+      TIMEOUT ${DEFAULT_TEST_TIMEOUT})
+    set_tests_properties(test_gdal PROPERTIES DEPENDS link_target)
+      
+  endif()
 endif ()
 MESSAGE("CMAKE_EXE_LINKER_FLAGS ${CMAKE_EXE_LINKER_FLAGS}")

tests/cunit/test_gdal.c

@@ -167,27 +167,26 @@ int test_gdal(int iosysid, int ioid, int num_flavors, int *flavor, int my_rank,
 	    ERR(ret);
 
 	  /* Check the results. */
-// TEMPORARILY DISABLED UNTIL A SEGFAULT IS DIAGNOSED
-//	  for (int f = 0; f < arraylen; f++)
-//	    {
-//	      switch (pio_type)
-//		{
-//		case PIO_INT:
-//		  if (test_data_int_in[f] != test_data_int[f])
-//		    return ERR_WRONG;
-//		  break;
-//		case PIO_FLOAT:
-//		  if (test_data_float_in[f] != test_data_float[f])
-//		    return ERR_WRONG;
-//		  break;
-//		case PIO_DOUBLE:
-//		  if (test_data_double_in[f] != test_data_double[f])
-//		    return ERR_WRONG;
-//		  break;
-//		default:
-//		  ERR(ERR_WRONG);
-//		}
-//	    }
+	  for (int f = 0; f < arraylen; f++)
+	    {
+	      switch (pio_type)
+		{
+		case PIO_INT:
+		  if (test_data_int_in[f] != test_data_int[f])
+		    return ERR_WRONG;
+		  break;
+		case PIO_FLOAT:
+		  if (test_data_float_in[f] != test_data_float[f])
+		    return ERR_WRONG;
+		  break;
+		case PIO_DOUBLE:
+		  if (test_data_double_in[f] != test_data_double[f])
+		    return ERR_WRONG;
+		  break;
+		default:
+		  ERR(ERR_WRONG);
+		}
+	    }
 
 	  /* Close the netCDF file. */
 	  if ((ret = PIOc_closefile(ncid2)))
@@ -247,7 +246,7 @@ int test_all_gdal(int iosysid, int num_flavors, int *flavor, int my_rank,
 int main(int argc, char **argv)
 {
 #define NUM_REARRANGERS_TO_TEST 2
-    int rearranger[NUM_REARRANGERS_TO_TEST] = {PIO_REARR_BOX, PIO_REARR_SUBSET};
+    int rearranger[NUM_REARRANGERS_TO_TEST] = {PIO_REARR_SUBSET, PIO_REARR_BOX};
     int my_rank;
     int ntasks;
     int num_flavors; /* Number of PIO netCDF flavors in this build. */
@@ -283,10 +282,14 @@ int main(int argc, char **argv)
         {
             /* Initialize the PIO IO system. This specifies how
              * many and which processors are involved in I/O. */
-            if ((ret = PIOc_Init_Intracomm(test_comm, TARGET_NTASKS, ioproc_stride,
+            if ((ret = PIOc_Init_Intracomm(test_comm, NUM_IO_PROCS, ioproc_stride,
                                            ioproc_start, rearranger[r], &iosysid)))
                 return ret;
 
+/*	    if ((ret = PIOc_set_rearr_opts(iosysid, PIO_REARR_COMM_P2P, PIO_REARR_COMM_FC_2D_DISABLE, false, false, PIO_REARR_COMM_UNLIMITED_PEND_REQ, false, false, PIO_REARR_COMM_UNLIMITED_PEND_REQ)))
+                return ret;
+*/
+	    
             /* Run tests. */
             if ((ret = test_all_gdal(iosysid, num_flavors, flavor, my_rank, test_comm)))
                 return ret;