fix netcdf4 read

Author: jedwards4b

CMakeLists.txt

@@ -121,7 +121,7 @@ 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(PIO_USE_GDAL "Enable support for Geospatial Data Abstraction Library" OFF)  
 option(BUILD_SHARED_LIBS "Build shared libraries" OFF)
 
 if(APPLE)

src/clib/CMakeLists.txt

@@ -28,7 +28,7 @@ set (src topology.c pio_file.c pioc_support.c pio_lists.c
 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.
+
 if (PIO_USE_GDAL)
   set (src ${src} pio_gdal.c)
 endif()

src/clib/pio_darray_int.c

@@ -999,8 +999,8 @@ recv_and_write_data(file_desc_t *file, const int *varids, const int *frame,
 #ifdef PIO_ENABLE_GDAL
 			if (file->iotype == PIO_IOTYPE_GDAL)
 			    ierr = GDALc_shp_write_float_field(file->pio_ncid, varids[nv], start, count, bufptr);
+			else
 #endif		        
-		      if (file->iotype == PIO_IOTYPE_NETCDF)
                         if ((ierr = nc_put_vara(file->fh, varids[nv], start, count, bufptr)))
                             return check_netcdf2(ios, NULL, ierr, __FILE__, __LINE__);
 		      }

tests/cunit/CMakeLists.txt

@@ -361,12 +361,11 @@ else ()
     add_custom_target(link_target ALL
                       COMMAND ${CMAKE_COMMAND} -E create_symlink
                       ${CMAKE_CURRENT_SOURCE_DIR}/data ${CMAKE_CURRENT_BINARY_DIR}/data)
+    add_dependencies(tests link_target)
     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

@@ -154,6 +154,8 @@ int test_gdal(int iosysid, int ioid, int num_flavors, int *flavor, int my_rank,
         {
 	  sprintf(filename, "data/cb_2018_us_region_20m.shp");
 
+	  assert(filename);
+	  
 	  test_data_in = test_data_float_in;
 	  /* Open the file. */
 	  if ((ret = GDALc_openfile(iosysid, &ncid2, &hDSp, &iotype, filename, PIO_NOWRITE)))

tests/cunit/test_pioc.c

@@ -170,18 +170,17 @@ int check_darray_file(int iosysid, int ntasks, int my_rank, char *filename)
     if ((ret = PIOc_read_darray(ncid, 0, ioid, arraylen, &data_in)))
         ERR(ret);
 
-    /* Check data. */
-    printf("my_rank %d data_in %f\n",my_rank, data_in);
-    if (data_in != my_rank * 10)
-        ERR(ERR_WRONG);
-
     /* Try to write, but this will fail because file was opened with
      * NOWRITE. */
     float fillvalue = 0.0;
     float test_data =  my_rank * 10;
     if (PIOc_write_darray(ncid, 0, ioid, arraylen, &test_data, &fillvalue) != PIO_EPERM)
         ERR(ret);
 
+    /* Check data. */
+    if (data_in != my_rank * 10)
+        ERR(ERR_WRONG);
+
     /* Close the file. */
     if ((ret = PIOc_closefile(ncid)))
         ERR(ret);
@@ -210,7 +209,7 @@ int test_darray(int iosysid, int ioid, int num_flavors, int *flavor, int my_rank
     {
         /* Create the filename. */
         sprintf(filename, "%s_flavor_%d_fv_%d.nc", TEST_NAME, flavor[fmt], fv);
-	printf("Creating file %s\n",filename);
+
         /* Create the netCDF output file. */
         if ((ret = PIOc_createfile(iosysid, &ncid, &(flavor[fmt]), filename, PIO_CLOBBER)))
             ERR(ret);
@@ -238,17 +237,10 @@ int test_darray(int iosysid, int ioid, int num_flavors, int *flavor, int my_rank
         float fillvalue = PIO_FILL_FLOAT;
         float *fillvaluep = fv ? &fillvalue : NULL;
         float test_data[arraylen];
-        for (int f = 0; f < arraylen; f++){
+        for (int f = 0; f < arraylen; f++)
             test_data[f] = my_rank * 10 + f;
-	    if (flavor[fmt] == 3)
-		printf("my_rank %d test_data[%d]%f\n",my_rank, f, test_data[f]);
-	}
-	if (flavor[fmt] == 3)
-	    PIOc_set_log_level(3);
         if ((ret = PIOc_write_darray(ncid, varid, ioid, arraylen, test_data, fillvaluep)))
             ERR(ret);
-	if (flavor[fmt] == 3)
-	    PIOc_set_log_level(0);
 
         /* Close the netCDF file. */
         if ((ret = PIOc_closefile(ncid)))