Merge pull request #1864 from jedwards4b/check_netcdf_errfix

fix error in check_netcdf call and in detecting dap
NCAR · Mar 18, 2021 · 357ca50 · 357ca50
2 parents 813e7c1 + 9a4e836
commit 357ca50
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Showing 7 changed files with 53 additions and 58 deletions.
diff --git a/.github/workflows/autotools.yml b/.github/workflows/autotools.yml
@@ -27,7 +27,7 @@ jobs:
         sudo apt-spy2 fix --commit
         # after selecting a specific mirror, we need to run 'apt-get update'
         sudo apt-get update
-        sudo apt-get install netcdf-bin libnetcdf-dev doxygen graphviz wget gfortran libjpeg-dev libz-dev openmpi-bin libopenmpi-dev 
+        sudo apt-get install netcdf-bin libnetcdf-dev doxygen graphviz wget gfortran libjpeg-dev libz-dev openmpi-bin libopenmpi-dev
     - name: cache-pnetcdf
       id: cache-pnetcdf
       uses: actions/cache@v2
@@ -50,6 +50,6 @@ jobs:
     - name: autoreconf
       run: autoreconf -i
     - name: configure
-      run: ./configure --enable-fortran --enable-docs
+      run: ./configure --enable-fortran --enable-docs  --with-mpiexec='mpiexec --oversubscribe'
     - name: make check
       run: make -j check
diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
@@ -54,7 +54,7 @@ jobs:
         set -x
         mkdir build
         cd build
-        cmake -Wno-dev -DNetCDF_C_LIBRARY=/usr/lib/x86_64-linux-gnu/libnetcdf.so -DNetCDF_C_INCLUDE_DIR=/usr/include -DPnetCDF_PATH='/home/runner/pnetcdf' -DPIO_ENABLE_FORTRAN=Off -DPIO_HDF5_LOGGING=On -DPIO_USE_MALLOC=On -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_TIMING=Off ..
+        cmake -Wno-dev -DNetCDF_C_LIBRARY=/usr/lib/x86_64-linux-gnu/libnetcdf.so -DNetCDF_C_INCLUDE_DIR=/usr/include -DPnetCDF_PATH='/home/runner/pnetcdf' -DPIO_ENABLE_FORTRAN=Off -DPIO_HDF5_LOGGING=On -DPIO_USE_MALLOC=On -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_TIMING=Off  -DMPIEXEC_PREFLAGS="--oversubscribe" ..
         make VERBOSE=1
         make tests VERBOSE=1
         ctest -VV
diff --git a/.github/workflows/strict_autotools_ubuntu_latest.yml b/.github/workflows/strict_autotools_ubuntu_latest.yml
@@ -27,7 +27,7 @@ jobs:
         sudo apt-spy2 fix --commit
         # after selecting a specific mirror, we need to run 'apt-get update'
         sudo apt-get update
-        sudo apt-get install netcdf-bin libnetcdf-dev doxygen graphviz wget gfortran libjpeg-dev libz-dev openmpi-bin libopenmpi-dev 
+        sudo apt-get install netcdf-bin libnetcdf-dev doxygen graphviz wget gfortran libjpeg-dev libz-dev openmpi-bin libopenmpi-dev
 
     - name: cache-pnetcdf
       id: cache-pnetcdf
@@ -56,7 +56,6 @@ jobs:
         export CFLAGS="-std=c99 -Wall"
         export FFLAGS="-Wall"
         export FCFLAGS="-Wall"
-        export DISTCHECK_CONFIGURE_FLAGS="--enable-fortran"
+        export DISTCHECK_CONFIGURE_FLAGS="--enable-fortran --with-mpiexec='/usr/bin/mpiexec --oversubscribe'"
         ./configure
         make -j distcheck
-        
diff --git a/CTestScript.cmake b/CTestScript.cmake
@@ -42,6 +42,8 @@ execute_process (COMMAND ${HOSTNAME_CMD}
 ## -- Set hostname ID (e.g., alcf, nwsc, nersc, ...)
 message ("hostname is ${HOSTNAME}")
 
+if (DEFINED HOSTNAME_ID)
+else()
 # UCAR/NWSC Machines
 if (HOSTNAME MATCHES "^yslogin" OR
     HOSTNAME MATCHES "^geyser" OR
@@ -51,7 +53,7 @@ if (HOSTNAME MATCHES "^yslogin" OR
 # New UCAR/NWSC SGI Machines
 elseif (HOSTNAME MATCHES "^laramie" OR
         HOSTNAME MATCHES "^chadmin" OR
-	HOSTNAME MATCHES "^cheyenne")
+        HOSTNAME MATCHES "^cheyenne")
    set (HOSTNAME_ID "nwscla")
 # ALCF/Argonne Machines
 elseif (HOSTNAME MATCHES "^mira" OR
@@ -87,10 +89,10 @@ else ()
      if (CMAKE_SYSTEM_NAME MATCHES "Catamount")
         set (HOSTNAME_ID "ncsa")
      else ()
-     	set (HOSTNAME_ID "unknown")
+        set (HOSTNAME_ID "unknown")
      endif ()
 endif ()
-
+endif()
 ## -- Get system info
 
 find_program (UNAME NAMES uname)

diff --git a/cmake/LibMPI.cmake b/cmake/LibMPI.cmake
@@ -33,9 +33,9 @@ function (platform_name RETURN_VARIABLE)
 
     if (SITENAME MATCHES "^laramie" OR
             SITENAME MATCHES "^cheyenne" OR
-	    SITENAME MATCHES "^chadmin")
+            SITENAME MATCHES "^chadmin")
 
-	set (${RETURN_VARIABLE} "nwscla" PARENT_SCOPE)
+        set (${RETURN_VARIABLE} "nwscla" PARENT_SCOPE)
 
     # ALCF/Argonne Machines
     elseif (SITENAME MATCHES "^mira" OR
@@ -67,7 +67,6 @@ function (platform_name RETURN_VARIABLE)
         set (${RETURN_VARIABLE} "unknown" PARENT_SCOPE)
 
     endif ()
-
 endfunction ()
 
 #==============================================================================

diff --git a/cmake/TryNetCDF_DAP.c b/cmake/TryNetCDF_DAP.c
@@ -5,9 +5,9 @@
 
 int main()
 {
-#if NC_HAS_DAP==1
-	return 0;
+#if NC_HAS_DAP==1 || NC_HAS_DAP2==1 || NC_HAS_DAP4==1
+        return 0;
 #else
-	XXX;
+        XXX;
 #endif
 }
diff --git a/src/clib/pio_getput_int.c b/src/clib/pio_getput_int.c
@@ -1140,6 +1140,8 @@ PIOc_put_vars_tc(int ncid, int varid, const PIO_Offset *start, const PIO_Offset
                 int *request;
 
                 PLOG((2, "PIOc_put_vars_tc calling pnetcdf function"));
+                flush_output_buffer(file, false, num_elem*typelen);
+
                 /*vdesc = &file->varlist[varid];*/
                 if ((ierr = get_var_desc(varid, &file->varlist, &vdesc)))
                     return pio_err(ios, file, ierr, __FILE__, __LINE__);
@@ -1148,47 +1150,42 @@ PIOc_put_vars_tc(int ncid, int varid, const PIO_Offset *start, const PIO_Offset
                                                    sizeof(int) * (vdesc->nreqs + PIO_REQUEST_ALLOC_CHUNK))))
                         return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
                 request = vdesc->request + vdesc->nreqs;
-                PLOG((2, "PIOc_put_vars_tc request = %d", vdesc->request));
+                PLOG((2, "PIOc_put_vars_tc request = %d size = %d", vdesc->request, num_elem*typelen));
 
-                /* Only the IO master actually does the call. */
-//                if (ios->iomaster == MPI_ROOT)
-//                {
-                    switch(xtype)
-                    {
-                    case NC_BYTE:
-                        ierr = ncmpi_bput_vars_schar(file->fh, varid, start, count, fake_stride, buf, request);
-                        break;
-                    case NC_CHAR:
-                        ierr = ncmpi_bput_vars_text(file->fh, varid, start, count, fake_stride, buf, request);
-                        break;
-                    case NC_SHORT:
-                        ierr = ncmpi_bput_vars_short(file->fh, varid, start, count, fake_stride, buf, request);
-                        break;
-                    case NC_INT:
-                        ierr = ncmpi_bput_vars_int(file->fh, varid, start, count, fake_stride, buf, request);
-                        break;
-                    case PIO_LONG_INTERNAL:
-                        ierr = ncmpi_bput_vars_long(file->fh, varid, start, count, fake_stride, buf, request);
-                        break;
-                    case NC_FLOAT:
-                        ierr = ncmpi_bput_vars_float(file->fh, varid, start, count, fake_stride, buf, request);
-                        break;
-                    case NC_DOUBLE:
-                        ierr = ncmpi_bput_vars_double(file->fh, varid, start, count, fake_stride, buf, request);
-                        break;
-                    default:
-                        return pio_err(ios, file, PIO_EBADTYPE, __FILE__, __LINE__);
-                    }
-                    PLOG((2, "PIOc_put_vars_tc io_rank 0 done with pnetcdf call, ierr=%d", ierr));
+                switch(xtype)
+                {
+                case NC_BYTE:
+                    ierr = ncmpi_bput_vars_schar(file->fh, varid, start, count, fake_stride, buf, request);
+                    break;
+                case NC_CHAR:
+                    ierr = ncmpi_bput_vars_text(file->fh, varid, start, count, fake_stride, buf, request);
+                    break;
+                case NC_SHORT:
+                    ierr = ncmpi_bput_vars_short(file->fh, varid, start, count, fake_stride, buf, request);
+                    break;
+                case NC_INT:
+                    ierr = ncmpi_bput_vars_int(file->fh, varid, start, count, fake_stride, buf, request);
+                    break;
+                case PIO_LONG_INTERNAL:
+                    ierr = ncmpi_bput_vars_long(file->fh, varid, start, count, fake_stride, buf, request);
+                    break;
+                case NC_FLOAT:
+                    ierr = ncmpi_bput_vars_float(file->fh, varid, start, count, fake_stride, buf, request);
+                    break;
+                case NC_DOUBLE:
+                    ierr = ncmpi_bput_vars_double(file->fh, varid, start, count, fake_stride, buf, request);
+                    break;
+                default:
+                    return pio_err(ios, file, PIO_EBADTYPE, __FILE__, __LINE__);
+                }
+                PLOG((2, "PIOc_put_vars_tc io_rank 0 done with pnetcdf call, ierr=%d", ierr));
 
-//                }
-//                else
-//                    *request = PIO_REQ_NULL;
 
                 vdesc->nreqs++;
-                flush_output_buffer(file, false, 0);
-                PLOG((2, "PIOc_put_vars_tc flushed output buffer"));
-                if(ierr == -40)
+//                flush_output_buffer(file, ierr == PIO_EINSUFFBUF, 0);
+//                PLOG((2, "PIOc_put_vars_tc flushed output buffer"));
+
+                if(ierr == PIO_EINVALCOORDS)
                     for(int i=0; i<ndims; i++)
                         PLOG((2,"start[%d] %ld count[%d] %ld\n",i,start[i],i,count[i]));
             } /* endif ndims == 0 */
@@ -1265,15 +1262,13 @@ PIOc_put_vars_tc(int ncid, int varid, const PIO_Offset *start, const PIO_Offset
         if (ndims && !stride_present)
             free(fake_stride);
 
-        if (ierr)
-            return check_netcdf(file, ierr, __FILE__, __LINE__);
     }
 
     /* Broadcast and check the return code. */
-    /* if ((mpierr = MPI_Bcast(&ierr, 1, MPI_INT, ios->ioroot, ios->my_comm))) */
-    /*     return check_mpi(NULL, file, mpierr, __FILE__, __LINE__); */
-    /* if (ierr) */
-    /*     return check_netcdf(file, ierr, __FILE__, __LINE__); */
+    if ((mpierr = MPI_Bcast(&ierr, 1, MPI_INT, ios->ioroot, ios->my_comm)))
+        return check_mpi(NULL, file, mpierr, __FILE__, __LINE__);
+    if (ierr)
+        return check_netcdf(file, ierr, __FILE__, __LINE__);
     PLOG((2, "PIOc_put_vars_tc bcast netcdf return code %d complete", ierr));
 
     return PIO_NOERR;