Merge pull request #1974 from jedwards4b/fix_scalar_write_issue

fix scalar write issue, fix serial build issue

.github/actions/parallelio_cmake/action.yml

@@ -137,5 +137,5 @@ runs:
         -DPnetCDF_C_LIBRARY=${{ inputs.pnetcdf_library }}  \
         $GITHUB_WORKSPACE/parallelio-src
         make VERBOSE=1
-        make tests
+        #make tests
         make install

.github/workflows/autotools.yml

@@ -52,6 +52,6 @@ jobs:
         cd $GITHUB_WORKSPACE
         make check
 
-    - name: Setup tmate session
-      if: ${{ failure() }}
-      uses: mxschmitt/action-tmate@v3
+#    - name: Setup tmate session
+#      if: ${{ failure() }}
+#      uses: mxschmitt/action-tmate@v3

.github/workflows/cmake.yml

@@ -26,6 +26,7 @@ jobs:
         sudo apt-get update
         sudo apt-get install netcdf-bin libnetcdf-dev doxygen graphviz wget gfortran \
         libjpeg-dev libz-dev openmpi-bin libopenmpi-dev cmake pnetcdf-bin libpnetcdf-dev libnetcdff-dev
+        nc-config --all
 
     - name: cmake build
       uses: ./.github/actions/parallelio_cmake

.github/workflows/intel.yml

@@ -121,11 +121,11 @@ jobs:
     - name: parallelio tests
       run: |
         pushd  $GITHUB_WORKSPACE/build
-        #make tests
+        make tests
         ctest -VV -E test_async_
         popd
       #     the following can be used by developers to login to the github server in case of errors
       #     see https://github.com/marketplace/actions/debugging-with-tmate for further details
-    - name: Setup tmate session
-      if: ${{ failure() }}
-      uses: mxschmitt/action-tmate@v3
+#    - name: Setup tmate session
+#      if: ${{ failure() }}
+#      uses: mxschmitt/action-tmate@v3

CMakeLists.txt

@@ -10,7 +10,7 @@ project (PIO C)
 # The project version number.
 set(VERSION_MAJOR   2   CACHE STRING "Project major version number.")
 set(VERSION_MINOR   6   CACHE STRING "Project minor version number.")
-set(VERSION_PATCH   1   CACHE STRING "Project patch version number.")
+set(VERSION_PATCH   2   CACHE STRING "Project patch version number.")
 mark_as_advanced(VERSION_MAJOR VERSION_MINOR VERSION_PATCH)
 
 # Create version info in autotools parlance for pio_meta.h.
@@ -358,8 +358,16 @@ int main() {return 0;}" HAVE_SZIP_WRITE)
 # Check to see if parallel filters are supported by HDF5/netcdf-c.
 ###
 if (HAVE_NETCDF_PAR)
-  check_function_exists(nc_inq_filter_avail HAVE_PAR_FILTERS)
+  CHECK_C_SOURCE_COMPILES("
+#include <netcdf_meta.h>
+#if !NC_HAS_PAR_FILTERS
+    choke me
+#endif
+int main() {return 0;}" HAVE_PAR_FILTERS)
+else()
+  set(HAVE_PAR_FILTERS 0)
 endif()
+
 ###
 # Check to see if this is netcdf-c-4.7.2, which won't work.
 ###

configure.ac

@@ -2,7 +2,7 @@
 ## Ed Hartnett 8/16/17
 
 # Initialize autoconf and automake.
-AC_INIT(pio, 2.6.1)
+AC_INIT(pio, 2.6.2)
 AC_CONFIG_SRCDIR(src/clib/pio_darray.c)
 AM_INIT_AUTOMAKE([foreign serial-tests])
 
@@ -11,15 +11,15 @@ AM_INIT_AUTOMAKE([foreign serial-tests])
 # AC_DEFINE_UNQUOTED for config.h.
 AC_SUBST([PIO_VERSION_MAJOR]) PIO_VERSION_MAJOR=2
 AC_SUBST([PIO_VERSION_MINOR]) PIO_VERSION_MINOR=6
-AC_SUBST([PIO_VERSION_PATCH]) PIO_VERSION_PATCH=1
+AC_SUBST([PIO_VERSION_PATCH]) PIO_VERSION_PATCH=2
 AC_DEFINE_UNQUOTED([PIO_VERSION_MAJOR], [$PIO_VERSION_MAJOR], [PIO major version])
 AC_DEFINE_UNQUOTED([PIO_VERSION_MINOR], [$PIO_VERSION_MINOR], [PIO minor version])
 AC_DEFINE_UNQUOTED([PIO_VERSION_PATCH], [$PIO_VERSION_PATCH], [PIO patch version])
 
 # Once more for the documentation.
 AC_SUBST([VERSION_MAJOR], [2])
 AC_SUBST([VERSION_MINOR], [6])
-AC_SUBST([VERSION_PATCH], [1])
+AC_SUBST([VERSION_PATCH], [2])
 
 
 # The m4 directory holds macros for autoconf.

src/clib/pio.h

@@ -1267,9 +1267,8 @@ extern "C" {
                                const long long *op);
     int PIOc_put_vard_ulonglong(int ncid, int varid, int decompid, const PIO_Offset recnum,
                                 const unsigned long long *op);
-/* use this variable in the NETCDF library (introduced in v4.9.0) to determine if the following
-   functions are available */
-#ifdef NC_HAS_MULTIFILTERS
+
+#ifdef NC_HAS_PAR_FILTERS
   int PIOc_def_var_filter(int ncid, int varid,unsigned int id, size_t nparams, unsigned int *params);
   int PIOc_inq_var_filter_ids(int ncid, int varid, size_t *nfiltersp, unsigned int *ids);
   int PIOc_inq_var_filter_info(int ncid, int varid, unsigned int id, size_t *nparamsp, unsigned int *params );

src/clib/pio_file.c

@@ -156,7 +156,7 @@ PIOc_createfile(int iosysid, int *ncidp, int *iotype, const char *filename,
 
     PLOG((1, "PIOc_createfile iosysid = %d iotype = %d filename = %s mode = %d",
           iosysid, *iotype, filename, mode));
-
+   
     /* Create the file. */
     if ((ret = PIOc_createfile_int(iosysid, ncidp, iotype, filename, mode, 0)))
         return pio_err(ios, NULL, ret, __FILE__, __LINE__);

src/clib/pio_getput_int.c

@@ -1085,100 +1085,51 @@ PIOc_put_vars_tc(int ncid, int varid, const PIO_Offset *start, const PIO_Offset
 #ifdef _PNETCDF
         if (file->iotype == PIO_IOTYPE_PNETCDF)
         {
-            if (ndims == 0) 
-                if ((ierr = ncmpi_begin_indep_data(file->fh)))
-                    return pio_err(ios, file, ierr, __FILE__, __LINE__);
             if (ios->iomain == MPI_ROOT)
             {
-                /* Scalars have to be handled differently. */
-                if (ndims == 0)
+                /* This is not a scalar var. */
+                var_desc_t *vdesc;
+
+                PLOG((2, "PIOc_put_vars_tc calling pnetcdf function"));
+
+                if ((ierr = get_var_desc(varid, &file->varlist, &vdesc)))
+                    return pio_err(ios, file, ierr, __FILE__, __LINE__);
+
+                switch(xtype)
                 {
-                    /* This is a scalar var. */
-                    PLOG((2, "pnetcdf writing scalar with ncmpi_put_vars_*() file->fh = %d varid = %d",
-                          file->fh, varid));
-                    pioassert(!start && !count && !stride, "expected NULLs", __FILE__, __LINE__);
-
-
-                    /* Only the IO main does the IO, so we are not really
-                     * getting parallel IO here. */
-
-                    switch(xtype)
-                    {
-                    case NC_BYTE:
-                        ierr = ncmpi_put_vars_schar(file->fh, varid, start, count, stride, buf);
-                        break;
-                    case NC_CHAR:
-                        ierr = ncmpi_put_vars_text(file->fh, varid, start, count, stride, buf);
-                        break;
-                    case NC_SHORT:
-                        ierr = ncmpi_put_vars_short(file->fh, varid, start, count, stride, buf);
-                        break;
-                    case NC_INT:
-                        ierr = ncmpi_put_vars_int(file->fh, varid, start, count, stride, buf);
-                        break;
-                    case PIO_LONG_INTERNAL:
-                        ierr = ncmpi_put_vars_long(file->fh, varid, start, count, stride, buf);
-                        break;
-                    case NC_FLOAT:
-                        ierr = ncmpi_put_vars_float(file->fh, varid, start, count, stride, buf);
-                        break;
-                    case NC_DOUBLE:
-                        ierr = ncmpi_put_vars_double(file->fh, varid, start, count, stride, buf);
-                        break;
-                    default:
-                        return pio_err(ios, file, PIO_EBADIOTYPE, __FILE__, __LINE__);
-                    }
+                case NC_BYTE:
+                    ierr = ncmpi_bput_vars_schar(file->fh, varid, start, count, fake_stride, buf, NULL);
+                    break;
+                case NC_CHAR:
+                    ierr = ncmpi_bput_vars_text(file->fh, varid, start, count, fake_stride, buf, NULL);
+                    break;
+                case NC_SHORT:
+                    ierr = ncmpi_bput_vars_short(file->fh, varid, start, count, fake_stride, buf, NULL);
+                    break;
+                case NC_INT:
+                    ierr = ncmpi_bput_vars_int(file->fh, varid, start, count, fake_stride, buf, NULL);
+                    break;
+                case PIO_LONG_INTERNAL:
+                    ierr = ncmpi_bput_vars_long(file->fh, varid, start, count, fake_stride, buf, NULL);
+                    break;
+                case NC_FLOAT:
+                    ierr = ncmpi_bput_vars_float(file->fh, varid, start, count, fake_stride, buf, NULL);
+                    break;
+                case NC_DOUBLE:
+                    ierr = ncmpi_bput_vars_double(file->fh, varid, start, count, fake_stride, buf, NULL);
+                    break;
+                default:
+                    return pio_err(ios, file, PIO_EBADTYPE, __FILE__, __LINE__);
                 }
-                else
-                {
-                    /* This is not a scalar var. */
-                    var_desc_t *vdesc;
-
-                    PLOG((2, "PIOc_put_vars_tc calling pnetcdf function"));
-
-                    if ((ierr = get_var_desc(varid, &file->varlist, &vdesc)))
-                        return pio_err(ios, file, ierr, __FILE__, __LINE__);
-
-                    switch(xtype)
-                    {
-                    case NC_BYTE:
-                        ierr = ncmpi_bput_vars_schar(file->fh, varid, start, count, fake_stride, buf, NULL);
-                        break;
-                    case NC_CHAR:
-                        ierr = ncmpi_bput_vars_text(file->fh, varid, start, count, fake_stride, buf, NULL);
-                        break;
-                    case NC_SHORT:
-                        ierr = ncmpi_bput_vars_short(file->fh, varid, start, count, fake_stride, buf, NULL);
-                        break;
-                    case NC_INT:
-                        ierr = ncmpi_bput_vars_int(file->fh, varid, start, count, fake_stride, buf, NULL);
-                        break;
-                    case PIO_LONG_INTERNAL:
-                        ierr = ncmpi_bput_vars_long(file->fh, varid, start, count, fake_stride, buf, NULL);
-                        break;
-                    case NC_FLOAT:
-                        ierr = ncmpi_bput_vars_float(file->fh, varid, start, count, fake_stride, buf, NULL);
-                        break;
-                    case NC_DOUBLE:
-                        ierr = ncmpi_bput_vars_double(file->fh, varid, start, count, fake_stride, buf, NULL);
-                        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));
-
-
-                    vdesc->nreqs++;
+                PLOG((2, "PIOc_put_vars_tc io_rank 0 done with pnetcdf call, ierr=%d", ierr));
+
+
+                vdesc->nreqs++;
 
                 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 */
             } /* end if MPI_ROOT */
-            /* Turn off independent access for pnetcdf file. */
-            if(ndims == 0)
-                if ((ierr = ncmpi_end_indep_data(file->fh)))
-                    return pio_err(ios, file, ierr, __FILE__, __LINE__);
         }
 #endif /* _PNETCDF */
 

src/clib/pio_internal.h

@@ -17,7 +17,7 @@
 #include <limits.h>
 #include <math.h>
 #include <netcdf.h>
-#ifdef PIO_HAS_PAR_FILTERS
+#ifdef NC_HAS_PAR_FILTERS
 #include <netcdf_filter.h>
 #include <netcdf_meta.h>
 #endif

src/clib/pio_nc4.c

@@ -1396,7 +1396,6 @@ PIOc_def_var_filter(int ncid, int varid, unsigned int id, size_t nparams, unsign
     return PIO_NOERR;
 }
 #ifdef PIO_HAS_PAR_FILTERS
-
 /**
  * Get the variable filter ids if any
  *
@@ -1794,8 +1793,10 @@ PIOc_inq_var_zstandard(int ncid, int varid, int* hasfilterp, int *levelp)
 
     return PIO_NOERR;
 }
+// NC_HAS_ZSTD
 #endif
-
+#endif
+#ifdef PIO_HAS_PAR_FILTERS
 /**
  *
  *
@@ -1875,7 +1876,9 @@ PIOc_inq_filter_avail(int ncid, unsigned int id )
 
     return ierr;
 }
-#endif
+// PIO_HAS_PAR_FILTERS
+#endif 
+// NC_HAS_MULTIFILTERS
 #endif
 #ifdef NC_HAS_QUANTIZE
 /**

src/clib/pioc_support.c

@@ -3111,15 +3111,15 @@ iotype_is_valid(int iotype)
         ret++;
 
     /* Some builds include netCDF-4. */
-#ifdef _NETCDF4
+#ifdef NC_HAS_NC4
     if (iotype == PIO_IOTYPE_NETCDF4C || iotype == PIO_IOTYPE_NETCDF4P)
         ret++;
 #endif /* _NETCDF4 */
 
     /* Some builds include pnetcdf. */
+#ifdef _PNETCDF
     if (iotype == PIO_IOTYPE_PNETCDF)
         ret++;
-#ifdef _PNETCDF
 #endif /* _PNETCDF */
 
     return ret;

src/flib/CMakeLists.txt

@@ -200,6 +200,7 @@ else ()
     target_compile_definitions (gptl
       PUBLIC NO_MPIMOD)
   endif()
+  target_compile_definitions (piof PUBLIC NO_MPIMOD)
 endif ()
 
 #===== GPTL =====

src/ncint/ncintdispatch.c

@@ -127,6 +127,7 @@ NC_Dispatch NCINT_dispatcher = {
     NC_NOTNC4_def_var_filter,
     NC_NOTNC4_set_var_chunk_cache,
     NC_NOTNC4_get_var_chunk_cache,
+#ifdef PIO_HAS_PAR_FILTERS
 #if NC_DISPATCH_VERSION == 2
     PIO_NCINT_filter_actions,
 #endif
@@ -141,6 +142,7 @@ NC_Dispatch NCINT_dispatcher = {
 #if NC_DISPATCH_VERSION >= 5
     PIOc_inq_filter_avail,
 #endif
+#endif
 };
 
 /**
@@ -229,10 +231,11 @@ PIO_NCINT_create(const char *path, int cmode, size_t initialsz, int basepe,
     if ((ret = nc4_file_list_add(ncid, path, cmode, NULL)))
         return ret;
 
-    /* Create the file with PIO. The final parameter tests
+    /* Create the file with PIO. The final parameter tells
      * createfile_int to accept the externally assigned ncid. */
     if ((ret = PIOc_createfile_int(diosysid, &ncid, &iotype, path, cmode, 1)))
         return ret;
+
 
     return PIO_NOERR;
 }

tests/cunit/test_intercomm2.c

@@ -338,6 +338,7 @@ int main(int argc, char **argv)
                 sprintf(filename[fmt], "test_intercomm2_%d.nc", flavor[fmt]);
 
                 /* Create a netCDF file with one dimension and one variable. */
+
                 if ((ret = PIOc_createfile(iosysid[my_comp_idx], &ncid, &flavor[fmt], filename[fmt],
                                            NC_CLOBBER)))
                     ERR(ret);

tests/cunit/test_pioc.c

@@ -1827,6 +1827,9 @@ int test_scalar(int iosysid, int num_flavors, int *flavor, int my_rank, int asyn
         int test_val = TEST_VAL_42;
         if ((ret = PIOc_put_var_int(ncid, varid, &test_val)))
             ERR(ret);
+        /* flush the write buffer */
+        if ((ret = PIOc_sync(ncid)))
+            ERR(ret);
 
         /* Check the scalar var. */
         if ((ret = check_scalar_var(ncid, varid, flavor[fmt], my_rank)))
@@ -2326,7 +2329,6 @@ int test_all(int iosysid, int num_flavors, int *flavor, int my_rank, MPI_Comm te
     /* This will be our file name for writing out decompositions. */
     sprintf(filename, "decomp_%d.txt", my_rank);
     sprintf(nc_filename, "decomp_%d.nc", my_rank);
-
     /* This is a simple test that just creates the decomp with
      * async. */
     if (async)