Merge pull request ESMCI#1278 from NCAR/ejh_test_4

Fixes to PIO for newer netCDF library versions
rfiorella · Jan 11, 2018 · 7c92c48 · 7c92c48
2 parents 4e42e46 + fda1302
commit 7c92c48
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Showing 7 changed files with 52 additions and 13 deletions.
diff --git a/src/clib/pio_darray.c b/src/clib/pio_darray.c
@@ -529,8 +529,10 @@ int PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *
         if ((ierr = find_var_fillvalue(file, varid, vdesc)))
             return pio_err(ios, file, PIO_EBADID, __FILE__, __LINE__);
 
-    /* Check that if the user passed a fill value, it is correct. */
-    if (fillvalue)
+    /* Check that if the user passed a fill value, it is correct. If
+     * use_fill is false, then find_var_fillvalue will not end up
+     * getting a fill value. */
+    if (fillvalue && vdesc->use_fill)
         if (memcmp(fillvalue, vdesc->fillvalue, vdesc->pio_type_size))
             return pio_err(ios, file, PIO_EINVAL, __FILE__, __LINE__);
 

diff --git a/src/clib/pio_darray_int.c b/src/clib/pio_darray_int.c
@@ -805,10 +805,16 @@ int pio_read_darray_nc(file_desc_t *file, io_desc_t *iodesc, int vid, void *iobu
            the mpitype. */
         region = iodesc->firstregion;
 
-        /* ??? */
+        /* There are different numbers of dims in the decomposition
+         * and the file. */
         if (fndims > ndims)
         {
             ndims++;
+
+            /* If the user did not call setframe, use a default frame
+             * of 0. This is required for backward compatibility. */
+            if (vdesc->record < 0)
+                vdesc->record = 0;
         }
 
         /* For each regions, read the data. */
@@ -833,7 +839,8 @@ int pio_read_darray_nc(file_desc_t *file, io_desc_t *iodesc, int vid, void *iobu
                 else
                     bufptr=(void *)((char *)iobuf + iodesc->mpitype_size * region->loffset);
 
-                LOG((2, "%d %d %d", iodesc->llen - region->loffset, iodesc->llen, region->loffset));
+                LOG((2, "iodesc->llen - region->loffset %d, iodesc->llen %d, region->loffset  %d vdesc->record %d",
+                     iodesc->llen - region->loffset, iodesc->llen, region->loffset, vdesc->record));
 
                 /* Get the start/count arrays. */
                 if (vdesc->record >= 0 && fndims > 1)
@@ -862,6 +869,11 @@ int pio_read_darray_nc(file_desc_t *file, io_desc_t *iodesc, int vid, void *iobu
                 }
             }
 
+#ifdef LOGGING
+            for (int i = 1; i < ndims; i++)
+                LOG((3, "start[%d] %d count[%d] %d", i, start[i], i, count[i]));
+#endif /* LOGGING */
+
             /* Do the read. */
             switch (file->iotype)
             {
@@ -1023,6 +1035,11 @@ int pio_read_darray_nc_serial(file_desc_t *file, io_desc_t *iodesc, int vid,
     if ((ierr = PIOc_inq_varndims(file->pio_ncid, vid, &fndims)))
         return pio_err(ios, file, ierr, __FILE__, __LINE__);
 
+    /* If setframe was not called, use a default value of 0. This is
+     * required for backward compatibility. */
+    if (fndims == ndims + 1 && vdesc->record < 0)
+        vdesc->record = 0;
+
     /* Confirm that we are being called with the correct ndims. */
     pioassert((fndims == ndims && vdesc->record < 0) ||
               (fndims == ndims + 1 && vdesc->record >= 0),
@@ -1043,6 +1060,12 @@ int pio_read_darray_nc_serial(file_desc_t *file, io_desc_t *iodesc, int vid,
            the mpitype. */
         region = iodesc->firstregion;
 
+        /* If setframe was not set before this call, assume a value of
+         * 0. This is required for backward compatibility. */
+        if (fndims > ndims)		
+            if (vdesc->record < 0)		
+                vdesc->record = 0;
+
         /* Put together start/count arrays for all regions. */
         for (int regioncnt = 0; regioncnt < iodesc->maxregions; regioncnt++)
         {

diff --git a/src/clib/pio_msg.c b/src/clib/pio_msg.c
@@ -1121,7 +1121,7 @@ int inq_var_fill_handler(iosystem_desc_t *ios)
     char fill_mode_present, fill_value_present;
     PIO_Offset type_size;
     int fill_mode, *fill_modep = NULL;
-    PIO_Offset *fill_value, *fill_valuep = NULL;
+    void *fill_value, *fill_valuep = NULL;
     int mpierr;
 
     assert(ios);
@@ -1154,12 +1154,21 @@ int inq_var_fill_handler(iosystem_desc_t *ios)
         fill_valuep = fill_value;
 
     /* Call the inq function to get the values. */
+    LOG((3, "inq_var_fill_handlder about to call inq_var_fill"));
     PIOc_inq_var_fill(ncid, varid, fill_modep, fill_valuep);
+    if (fill_modep)
+        LOG((3, "after inq_var_fill fill_modep %d", *fill_modep));
 
     /* Free fill value storage if we allocated some. */
     if (fill_value_present)
+    {
+        LOG((3, "about to free fill_value"));
         free(fill_value);
+        LOG((3, "freed fill_value"));
+    }
 
+    if (fill_modep)
+        LOG((3, "done with inq_var_fill_handler", *fill_modep));
     return PIO_NOERR;
 }
 

diff --git a/src/clib/pio_nc.c b/src/clib/pio_nc.c
@@ -2208,8 +2208,8 @@ int PIOc_def_var_fill(int ncid, int varid, int fill_mode, const void *fill_value
             return check_netcdf(file, ierr, __FILE__, __LINE__);
         if ((ierr = PIOc_inq_type(ncid, xtype, NULL, &type_size)))
             return check_netcdf(file, ierr, __FILE__, __LINE__);
+        LOG((2, "PIOc_def_var_fill type_size = %d", type_size));
     }
-    LOG((2, "PIOc_def_var_fill type_size = %d", type_size));
 
     /* If async is in use, and this is not an IO task, bcast the parameters. */
     if (ios->async)
@@ -2264,7 +2264,11 @@ int PIOc_def_var_fill(int ncid, int varid, int fill_mode, const void *fill_value
         {
             LOG((2, "defining fill value attribute for netCDF classic file"));
             if (file->do_io)
-                ierr = nc_put_att(file->fh, varid, _FillValue, xtype, 1, fill_valuep);
+            {
+                ierr = nc_set_fill(file->fh, NC_FILL, NULL);
+                if (!ierr)
+                    ierr = nc_put_att(file->fh, varid, _FillValue, xtype, 1, fill_valuep);
+            }
         }
         else
         {

diff --git a/src/clib/pioc.c b/src/clib/pioc.c
@@ -220,7 +220,6 @@ int PIOc_setframe(int ncid, int varid, int frame)
 
     /* Set the record dimension value for this variable. This will be
      * used by the write_darray functions. */
-    /* file->varlist[varid].record = frame; */
     vdesc->record = frame;
 
     return PIO_NOERR;

diff --git a/tests/cunit/test_darray_1d.c b/tests/cunit/test_darray_1d.c
@@ -579,11 +579,9 @@ int test_darray_fill_unlim(int iosysid, int ioid, int pio_type, int num_flavors,
         if (!(test_data_in = malloc(type_size * arraylen)))
             ERR(PIO_ENOMEM);
 
-        /* Set the record number for the unlimited dimension. */
-        if ((ret = PIOc_setframe(ncid, varid, 0)))
-            ERR(ret);
-
-        /* Read the data. */
+        /* Read the data. We don't have to set the record number for
+         * the unlimited dimension. If we don't set it, PIO will
+         * assume a value of 0. */
         if ((ret = PIOc_read_darray(ncid, varid, ioid, arraylen, test_data_in)))
             ERR(ret);
 

diff --git a/tests/cunit/test_darray_2sync.c b/tests/cunit/test_darray_2sync.c
@@ -189,6 +189,10 @@ int darray_fill_test(int iosysid, int my_rank, int num_iotypes, int *iotype,
             if ((ret = PIOc_def_var(ncid, VAR_NAME, test_type[t], NDIM1, &dimid, &varid)))
                 ERR(ret);
 
+            /* Turn on fill mode for this var. */
+            if ((ret = PIOc_def_var_fill(ncid, varid, 0, default_fillvalue)))
+                ERR(ret);
+
             /* End define mode. */
             if ((ret = PIOc_enddef(ncid)))
                 ERR(ret);