HDF5: Fix chunking warning (AMReX-Codes#4033) (AMReX-Codes#4034)

## Summary Fixes AMReX-Codes#4033, where chunk value is read regardless of storage format. ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] include documentation in the code and/or rst files, if appropriate
JBlaschke · Jul 17, 2024 · 8b3ffe6 · 8b3ffe6
1 parent dcb9cc0
commit 8b3ffe6
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Showing 2 changed files with 22 additions and 15 deletions.
diff --git a/Src/Extern/HDF5/AMReX_ParticleHDF5.H b/Src/Extern/HDF5/AMReX_ParticleHDF5.H
@@ -765,9 +765,11 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
 /* #endif */
 
     hsize_t chunk_size;
-    if (H5Pget_chunk(dcpl_int, 1, &chunk_size) > -1) {
-        if ((int)chunk_size > total_int_size) {
-            H5Pset_chunk(dcpl_int, 1, &total_int_size);
+    if (H5Pget_layout(dcpl_int) == H5D_CHUNKED) {
+        if (H5Pget_chunk(dcpl_int, 1, &chunk_size) > -1) {
+            if ((int)chunk_size > total_int_size) {
+                H5Pset_chunk(dcpl_int, 1, &total_int_size);
+            }
         }
     }
 
@@ -806,10 +808,11 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
         }
     }
 #endif
-
-    if (H5Pget_chunk(dcpl_real, 1, &chunk_size) > -1) {
-        if ((int)chunk_size > total_real_size) {
-            H5Pset_chunk(dcpl_real, 1, &total_real_size);
+    if (H5Pget_layout(dcpl_real) == H5D_CHUNKED) {
+        if (H5Pget_chunk(dcpl_real, 1, &chunk_size) > -1) {
+            if ((int)chunk_size > total_real_size) {
+                H5Pset_chunk(dcpl_real, 1, &total_real_size);
+            }
         }
     }
 

diff --git a/Src/Extern/HDF5/AMReX_PlotFileUtilHDF5.cpp b/Src/Extern/HDF5/AMReX_PlotFileUtilHDF5.cpp
@@ -720,10 +720,12 @@ void WriteMultiLevelPlotfileHDF5SingleDset (const std::string& plotfilename,
 #endif
 
         // Force maximum chunk size to be size of write
-        hsize_t chunk_size;
-        if (H5Pget_chunk(lev_dcpl_id, 1, &chunk_size) > -1) {
-            if ((int)chunk_size > hs_allprocsize[0]) {
-                H5Pset_chunk(lev_dcpl_id, 1, hs_allprocsize);
+        if (H5Pget_layout(lev_dcpl_id) == H5D_CHUNKED) {
+            hsize_t chunk_size;
+            if (H5Pget_chunk(lev_dcpl_id, 1, &chunk_size) > -1) {
+                if ((int)chunk_size > hs_allprocsize[0]) {
+                    H5Pset_chunk(lev_dcpl_id, 1, hs_allprocsize);
+                }
             }
         }
 
@@ -1190,10 +1192,12 @@ void WriteMultiLevelPlotfileHDF5MultiDset (const std::string& plotfilename,
             hid_t dataspace    = H5Screate_simple(1, hs_allprocsize, NULL);
             snprintf(dataname, sizeof dataname, "data:datatype=%d", jj);
             // Force maximum chunk size to be size of write
-            hsize_t chunk_size;
-            if (H5Pget_chunk(lev_dcpl_id, 1, &chunk_size) > -1) {
-                if ((int)chunk_size > hs_allprocsize[0]) {
-                    H5Pset_chunk(lev_dcpl_id, 1, hs_allprocsize);
+            if (H5Pget_layout(lev_dcpl_id) == H5D_CHUNKED) {
+                hsize_t chunk_size;
+                if (H5Pget_chunk(lev_dcpl_id, 1, &chunk_size) > -1) {
+                    if ((int)chunk_size > hs_allprocsize[0]) {
+                        H5Pset_chunk(lev_dcpl_id, 1, hs_allprocsize);
+                    }
                 }
             }
 #ifdef AMREX_USE_HDF5_ASYNC