amrex.hdf5.patch

diff --git a/Src/Extern/HDF5/AMReX_PlotFileUtilHDF5.cpp b/Src/Extern/HDF5/AMReX_PlotFileUtilHDF5.cpp
index 7573b195c..90af31464 100644
--- a/Src/Extern/HDF5/AMReX_PlotFileUtilHDF5.cpp
+++ b/Src/Extern/HDF5/AMReX_PlotFileUtilHDF5.cpp
@@ -588,7 +588,7 @@ void WriteMultiLevelPlotfileHDF5SingleDset (const std::string& plotfilename,
 #endif
         if(centerdataset < 0) { std::cout << "Create center dataset failed! ret = " << centerdataset << std::endl; break;}
 
-        Vector<unsigned long long> offsets(sortedGrids.size() + 1);
+        Vector<unsigned long long> offsets(sortedGrids.size() + 1, 0);
         unsigned long long currentOffset(0L);
         for(int b(0); b < sortedGrids.size(); ++b) {
             offsets[b] = currentOffset;
@@ -596,21 +596,23 @@ void WriteMultiLevelPlotfileHDF5SingleDset (const std::string& plotfilename,
         }
         offsets[sortedGrids.size()] = currentOffset;
 
-        Vector<unsigned long long> procOffsets(nProcs);
-        int posCount(0);
-        Vector<unsigned long long> procBufferSize(nProcs);
+        Vector<unsigned long long> procOffsets(nProcs, 0);
+        Vector<unsigned long long> procBufferSize(nProcs, 0);
         unsigned long long totalOffset(0);
         for(auto it = gridMap.begin(); it != gridMap.end(); ++it) {
             int proc = it->first;
             Vector<Box> &boxesAtProc = it->second;
-            /* BL_ASSERT(posCount == proc); */
-            procOffsets[posCount] = totalOffset;
-            ++posCount;
+            procOffsets[proc] = totalOffset;
             procBufferSize[proc] = 0L;
             for(int b(0); b < boxesAtProc.size(); ++b) {
                 procBufferSize[proc] += boxesAtProc[b].numPts() * ncomp;
             }
             totalOffset += procBufferSize[proc];
+
+            /* if (level == 2) { */
+            /*     fprintf(stderr, "Rank %d: level %d, proc %d, offset %ld, size %ld, all size %ld\n", */
+            /*             myProc, level, proc, procOffsets[proc], procBufferSize[proc], totalOffset); */
+            /* } */
         }
 
         if(ParallelDescriptor::IOProcessor()) {
@@ -658,7 +660,12 @@ void WriteMultiLevelPlotfileHDF5SingleDset (const std::string& plotfilename,
         hid_t dataspace    = H5Screate_simple(1, hs_allprocsize, NULL);
         hid_t memdataspace = H5Screate_simple(1, hs_procsize, NULL);
 
-        H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, ch_offset, NULL, hs_procsize, NULL);
+        /* fprintf(stderr, "Rank %d: level %d, offset %ld, size %ld, all size %ld\n", myProc, level, ch_offset[0], hs_procsize[0], hs_allprocsize[0]); */
+
+        if (hs_procsize[0] == 0)
+            H5Sselect_none(dataspace);
+        else
+            H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, ch_offset, NULL, hs_procsize, NULL);
 
         Vector<Real> a_buffer(procBufferSize[myProc], -1.0);
         const MultiFab* data;
@@ -1019,15 +1026,12 @@ void WriteMultiLevelPlotfileHDF5MultiDset (const std::string& plotfilename,
         offsets[sortedGrids.size()] = currentOffset;
 
         Vector<unsigned long long> procOffsets(nProcs);
-        int posCount(0);
         Vector<unsigned long long> procBufferSize(nProcs);
         unsigned long long totalOffset(0);
         for(auto it = gridMap.begin(); it != gridMap.end(); ++it) {
             int proc = it->first;
             Vector<Box> &boxesAtProc = it->second;
-            /* BL_ASSERT(posCount == proc); */
-            procOffsets[posCount] = totalOffset;
-            ++posCount;
+            procOffsets[proc] = totalOffset;
             procBufferSize[proc] = 0L;
             for(int b(0); b < boxesAtProc.size(); ++b) {
                 /* procBufferSize[proc] += boxesAtProc[b].numPts() * ncomp; */
@@ -1081,7 +1085,10 @@ void WriteMultiLevelPlotfileHDF5MultiDset (const std::string& plotfilename,
         hid_t dataspace    = H5Screate_simple(1, hs_allprocsize, NULL);
         hid_t memdataspace = H5Screate_simple(1, hs_procsize, NULL);
 
-        H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, ch_offset, NULL, hs_procsize, NULL);
+        if (hs_procsize[0] == 0)
+            H5Sselect_none(dataspace);
+        else
+            H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, ch_offset, NULL, hs_procsize, NULL);
 
         Vector<Real> a_buffer(procBufferSize[myProc]*ncomp, -1.0);
         Vector<Real> a_buffer_ind(procBufferSize[myProc], -1.0);