`CheckpointPostHDF5` appends text data to HDF5 binary file

[WeiqunZhang]

• Type: Bug / Data corruption
• Severity: High
• Component: HDF5 particle checkpoint post-processing
• Location: Src/Extern/HDF5/AMReX_ParticleHDF5.H:512-513

Problem

CheckpointPostHDF5 opens HdrFileNamePrePost with std::ofstream in append mode and writes per-grid metadata as text:

std::ofstream HdrFile;
HdrFile.open(HdrFileNamePrePost.c_str(), std::ios::out | std::ios::app);
// ...
HdrFile << whichPrePost[lev][j] << ' ' << countPrePost[lev][j] << ' '
        << wherePrePost[lev][j] << '\n';

However, HdrFileNamePrePost is set in WriteHDF5ParticleDataSync (line 228 of AMReX_WriteBinaryParticleDataHDF5.H) to an .h5 file:

HDF5FileName += ".h5";
pc.HdrFileNamePrePost = HDF5FileName;

Appending raw text to an HDF5 binary file corrupts the HDF5 structure. HDF5 files have a specific binary format with a superblock, B-tree indices, and heap structures. Appending arbitrary bytes beyond the HDF5 end-of-file marker makes the file unreadable by most HDF5 tools and prevents subsequent H5Fopen from working correctly.

Impact

• Any use of the pre/post checkpoint path with HDF5 (usePrePost = true) produces corrupt HDF5 files.
• The non-HDF5 CheckpointPost correctly writes to a separate text header file, but CheckpointPostHDF5 reuses the .h5 filename without adaptation.

Suggested patch

The per-grid metadata (which, count, where) should be written as HDF5 attributes or datasets, not appended as text. One approach:

--- a/Src/Extern/HDF5/AMReX_ParticleHDF5.H
+++ b/Src/Extern/HDF5/AMReX_ParticleHDF5.H
@@ -509,8 +509,14 @@

     const int IOProcNumber = ParallelDescriptor::IOProcessorNumber();
-    std::ofstream HdrFile;
-    HdrFile.open(HdrFileNamePrePost.c_str(), std::ios::out | std::ios::app);
+    hid_t fid = -1;
+    if (ParallelDescriptor::IOProcessor()) {
+        fid = H5Fopen(HdrFileNamePrePost.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
+        if (fid < 0) {
+            amrex::Abort("ParticleContainer::CheckpointPostHDF5(): "
+                         "unable to open HDF5 file for post metadata");
+        }
+    }

     for(int lev(0); lev <= finestLevel(); ++lev) {
         ParallelDescriptor::ReduceIntSum (...);
@@ // write which/count/where as HDF5 datasets per level instead of text

The exact HDF5 schema (attributes vs. datasets, naming) should match whatever the corresponding RestartHDF5 expects.

Prepared by Claude