CarpetIOHDF5: implement "out_unchunked" option for individual variables to be output

Apart from setting the parameter IO::out_unchunked to choose the output mode
for all variables, this can be overridden for individual variables in an option
string appended to the variable's name in the IOHDF5::out_vars parameter.

darcs-hash:20051005100152-776a0-9f6f2e4b691a46b12aefab555440625f39836aaf.gz

2 files changed, 28 insertions, 6 deletions

diff --git a/Carpet/CarpetIOHDF5/doc/documentation.tex b/Carpet/CarpetIOHDF5/doc/documentation.tex
index 28176c549..ef401153e 100644
--- a/Carpet/CarpetIOHDF5/doc/documentation.tex
+++ b/Carpet/CarpetIOHDF5/doc/documentation.tex
@@ -94,8 +94,9 @@ Parameters to control the \ThisThorn\ I/O method are:
         all variables. Multiple names must be separated by whitespaces.
 
         Each group/variable name can have an option string attached in which you
-        can specify a different output frequency for that individual variable
-	or a set of individual refinement levels to be output, e.g.
+        can specify a different output frequency for that individual variable,
+	a set of individual refinement levels to be output, or an individual
+        output mode, e.g.
 \begin{verbatim}
   IOHDF5::out_vars = "wavetoy::phi{ out_every = 4 refinement_levels = { 1 2 } }"
 \end{verbatim}
@@ -152,9 +153,20 @@ for a global view on the data.
 The default is to output distributed grid variables in parallel, each processor
 writing a file
 {\tt \textless varname\textgreater.file\_\textless processor ID\textgreater.h5}.
+The chunked/unchunked mode can also be set individually in a key/value
+option string (with the key {\tt out\_unchunked} and possible string values
+{\tt "true|false|yes|no"}) appended to a group/variable name in the
+{\tt out\_vars} parameter, eg.
+\begin{verbatim}
+  IOHDF5::out_vars = "wavetoy::phi{out_unchunked = 'true'}  grid::coordinates"
+\end{verbatim}
+will cause the variable {\tt phi} to be output into a single unchunked file
+whereas other variables will still be output into separate chunked files
+(assuming the output mode is left to its default).
 Grid scalars
 and {\tt DISTRIB = CONST} grid arrays are always output as unchunked data
-on processor 0 only.\\
+on processor 0 only.
+
 Parallel output in a parallel simulation will ensure maximum I/O
 performance. Note that changing the output mode to serial I/O might only be
 necessary if the data analysis and visualisation tools cannot deal with
diff --git a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
index bbace4a4b..74de7fe48 100644
--- a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
+++ b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
@@ -566,7 +566,12 @@ static int OutputVarAs (const cGH* const cctkGH, const char* const fullname,
   }
 
   // get the default I/O request for this variable
-  ioRequest* request = IOUtil_DefaultIORequest (cctkGH, vindex, 1);
+  const CarpetIOHDF5GH *myGH =
+    (CarpetIOHDF5GH *) CCTK_GHExtension (cctkGH, CCTK_THORNSTRING);
+  ioRequest* request = myGH->requests[vindex];
+  if (not request) {
+    request = IOUtil_DefaultIORequest (cctkGH, vindex, 1);
+  }
 
   // Get grid hierarchy extentsion from IOUtil
   const ioGH * const iogh = (const ioGH *) CCTK_GHExtension (cctkGH, "IO");
@@ -574,12 +579,11 @@ static int OutputVarAs (const cGH* const cctkGH, const char* const fullname,
 
   // Invent a file name
   int ioproc = 0, nioprocs = 1;
-  const CarpetIOHDF5GH *myGH =
-    (CarpetIOHDF5GH *) CCTK_GHExtension (cctkGH, CCTK_THORNSTRING);
   string filename;
   filename.append (myGH->out_dir);
   filename.append (alias);
   if (not (CCTK_EQUALS (out_mode, "onefile") or
+           request->out_unchunked or
            groupdata.disttype == CCTK_DISTRIB_CONSTANT or
            dist::size() == 1)) {
     char buffer[32];
@@ -654,6 +658,7 @@ static int OutputVarAs (const cGH* const cctkGH, const char* const fullname,
                 fullname, mglevel, reflevel);
   }
   if ((CCTK_EQUALS (out_mode, "onefile") and io_out_unchunked) or
+      request->out_unchunked or
       groupdata.disttype == CCTK_DISTRIB_CONSTANT) {
     WriteVarUnchunked (cctkGH, file, request, false);
   } else if (CCTK_EQUALS (out_mode, "onefile")) {
@@ -662,6 +667,11 @@ static int OutputVarAs (const cGH* const cctkGH, const char* const fullname,
     WriteVarChunkedParallel (cctkGH, file, request, false);
   }
 
+  // free I/O request structure
+  if (request != myGH->requests[vindex]) {
+    IOUtil_FreeIORequest (&request);
+  }
+
   // Close the file
   if (file >= 0) {
     HDF5_ERROR (H5Fclose (file));