H5Part development and discussion

[John Biddiscombe <biddisco AT cscs.ch>]

Fix 1 : If you run using MPI and Parallel IO, (mpirun -np 1 ...) but 
only have one processor there is a small bug which causes a crash, the 
f->pnparticles array is set to null (because 1 proc), but MPI_AllGather 
is still called. This patch fixes it by skipping the MPI_AllGather and 
setting the total to N prior to setting mem/dataspaces etc. (can we just 
use H5_ALL instead of creating a simple dataspace in this case).

Addition 1 : H5PartGetNativeDatasetType
I've added a function which returns a type, I need this because I'm 
storing int/float/double/byte/char/long/long long/ etc all possible 
types signed/unsigned into H5Part files and querying types when reading 
the data back. I have not yet integrated my 'all types' support into 
H5Part itself, but I would like to eventually, In the meantime this 
functions is useful, small and does no harm, so it'd be nice to add it it.

Additon 2: H5PartHasStep
I use H5Part files to cache results when loadiing from other file 
formats as well as storing from simulation, To check if a step exists 
this function is convenient (I am aware that I could use SetStep which 
fails if the step exists, but from a puerist's viewpoint having a 
specific H5HasStep is more appealing).

Thanks in anticipation

JB
Index: src/H5Part.c
===================================================================
--- src/H5Part.c        (revision 2908)
+++ src/H5Part.c        (working copy)
@@ -535,36 +535,42 @@
        /*
          acquire the number of particles to be written from each MPI process
        */
-       r = MPI_Allgather (
-               &nparticles, 1, MPI_LONG_LONG,
-               f->pnparticles, 1, MPI_LONG_LONG,
-               f->comm);
-       if ( r != MPI_SUCCESS) {
-               return HANDLE_MPI_ALLGATHER_ERR;
-       }
-       if ( f->myproc == 0 ) {
-               _H5Part_print_debug ( "Particle offsets:" );
-               for(i=0;i<f->nprocs;i++) 
-                       _H5Part_print_debug ( "\tnp=%lld",
-                                             (long long) f->pnparticles[i] );
-       }
-       /* should I create a selection here? */
+      if (f->nprocs==1) {
+        /* serial mode f->pnparticles is NULL */
+        total = nparticles;
+      }
+      else {
+         r = MPI_Allgather (
+                 &nparticles, 1, MPI_LONG_LONG,
+                 f->pnparticles, 1, MPI_LONG_LONG,
+                 f->comm);
+         if ( r != MPI_SUCCESS) {
+                 return HANDLE_MPI_ALLGATHER_ERR;
+         }
+         if ( f->myproc == 0 ) {
+                 _H5Part_print_debug ( "Particle offsets:" );
+                 for(i=0;i<f->nprocs;i++) 
+                         _H5Part_print_debug ( "\tnp=%lld",
+                                               (long long) f->pnparticles[i] 
);
+         }
+         /* should I create a selection here? */
+    
+         /* compute start offsets */
+         stride[0] = 1;
+         start[0] = 0;
+         for (i=0; i<f->myproc; i++) {
+                 start[0] += f->pnparticles[i];
+         }
+       
 
-       /* compute start offsets */
-       stride[0] = 1;
-       start[0] = 0;
-       for (i=0; i<f->myproc; i++) {
-               start[0] += f->pnparticles[i];
-       }
-       
 
+          /* compute total nparticles */
+         total = 0;
+         for (i=0; i < f->nprocs; i++) {
+                 total += f->pnparticles[i];
+         }
+      }
 
-        /* compute total nparticles */
-       total = 0;
-       for (i=0; i < f->nprocs; i++) {
-               total += f->pnparticles[i];
-       }
-
        /* declare overall datasize */
        f->shape = H5Screate_simple (1, &total, &total);
        if (f->shape < 0) return HANDLE_H5S_CREATE_SIMPLE_ERR ( total );
@@ -579,14 +585,16 @@
        if (f->memshape < 0)
                return HANDLE_H5S_CREATE_SIMPLE_ERR ( f->nparticles );
 
-       count[0] = nparticles;
-       r = H5Sselect_hyperslab (
-               f->diskshape,
-               H5S_SELECT_SET,
-               start,
-               stride,
-               count, NULL );
-       if ( r < 0 ) return HANDLE_H5S_SELECT_HYPERSLAB_ERR;
+    if (f->nprocs>1) {
+         count[0] = nparticles;
+         r = H5Sselect_hyperslab (
+                 f->diskshape,
+                 H5S_SELECT_SET,
+                 start,
+                 stride,
+                 count, NULL );
+         if ( r < 0 ) return HANDLE_H5S_SELECT_HYPERSLAB_ERR;
+    }
 
        if ( f->timegroup < 0 ) {
                r = _H5Part_set_step ( f, 0 );
@@ -1506,6 +1514,35 @@
 /*!
   \ingroup h5part_read
 
+  Query whether a particular step already exists in the file
+  \c f.
+
+  It works for both reading and writing of files
+
+  \return      1 or 0 for true or false
+*/
+h5part_int64_t
+H5PartHasStep (
+       H5PartFile *f,                  /*!< [in]  Handle to open file */
+  h5part_int64_t step /*!< [in]  Step number to query */
+       ) {
+
+       SET_FNAME ( "H5PartHasStep" );
+
+       CHECK_FILEHANDLE( f );
+
+       char name[128];
+       sprintf ( name, "%s#%0*lld", f->groupname_step, f->stepno_width, 
(long long) step );
+       herr_t herr = H5Gget_objinfo( f->file, name, 1, NULL );
+       if ( herr >= 0 ) {
+               return 1;
+       }
+  return 0;
+}
+
+/*!
+  \ingroup h5part_read
+
   Get the number of time-steps that are currently stored in the file
   \c f.
 
@@ -2283,6 +2320,29 @@
        return H5PART_SUCCESS;
 }
 
+/*!
+  \ingroup h5part_utility
+
+  This function can be used to query the Type of a dataset
+  It is not used by the core H5Part library but is useful when 
+  reading generic data from the file. 
+  An example of usage would be (H5Tequal(datatype,H5T_NATIVE_FLOAT)) 
+  any NATIVE type can be used to test.
+  
+  \return      \c an hdf5 handle to the native type of the data
+*/
+hid_t H5PartGetNativeDatasetType(H5PartFile *f, const char *name)
+{
+  hid_t dataset, datatype, datatypen;
+  if(!f->timegroup) H5PartSetStep(f,f->timestep); /* choose current step */
+  dataset=H5Dopen(f->timegroup,name);
+  datatype  = H5Dget_type(dataset);
+  datatypen = H5Tget_native_type(datatype, H5T_DIR_DEFAULT);
+  H5Tclose(datatype);
+  H5Dclose(dataset);
+  return datatypen;
+}
+
 /****************** error handling ******************/
 
 /*!
Index: src/H5Part.h
===================================================================
--- src/H5Part.h        (revision 2908)
+++ src/H5Part.h        (working copy)
@@ -97,6 +97,12 @@
        );
 
 h5part_int64_t
+H5PartHasStep (
+       H5PartFile *f,
+  h5part_int64_t step
+       );
+
+h5part_int64_t
 H5PartGetNumSteps (
        H5PartFile *f
        );
@@ -306,6 +312,13 @@
        ...
        );
 
+/*================== Utility Routines =================*/
+hid_t 
+H5PartGetNativeDatasetType(
+  H5PartFile *f, 
+  const char *name
+);
+
 #ifdef __cplusplus
 }
 #endif
Index: src/H5PartTypes.h
===================================================================
--- src/H5PartTypes.h   (revision 2908)
+++ src/H5PartTypes.h   (working copy)
@@ -6,7 +6,7 @@
 #define _H5PARTTYPES_H_
 
 #ifdef   WIN32
-typdef __int64                 int64_t;
+typedef __int64                        int64_t;
 #endif /* WIN32 */
 
 typedef int64_t                        h5part_int64_t;