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git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@3 7842ec3a-9562-4be5-9c5b-06ba18f2b668

1 files changed, 430 insertions, 0 deletions

diff --git a/src/DumpUtils.c b/src/DumpUtils.c
new file mode 100644
index 0000000..73d7fe3
--- /dev/null
+++ b/src/DumpUtils.c
@@ -0,0 +1,430 @@
+ /*@@
+   @file      DumpUtils.c
+   @date      Fri Oct 6 2000
+   @author    Thomas Radke
+   @desc 
+              Utility routines for dumping data into HDF5 files.
+   @enddesc 
+   @version   $Id$
+ @@*/
+
+
+#include <stdlib.h>
+
+#include "cctk.h"
+#include "cctk_Parameters.h"
+#include "CactusBase/IOUtil/src/ioGH.h"
+#include "CactusBase/IOUtil/src/ioutil_CheckpointRecovery.h"
+#include "ioHDF5UtilGH.h"
+
+/* the rcs ID and its dummy function to use it */
+static char *rcsid = "$Id$";
+CCTK_FILEVERSION(BetaThorns_IOHDF5Util_DumpUtils_c)
+
+
+/*@@
+   @routine    IOHDF5Util_DumpGH
+   @date       Tue Oct 10 2000
+   @author     Thomas Radke
+   @desc
+               Dump all variables of the given GH along with
+               the global attributes and parameters
+               to the (already opened) HDF5 checkpoint file.
+   @enddesc
+   @var        GH
+   @vdesc      Pointer to CCTK grid hierarchy
+   @vtype      cGH *
+   @vio        in
+   @endvar
+   @var        timers
+   @vdesc      array of timers for timing the checkpointing
+   @vtype      int []
+   @vio        in
+   @endvar
+   @var        file
+   @vdesc      HDF5 file handle
+   @vtype      hid_t
+   @vio        in
+   @endvar
+
+   @returntype int
+   @returndesc
+               always 0 (for success)
+   @endreturndesc
+@@*/
+int IOHDF5Util_DumpGH (cGH *GH,
+                       int timers[],
+                       hid_t file)
+{
+  DECLARE_CCTK_PARAMETERS
+  int index;
+  int maxdim;
+  int timelevel, current_timelevel;
+  int *old_downsample;
+  int old_out_single;
+  ioGH *ioUtilGH;
+  const char *thorn;
+  const char *impl;
+  ioHDF5Geo_t slab;
+
+
+  /* Get the GH extension for IOUtil */
+  ioUtilGH = (ioGH *) CCTK_GHExtension (GH, "IO");
+
+  /* disable downsampling after saving original downsampling params */
+  maxdim = CCTK_MaxDim ();
+  old_downsample = (int *) malloc (maxdim * sizeof (int));
+  for (index = 0; index < maxdim; index++)
+  {
+    old_downsample[index] = ioUtilGH->downsample[index];
+    ioUtilGH->downsample[index] = 1;
+    slab.direction[index] = index;
+    slab.downsample[index] = 1;
+  }
+
+  /* disable output in single precision */
+  old_out_single = ioUtilGH->out_single;
+  ioUtilGH->out_single = 0;
+
+  /* sync all active groups */
+  for (index = CCTK_NumGroups () - 1; index >= 0; index--)
+  {
+    if (CCTK_IsImplementationActive (
+           CCTK_ImpFromVarI (CCTK_FirstVarIndexI (index))))
+    {
+      CCTK_SyncGroupI (GH, index);
+    }
+  }
+
+  /* start CP_PARAMETERS_TIMER timer */
+  if (timers)
+  {
+    CCTK_TimerResetI (timers[CP_PARAMETERS_TIMER]);
+    CCTK_TimerStartI (timers[CP_PARAMETERS_TIMER]);
+  }
+
+  /* Great; Now start dumping away! */
+  if (file >= 0)
+  {
+    /* all GH extension variables and parameter stuff which is not
+       specific to any dataset goes into dedicated groups */
+    if (out3D_parameters)
+    {
+      IOHDF5Util_DumpParameters (GH, file);
+    }
+
+    IOHDF5Util_DumpGHExtensions (GH, file);
+  }
+
+  if (verbose)
+  {
+    CCTK_INFO ("Dumping variables ...");
+  }
+
+  /* stop CP_PARAMETERS_TIMER timer and start CP_VARIABLES_TIMER */
+  if (timers)
+  {
+    CCTK_TimerStopI  (timers[CP_PARAMETERS_TIMER]);
+    CCTK_TimerResetI (timers[CP_VARIABLES_TIMER]);
+    CCTK_TimerStartI (timers[CP_VARIABLES_TIMER]);
+  }
+
+  /* ... now the variables */
+  for (index = CCTK_NumVars () - 1; index >= 0; index--)
+  {
+    /* find out the thorn implementing variable with index */
+    impl = CCTK_ImpFromVarI (index);
+    thorn = CCTK_ImplementationThorn (impl);
+    if (! thorn)
+    {
+      thorn = impl;
+    }
+
+    /* let only variables pass which belong to an active thorn and
+       have storage assigned */
+    if (! CCTK_IsThornActive (thorn) ||
+        ! CCTK_QueryGroupStorageI (GH, CCTK_GroupIndexFromVarI (index)))
+    {
+      continue;
+    }
+
+    if (verbose && file >= 0)
+    {
+      CCTK_VInfo (CCTK_THORNSTRING, "  %s", CCTK_VarName (index));
+    }
+
+    /* get the current timelevel */
+    current_timelevel = CCTK_NumTimeLevelsFromVarI (index) - 1;
+    if (current_timelevel > 0)
+    {
+      current_timelevel--;
+    }
+
+    slab.sdim = slab.vdim = CCTK_GroupDimFromVarI (index);
+
+    /* now dump all timelevels up to the current */
+    for (timelevel = 0; timelevel <= current_timelevel; timelevel++)
+    {
+      IOHDF5Util_DumpVar (GH, index, timelevel, &slab, file, 0);
+    }
+
+  } /* end of loop over all variables */
+
+  /* stop CP_VARIABLES_TIMER timer */
+  if (timers)
+  {
+    CCTK_TimerStopI (timers[CP_VARIABLES_TIMER]);
+  }
+
+  /* restore output precision flag */
+  ioUtilGH->out_single = old_out_single;
+
+  /* restore original downsampling params */
+  memcpy (ioUtilGH->downsample, old_downsample, maxdim * sizeof (int));
+  free (old_downsample);
+
+  return (0);
+}
+
+
+/*@@
+   @routine    IOHDF5Util_DumpCommonAttributes
+   @date       May 21 1999
+   @author     Thomas Radke
+   @desc
+               Add "Common" attributes to the given dataset, these are:
+               <ul>
+                 <li> the variable's groupname
+                 <li> the grouptype
+                 <li> number of timelevels
+                 <li> simulation time
+                 <li> origin
+                 <li> bounding box
+                 <li> gridspacings
+                 <li> global grid size
+               </ul>
+   @enddesc
+   @var        GH
+   @vdesc      Pointer to CCTK grid hierarchy
+   @vtype      cGH *
+   @vio        in
+   @endvar
+   @var        index
+   @vdesc      CCTK index of the variable to dump
+   @vtype      int
+   @vio        in
+   @endvar
+   @var        timelevel
+   @vdesc      timelevel of the variable to dump
+   @vtype      int
+   @vio        in
+   @endvar
+   @var        global_shape
+   @vdesc      global shape of the grid
+   @vtype      CCTK_INT []
+   @vio        in
+   @endvar
+   @var        slab
+   @vdesc      pointer to hyperslab structure describing the dataset
+   @vtype      ioHDF5Geo_t *
+   @vio        in
+   @endvar
+   @var        dataset
+   @vdesc      the dataset handle where the attributes should be attached to
+   @vtype      hid_t
+   @vio        in
+   @endvar
+@@*/
+void IOHDF5Util_DumpCommonAttributes (cGH *GH,
+                                      int index,
+                                      int timelevel,
+                                      CCTK_INT global_shape[],
+                                      ioHDF5Geo_t *slab,
+                                      hid_t dataset)
+{
+  DECLARE_CCTK_PARAMETERS
+  int dim;
+  char *groupname;
+  CCTK_INT attr_int;
+  CCTK_REAL *attr_real;
+  ioHDF5UtilGH *myGH;
+
+
+  /* Get the handle for IOHDF5Util extensions */
+  myGH = (ioHDF5UtilGH *) CCTK_GHExtension (GH, "IOHDF5Util");
+
+  /* attributes describing the variable */
+  dim = CCTK_GroupDimI (CCTK_GroupIndexFromVarI (index));
+  groupname = CCTK_GroupNameFromVarI (index);
+  WRITE_ATTRIBUTE ("groupname", groupname, dataset,
+                   myGH->scalar_dataspace, 0, myGH->IOHDF5_STRING);
+  free (groupname);
+  attr_int = CCTK_GroupTypeFromVarI (index);
+  WRITE_ATTRIBUTE ("grouptype", &attr_int, dataset,
+                   myGH->scalar_dataspace, 0, IOHDF5_INT);
+  attr_int = CCTK_NumTimeLevelsFromVarI (index);
+  WRITE_ATTRIBUTE ("ntimelevels", &attr_int, dataset,
+                   myGH->scalar_dataspace, 0, IOHDF5_INT);
+  WRITE_ATTRIBUTE ("global_size", global_shape, dataset,
+                   myGH->array_dataspace, dim, IOHDF5_INT);
+  WRITE_ATTRIBUTE ("time", &GH->cctk_time, dataset,
+                   myGH->scalar_dataspace, 0, IOHDF5_REAL);
+
+  /* attributes describing the underlying grid */
+  dim = CCTK_MaxDim ();
+  attr_real = (CCTK_REAL *) malloc (2 * dim * sizeof (CCTK_REAL));
+  CCTK_CoordRange (GH, &attr_real[0], &attr_real[dim + 0], -1, "x", "cart3d");
+  CCTK_CoordRange (GH, &attr_real[1], &attr_real[dim + 1], -1, "y", "cart3d");
+  CCTK_CoordRange (GH, &attr_real[2], &attr_real[dim + 2], -1, "z", "cart3d");
+
+  WRITE_ATTRIBUTE ("origin", attr_real, dataset,
+                   myGH->array_dataspace, dim, IOHDF5_REAL);
+  WRITE_ATTRIBUTE ("min_ext", attr_real, dataset,
+                   myGH->array_dataspace, dim, IOHDF5_REAL);
+  WRITE_ATTRIBUTE ("max_ext", attr_real + dim, dataset,
+                   myGH->array_dataspace, dim, IOHDF5_REAL);
+  WRITE_ATTRIBUTE ("delta", GH->cctk_delta_space, dataset,
+                   myGH->array_dataspace, dim, IOHDF5_REAL);
+  free (attr_real);
+
+  /* attributes describing the hyperslab */
+  if (slab)
+  {
+    attr_real = (CCTK_REAL *) malloc (4 * slab->sdim * sizeof (CCTK_REAL));
+    for (dim = 0; dim < slab->sdim; dim++)
+    {
+      attr_real[dim + 0*slab->sdim] =
+        slab->origin[slab->direction[dim]] *
+        GH->cctk_delta_space[slab->direction[dim]];
+      attr_real[dim + 1*slab->sdim] =
+        slab->origin[dim] * GH->cctk_delta_space[dim];
+      attr_real[dim + 2*slab->sdim] =
+        (slab->origin[dim] + slab->actlen[dim]-1) *
+        GH->cctk_delta_space[dim] * slab->downsample[dim];
+      attr_real[dim + 3*slab->sdim] =
+        GH->cctk_delta_space[slab->direction[dim]] *
+        slab->downsample[slab->direction[dim]];
+    }
+    WRITE_ATTRIBUTE ("origin_slab",  attr_real + 0*dim, dataset,
+                     myGH->array_dataspace, dim, IOHDF5_REAL);
+    WRITE_ATTRIBUTE ("min_ext_slab", attr_real + 1*dim, dataset,
+                     myGH->array_dataspace, dim, IOHDF5_REAL);
+    WRITE_ATTRIBUTE ("max_ext_slab", attr_real + 2*dim, dataset,
+                     myGH->array_dataspace, dim, IOHDF5_REAL);
+    WRITE_ATTRIBUTE ("delta_slab",   attr_real + 3*dim, dataset,
+                     myGH->array_dataspace, dim, IOHDF5_REAL);
+    free (attr_real);
+  }
+}
+
+
+ /*@@
+   @routine    IOHDF5Util_DumpParameters
+   @date       Thu Jan 20 2000
+   @author     Thomas Radke
+   @desc
+               Collects the parameters of all active implementations
+               into a single string and writes it as an attribute
+               attached to the CACTUS_PARAMETERS_GROUP group in the HDF5 file.
+   @enddesc
+   @var        GH
+   @vdesc      Pointer to CCTK grid hierarchy
+   @vtype      cGH *
+   @vio        in
+   @endvar
+   @var        file
+   @vdesc      the HDF5 file handle
+   @vtype      hid_t
+   @vio        in
+   @endvar
+@@*/
+void IOHDF5Util_DumpParameters (cGH *GH,
+                                hid_t file)
+{
+  DECLARE_CCTK_PARAMETERS
+  ioHDF5UtilGH *myGH;
+  char *parameters;
+  hid_t group;
+
+
+  if (verbose)
+  {
+    CCTK_INFO ("Dumping GH extensions ...");
+  }
+
+  /* Get the parameter string buffer */
+  parameters = IOUtil_GetAllParameters (GH);
+
+  if (parameters)
+  {
+    /* Get the handle for IOHDF5Util extensions */
+    myGH = (ioHDF5UtilGH *) CCTK_GHExtension (GH, "IOHDF5Util");
+
+    IOHDF5_ERROR (group = H5Gcreate (file, CACTUS_PARAMETERS_GROUP, 0));
+    WRITE_ATTRIBUTE (ALL_PARAMETERS, parameters, group,
+                     myGH->scalar_dataspace, 0, myGH->IOHDF5_STRING);
+    IOHDF5_ERROR (H5Gclose (group));
+
+    free (parameters);
+  }
+}
+
+
+ /*@@
+   @routine    IOHDF5Util_DumpGHExtensions
+   @date       Thu Jan 20 2000
+   @author     Thomas Radke
+   @desc
+               Attaches the current values of important flesh and IO variables
+               as attributes to the GLOBAL_ATTRIBUTES_GROUP group
+               in the HDF5 file.
+   @enddesc
+   @var        GH
+   @vdesc      Pointer to CCTK grid hierarchy
+   @vtype      cGH *
+   @vio        in
+   @endvar
+   @var        file
+   @vdesc      the HDF5 file handle
+   @vtype      hid_t
+   @vio        in
+   @endvar
+@@*/
+void IOHDF5Util_DumpGHExtensions (cGH *GH,
+                                  hid_t file)
+{
+  DECLARE_CCTK_PARAMETERS
+  int value;
+  hid_t group;
+  ioGH *ioUtilGH;
+  ioHDF5UtilGH *myGH;
+
+
+  if (verbose)
+  {
+    CCTK_INFO ("Dumping GH extensions ...");
+  }
+
+  /* Get the handles for IOUtil and IOHDF5 extensions */
+  ioUtilGH = (ioGH *) CCTK_GHExtension (GH, "IO");
+  myGH = (ioHDF5UtilGH *) CCTK_GHExtension (GH, "IOHDF5Util");
+
+  IOHDF5_ERROR (group = H5Gcreate (file, GLOBAL_ATTRIBUTES_GROUP, 0));
+
+  value = CCTK_MainLoopIndex ();
+  WRITE_ATTRIBUTE ("main_loop_index", &value, group,
+                   myGH->scalar_dataspace, 0, H5T_NATIVE_INT);
+  value = CCTK_nProcs (GH);
+  WRITE_ATTRIBUTE ("nprocs", &value, group,
+                   myGH->scalar_dataspace, 0, H5T_NATIVE_INT);
+  WRITE_ATTRIBUTE ("ioproc_every", &ioUtilGH->ioproc_every, group,
+                   myGH->scalar_dataspace, 0, H5T_NATIVE_INT);
+  WRITE_ATTRIBUTE ("unchunked", &ioUtilGH->unchunked, group,
+                   myGH->scalar_dataspace, 0, H5T_NATIVE_INT);
+  WRITE_ATTRIBUTE ("cctk_time", &GH->cctk_time, group,
+                   myGH->scalar_dataspace, 0, IOHDF5_REAL);
+  WRITE_ATTRIBUTE ("cctk_iteration", &GH->cctk_iteration, group,
+                   myGH->scalar_dataspace, 0, H5T_NATIVE_INT);
+
+  IOHDF5_ERROR (H5Gclose (group));
+}