Parameter names changes as announced in today's mail to users@cactuscode.org.

You must also update thorns IOHDF5Util and IOUtil now.

This thorn will be moved from AlphaThorns to CactusPUGHIO now.


git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5/trunk@127 4825ed28-b72c-4eae-9704-e50c059e567d

7 files changed, 91 insertions, 123 deletions

diff --git a/src/DumpGH.c b/src/DumpGH.c
index b9d5674..952cbc0 100644
--- a/src/DumpGH.c
+++ b/src/DumpGH.c
@@ -16,7 +16,7 @@
 #include "cctk_Parameters.h"
 #include "CactusBase/IOUtil/src/ioGH.h"
 #include "CactusBase/IOUtil/src/ioutil_CheckpointRecovery.h"
-#include "BetaThorns/IOHDF5Util/src/ioHDF5UtilGH.h"
+#include "CactusPUGHIO/IOHDF5Util/src/ioHDF5UtilGH.h"
 #ifdef CCTK_MPI
 #include "CactusPUGH/PUGH/src/include/pugh.h"
 #endif
@@ -30,7 +30,7 @@
 
 /* the rcs ID and its dummy function to use it */
 static const char *rcsid = "$Header$";
-CCTK_FILEVERSION(AlphaThorns_IOHDF5_DumpGH_c)
+CCTK_FILEVERSION(CactusPUGHIO_IOHDF5_DumpGH_c)
 
 
 /********************************************************************
@@ -102,7 +102,7 @@ void IOHDF5_EvolutionCheckpoint (const cGH *GH)
       ((checkpoint_every > 0 && GH->cctk_iteration % checkpoint_every == 0) ||
        checkpoint_next))
   {
-    if (verbose)
+    if (! CCTK_Equals (verbose, "none"))
     {
       CCTK_INFO("------------------------------------------------------------");
       CCTK_VInfo (CCTK_THORNSTRING, "Dumping periodic checkpoint file at "
@@ -232,7 +232,7 @@ static int Checkpoint (const cGH *GH, int called_from)
   /* Now open the file */
   if (myproc == ioUtilGH->ioproc)
   {
-    if (verbose)
+    if (CCTK_Equals (verbose, "full"))
     {
       CCTK_VInfo (CCTK_THORNSTRING, "Creating checkpoint file '%s'",
                   cp_tempname);
@@ -269,7 +269,7 @@ static int Checkpoint (const cGH *GH, int called_from)
   /* close the temporary checkpoint file and rename it to the real file */
   if (myproc == ioUtilGH->ioproc)
   {
-    if (verbose)
+    if (CCTK_Equals (verbose, "full"))
     {
       CCTK_VInfo (CCTK_THORNSTRING, "Closing temporary checkpoint file '%s' "
                                     "and renaming it to '%s'",
@@ -281,7 +281,7 @@ static int Checkpoint (const cGH *GH, int called_from)
       HDF5_ERROR (H5Fclose (file));
     }
 
-    /* delete the oldest checkpoint file if checkpoint_keep_all isn't set
+    /* delete the oldest checkpoint file if requested
        and put the new filename into the ring buffer */
     if (retval == 0)
     {
@@ -301,14 +301,14 @@ static int Checkpoint (const cGH *GH, int called_from)
       {
         if (myGH->cp_filename_list[myGH->cp_filename_index])
         {
-          if (! checkpoint_keep_all)
+          if (checkpoint_keep > 0)
           {
             remove (myGH->cp_filename_list[myGH->cp_filename_index]);
           }
           free (myGH->cp_filename_list[myGH->cp_filename_index]);
         }
         myGH->cp_filename_list[myGH->cp_filename_index] = strdup (cp_filename);
-        myGH->cp_filename_index = (myGH->cp_filename_index+1) % checkpoint_keep;
+        myGH->cp_filename_index = (myGH->cp_filename_index+1) % abs (checkpoint_keep);
       }
     }
   }
diff --git a/src/Output.c b/src/Output.c
index b06e979..fb0f0d9 100644
--- a/src/Output.c
+++ b/src/Output.c
@@ -16,8 +16,8 @@
 #include "ioHDF5GH.h"
 
 /* the rcs ID and its dummy function to use it */
-static const char *rcsid = "$Id$";
-CCTK_FILEVERSION(AlphaThorns_IOHDF5_Output_c)
+static const char *rcsid = "$Header$";
+CCTK_FILEVERSION(CactusPUGHIO_IOHDF5_Output_c)
 
 
 /********************************************************************
@@ -35,10 +35,10 @@ static void CheckSteerableParameters (const cGH *GH);
    @enddesc
 
    @calls      IOHDF5_TimeFor
-               IOHDF5_OutputVarAs
+               IOHDF5_Write
 
    @var        GH
-   @vdesc      Pointer to CCTK GH
+   @vdesc      pointer to CCTK GH
    @vtype      const cGH *
    @vio        in
    @endvar
@@ -52,43 +52,21 @@ static void CheckSteerableParameters (const cGH *GH);
 int IOHDF5_OutputGH (const cGH *GH)
 {
   int vindex, retval;
-  ioHDF5GH *myGH;
-  char *fullname;
-  const char *name;
-  DECLARE_CCTK_PARAMETERS
-
-
-  myGH = (ioHDF5GH *) CCTK_GHExtension (GH, "IOHDF5");
+  const ioHDF5GH *myGH;
 
-  CheckSteerableParameters (GH);
 
-  if (myGH->out_every <= 0)
-  {
-    return (0);
-  }
+  retval = 0;
+  myGH = (const ioHDF5GH *) CCTK_GHExtension (GH, "IOHDF5");
 
   /* loop over all variables */
-  for (vindex = retval = 0; vindex < CCTK_NumVars (); vindex++)
+  for (vindex = CCTK_NumVars () - 1; vindex >= 0; vindex--)
   {
-    if (IOHDF5_TimeFor (GH, vindex))
+    if (IOHDF5_TimeFor (GH, vindex) &&
+        IOHDF5_Write (GH, vindex, CCTK_VarName (vindex)) == 0)
     {
-      name     = CCTK_VarName (vindex);
-      fullname = CCTK_FullName (vindex);
-
-      if (verbose)
-      {
-        CCTK_VInfo (CCTK_THORNSTRING, "IOHDF5_OutputGH: (fullname, name) = "
-                                      "(%s, %s)", fullname, name);
-      }
-
-      if (IOHDF5_OutputVarAs (GH, fullname, name) == 0)
-      {
-        /* register variable as having output this iteration */
-        myGH->out_last[vindex] = GH->cctk_iteration;
-        retval++;
-      }
-
-      free (fullname);
+      /* register variable as having output this iteration */
+      myGH->out_last[vindex] = GH->cctk_iteration;
+      retval++;
     }
   }
 
@@ -107,7 +85,7 @@ int IOHDF5_OutputGH (const cGH *GH)
    @calls      IOHDF5_Write
 
    @var        GH
-   @vdesc      Pointer to CCTK GH
+   @vdesc      pointer to CCTK GH
    @vtype      const cGH *
    @vio        in
    @endvar
@@ -137,7 +115,7 @@ int IOHDF5_OutputVarAs (const cGH *GH, const char *fullname, const char *alias)
 
   vindex = CCTK_VarIndex (fullname);
 
-  if (verbose)
+  if (CCTK_Equals (verbose, "full"))
   {
     CCTK_VInfo (CCTK_THORNSTRING, "IOHDF5_OutputVarAs: fullname, alias, "
                 "index = (%s, %s, %d)", fullname, alias, vindex);
@@ -175,7 +153,7 @@ int IOHDF5_OutputVarAs (const cGH *GH, const char *fullname, const char *alias)
    @calls      CheckSteerableParameters
 
    @var        GH
-   @vdesc      Pointer to CCTK GH
+   @vdesc      pointer to CCTK GH
    @vtype      const cGH *
    @vio        in
    @endvar
@@ -233,7 +211,7 @@ int IOHDF5_TimeFor (const cGH *GH, int vindex)
    @calls      IOHDF5_Write
 
    @var        GH
-   @vdesc      Pointer to CCTK GH
+   @vdesc      pointer to CCTK GH
    @vtype      const cGH *
    @vio        in
    @endvar
@@ -261,7 +239,7 @@ int IOHDF5_TriggerOutput (const cGH *GH, int vindex)
 
   myGH = (ioHDF5GH *) CCTK_GHExtension (GH, "IOHDF5");
 
-  if (verbose)
+  if (CCTK_Equals (verbose, "full"))
   {
     fullname = CCTK_FullName (vindex);
     CCTK_VInfo (CCTK_THORNSTRING, "IOHDF5_TriggerOutput: "
@@ -298,7 +276,7 @@ int IOHDF5_TriggerOutput (const cGH *GH, int vindex)
    @calls      IOHDF5Util_ParseVarsForOutput
 
    @var        GH
-   @vdesc      Pointer to CCTK grid hierarchy
+   @vdesc      pointer to CCTK grid hierarchy
    @vtype      const cGH *
    @vio        in
    @endvar
diff --git a/src/RecoverGH.c b/src/RecoverGH.c
index e8c4b8d..4732cea 100644
--- a/src/RecoverGH.c
+++ b/src/RecoverGH.c
@@ -26,7 +26,7 @@
 
 
 /* the rcs ID and its dummy function to use it */
-static const char *rcsid = "$Id$";
+static const char *rcsid = "$Header$";
 CCTK_FILEVERSION(CactusPUGHIO_IOHDF5_RecoverGH_c)
 
 
@@ -138,7 +138,7 @@ int IOHDF5_Recover (cGH *GH, const char *basefilename, int called_from)
   /* Recover GH extensions */
   if (called_from == CP_RECOVER_DATA)
   {
-    if (verbose)
+    if (CCTK_Equals (verbose, "full"))
     {
       CCTK_INFO ("Recovering GH extensions");
     }
@@ -148,7 +148,7 @@ int IOHDF5_Recover (cGH *GH, const char *basefilename, int called_from)
   if (! result)
   {
     /* Recover variables */
-    if (verbose)
+    if (CCTK_Equals (verbose, "full"))
     {
       CCTK_VInfo (CCTK_THORNSTRING, "Recovering %schunked data with ioproc %d, "
                   "ioproc_every %d", fileinfo.unchunked ? "un" : "",
@@ -160,7 +160,7 @@ int IOHDF5_Recover (cGH *GH, const char *basefilename, int called_from)
   /* Close the file and remove it if requested by the user */
   if (CCTK_MyProc (GH) == fileinfo.ioproc)
   {
-    if (verbose)
+    if (CCTK_Equals (verbose, "full"))
     {
       if (called_from == CP_RECOVER_DATA)
       {
@@ -177,7 +177,7 @@ int IOHDF5_Recover (cGH *GH, const char *basefilename, int called_from)
 
     if (called_from == CP_RECOVER_DATA && recover_and_remove)
     {
-      if (verbose)
+      if (CCTK_Equals (verbose, "full"))
       {
         CCTK_VInfo (CCTK_THORNSTRING, "Old checkpoint file '%s' will be removed"
                                       " after next successful checkpoint",
@@ -337,7 +337,7 @@ static int OpenFile (cGH *GH, const char *basefilename, int called_from,
 
   if (myproc == 0)
   {
-    if (verbose)
+    if (CCTK_Equals (verbose, "full"))
     {
       CCTK_VInfo (CCTK_THORNSTRING, "Opening file '%s'", filename);
     }
@@ -361,7 +361,7 @@ static int OpenFile (cGH *GH, const char *basefilename, int called_from,
                                 fileinfo->unchunked);
         strcat (filename, ".h5");
 
-        if (verbose)
+        if (CCTK_Equals (verbose, "full"))
         {
           CCTK_VInfo (CCTK_THORNSTRING, "Trying now file '%s'...", filename);
         }
@@ -417,7 +417,7 @@ static int OpenFile (cGH *GH, const char *basefilename, int called_from,
       if ((fileinfo->ioproc_every == nprocs && nprocs > 1) ||
           fileinfo->unchunked)
       {
-        if (verbose)
+        if (! CCTK_Equals (verbose, "none"))
         {
           CCTK_VInfo (CCTK_THORNSTRING, "Recovering from one %schunked file",
                                         fileinfo->unchunked ? "un" : "");
@@ -435,7 +435,7 @@ static int OpenFile (cGH *GH, const char *basefilename, int called_from,
         }
         else
         {
-          if (verbose)
+          if (! CCTK_Equals (verbose, "none"))
           {
             CCTK_VInfo (CCTK_THORNSTRING, "Recovering from %d chunked files",
                         nprocs / fileinfo->ioproc_every +
@@ -481,7 +481,7 @@ static int OpenFile (cGH *GH, const char *basefilename, int called_from,
     /* Open chunked files on other IO processors */
     if (myproc == fileinfo->ioproc && myproc != 0)
     {
-      if (verbose)
+      if (CCTK_Equals (verbose, "full"))
       {
         CCTK_VInfo (CCTK_THORNSTRING, "Opening chunked file '%s' on "
                                       "processor %d", filename, myproc);
diff --git a/src/Startup.c b/src/Startup.c
index 28efa08..15b7049 100644
--- a/src/Startup.c
+++ b/src/Startup.c
@@ -19,8 +19,8 @@
 #include "ioHDF5GH.h"
 
 /* the rcs ID and its dummy function to use it */
-static const char *rcsid = "$Id$";
-CCTK_FILEVERSION(AlphaThorns_IOHDF5_Startup_c)
+static const char *rcsid = "$Header$";
+CCTK_FILEVERSION(CactusPUGHIO_IOHDF5_Startup_c)
 
 
 /********************************************************************
@@ -130,51 +130,55 @@ static void *SetupGH (tFleshConfig *config, int conv_level, cGH *GH)
   myGH            = (ioHDF5GH *) malloc (sizeof (ioHDF5GH));
   myGH->out_last  = (int *) malloc (numvars * sizeof (int));
   myGH->requests  = (ioRequest **) calloc (numvars, sizeof (ioRequest *));
-  myGH->cp_filename_list = (char **) calloc (checkpoint_keep, sizeof (char *));
+  myGH->cp_filename_list = (char **) calloc (abs (checkpoint_keep),
+                                             sizeof (char *));
   myGH->cp_filename_index = 0;
 
-  /* Check whether "IOHDF5::outdir" was set.
-     If so take this directory otherwise default to "IO::outdir" */
-  if (CCTK_ParameterQueryTimesSet ("outdir", CCTK_THORNSTRING) > 0 ||
-      CCTK_ParameterQueryTimesSet ("outdir_HDF5", CCTK_THORNSTRING) > 0)
+  /* get the name of IOHDF5's output directory */
+  if (*out_dir == 0)
   {
-    if (CCTK_ParameterQueryTimesSet ("outdir", CCTK_THORNSTRING) <= 0)
-    {
-      CCTK_WARN (1, "Parameter 'IOHDF5::outdir_HDF5 is depricated in BETA12, "
-                    "please use 'IOHDF5::outdir' instead");
-      outdir = outdir_HDF5;
-    }
+    out_dir = *(const char **)
+              CCTK_ParameterGet ("out_dir", CCTK_ImplementationThorn ("IO"),
+                                 NULL);
+  }
 
-    if (CCTK_Equals (out3D_mode, "onefile") || ! strstr (outdir, "%u"))
+  /* skip the directory pathname if output goes into current directory */
+  if (strcmp (out_dir, "."))
+  {
+    i = strlen (out_dir);
+    if (CCTK_Equals (out_mode, "onefile") || ! strstr (out_dir, "%u"))
     {
-      myGH->outdir = strdup (outdir);
+      myGH->out_dir = (char *) malloc (i + 2);
+      strcpy (myGH->out_dir, out_dir);
+      myGH->out_dir[i] = '/';
+      myGH->out_dir[i+1] = 0;
     }
     else
     {
-      myGH->outdir = (char *) malloc (strlen (outdir) + 20);
-      sprintf (myGH->outdir, outdir, CCTK_MyProc (GH));
+      myGH->out_dir = (char *) malloc (i + 20);
+      sprintf (myGH->out_dir, out_dir, CCTK_MyProc (GH));
+      strcat (myGH->out_dir, "/");
     }
   }
   else
   {
-    myGH->outdir = CCTK_ParameterValString ("outdir",
-                                            CCTK_ImplementationThorn ("IO"));
+    myGH->out_dir = strdup ("");
   }
 
-  /* Create the output directory */
+  /* create the output directory */
   ioUtilGH = (const ioGH *) CCTK_GHExtension (GH, "IO");
-  i = IOUtil_CreateDirectory (GH, myGH->outdir,
-                              ! CCTK_Equals (out3D_mode, "onefile"),
+  i = IOUtil_CreateDirectory (GH, myGH->out_dir,
+                              ! CCTK_Equals (out_mode, "onefile"),
                               ioUtilGH->ioproc);
   if (i < 0)
   {
     CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
-                "Problem creating HDF5 output directory '%s'", myGH->outdir);
+                "Problem creating HDF5 output directory '%s'", myGH->out_dir);
   }
-  else if (i > 0 && CCTK_Equals (newverbose, "full"))
+  else if (i > 0 && CCTK_Equals (verbose, "full"))
   {
     CCTK_VInfo (CCTK_THORNSTRING,
-                "HDF5 output directory '%s' already exists", myGH->outdir);
+                "HDF5 output directory '%s' already exists", myGH->out_dir);
   }
 
   for (i = 0; i < numvars; i++)
diff --git a/src/Write.c b/src/Write.c
index b21c2d2..c4d3b50 100644
--- a/src/Write.c
+++ b/src/Write.c
@@ -21,7 +21,7 @@
 
 /* the rcs ID and its dummy funtion to use it */
 static const char *rcsid = "$Header$";
-CCTK_FILEVERSION(AlphaThorns_IOHDF5_Write_c)
+CCTK_FILEVERSION(CactusPUGHIO_IOHDF5_Write_c)
 
 
 /********************************************************************
@@ -113,7 +113,7 @@ int IOHDF5_Write (const cGH *GH, int vindex, const char *alias)
   }
   else
   {
-    if (verbose)
+    if (CCTK_Equals (verbose, "full"))
     {
       CCTK_VInfo (CCTK_THORNSTRING, "%s HDF5 output file '%s'",
                   is_new_file ? "Opening" : "Appending", filename);
@@ -154,9 +154,10 @@ int IOHDF5_Write (const cGH *GH, int vindex, const char *alias)
   {
     /* all GH extension variables and parameter stuff which is not
        specific to any dataset goes into dedicated groups */
-    if (strcmp (out3D_parameters, "no"))
+    if (! CCTK_Equals (out_save_parameters, "no"))
     {
-      IOHDF5Util_DumpParameters (GH, ! strcmp (out3D_parameters, "all"), file);
+      IOHDF5Util_DumpParameters (GH, CCTK_Equals (out_save_parameters, "all"),
+                                 file);
     }
 
     IOHDF5Util_DumpGHExtensions (GH, file);
@@ -168,16 +169,15 @@ int IOHDF5_Write (const cGH *GH, int vindex, const char *alias)
   /* close the file */
   if (file >= 0)
   {
-    if (verbose)
+    if (CCTK_Equals (verbose, "full"))
     {
       CCTK_INFO ("Closing HDF5 output file from this iteration");
     }
     HDF5_ERROR (H5Fclose (file));
   }
 
-  /* free the filename if it was not registered for re-opening
-     in IOHDF5_net3D_filename () */
-  if (out3D_septimefiles)
+  /* free the filename if it was not registered for re-opening */
+  if (out_timesteps_per_file > 0)
   {
     free (filename);
   }
@@ -259,7 +259,7 @@ static char *IOHDF5_GetFilename (const cGH *GH,
 
   myproc = CCTK_MyProc (GH);
 
-  if (out3D_septimefiles)
+  if (out_timesteps_per_file > 0)
   {
     tmp = extra;
     sprintf (extra, "%s.time_%7.3f", extra, GH->cctk_time);
@@ -289,26 +289,18 @@ static char *IOHDF5_GetFilename (const cGH *GH,
     sprintf (extra, "%s.file_%d", extra, myproc / ioUtilGH->ioproc_every);
 
     /* If necessary create the output directory */
-    outputdir = (char *) malloc (strlen (myGH->outdir) + strlen (varname) + 5);
-
-    if (strcmp (myGH->outdir, "."))
-    {
-      sprintf (outputdir, "%s/%s_3d", myGH->outdir, varname);
-    }
-    else
-    {
-      sprintf (outputdir, "%s_3d", varname);
-    }
+    outputdir = (char *) malloc (strlen (myGH->out_dir) + strlen (varname) + 5);
+    sprintf (outputdir, "%s%s_3d", myGH->out_dir, varname);
 
     result = IOUtil_CreateDirectory (GH, outputdir,
-                                     ! CCTK_Equals (out3D_mode, "onefile"),
+                                     ! CCTK_Equals (out_mode, "onefile"),
                                      ioUtilGH->ioproc);
     if (result < 0)
     {
       CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
                   "Problem creating output directory '%s'", outputdir);
     }
-    else if (result > 0 && CCTK_Equals (newverbose, "full"))
+    else if (result > 0 && CCTK_Equals (verbose, "full"))
     {
       CCTK_VInfo (CCTK_THORNSTRING,
                   "Output directory '%s' already exists", outputdir);
@@ -327,23 +319,16 @@ static char *IOHDF5_GetFilename (const cGH *GH,
 
   /* CREATE THE COMPLETE OUTPUT FILENAME
      ----------------------------------- */
-  filename = (char *) malloc (strlen (myGH->outdir) +
+  filename = (char *) malloc (strlen (myGH->out_dir) +
                               strlen (extradir) +
                               strlen (varname) +
                               strlen (extra) +
                               strlen (GH->identity) + 8);
-  if (strcmp (myGH->outdir, "."))
-  {
-    sprintf (filename, "%s/%s%s%s%s.h5",
-             myGH->outdir, extradir, varname, extra, GH->identity);
-  }
-  else
-  {
-    sprintf (filename, "%s%s%s%s.h5", extradir, varname, extra, GH->identity);
-  }
+  sprintf (filename, "%s%s%s%s%s.h5",
+           myGH->out_dir, extradir, varname, extra, GH->identity);
 
   /* no need to store filenames if used only once */
-  if (! out3D_septimefiles)
+  if (out_timesteps_per_file < 0)
   {
     if (myproc == ioUtilGH->ioproc)
     {
diff --git a/src/WriteIsosurface.c b/src/WriteIsosurface.c
index 3e7e573..be12eb8 100644
--- a/src/WriteIsosurface.c
+++ b/src/WriteIsosurface.c
@@ -16,8 +16,8 @@
 #include "ioHDF5GH.h"
 
 /* the rcs ID and its dummy funtion to use it */
-static const char *rcsid = "$Id$";
-CCTK_FILEVERSION(AlphaThorns_IOHDF5_WriteIsosurface_c)
+static const char *rcsid = "$Header$";
+CCTK_FILEVERSION(CactusPUGHIO_IOHDF5_WriteIsosurface_c)
 
 
 #define SOCKET_URL_PREFIX      "sock://"
diff --git a/src/ioHDF5GH.h b/src/ioHDF5GH.h
index 1c2fc5a..31c5fc0 100644
--- a/src/ioHDF5GH.h
+++ b/src/ioHDF5GH.h
@@ -4,14 +4,15 @@
    @author    Thomas Radke
    @desc 
               The extensions to the GH structure from IOHDF5.
-   @version $Id$
+   @enddesc
+   @version   $Header$
  @@*/
 
 #ifndef _IOHDF5_IOHDF5GH_H_
-#define _IOHDF5_IOHDF5GH_H_
+#define _IOHDF5_IOHDF5GH_H_ 1
 
-#include "BetaThorns/IOHDF5Util/src/ioHDF5UtilGH.h"
 #include "StoreNamedData.h"
+#include "CactusPUGHIO/IOHDF5Util/src/ioHDF5UtilGH.h"
 
 /* IOHDF5 GH extension structure */
 typedef struct
@@ -20,8 +21,8 @@ typedef struct
   /* how often to output */
   int  out_every;
 
-  /* directories in which to output */
-  char  *outdir;
+  /* directory in which to output */
+  char  *out_dir;
 
   /* the last iteration output */
   int   *out_last;