Moved the I/O request description and parsing routines from IOHDF5Util to IOUtil

so that they can be shared by all I/O thorns now.


git-svn-id: http://svn.cactuscode.org/arrangements/CactusBase/IOUtil/trunk@158 b32723a9-ab3a-4a60-88e2-2e5d99d7c17a

3 files changed, 468 insertions, 49 deletions

diff --git a/src/Utils.c b/src/Utils.c
index 7abec4d..c6a1c98 100644
--- a/src/Utils.c
+++ b/src/Utils.c
@@ -3,7 +3,7 @@
    @date      Tue 4th July 2000
    @author    Gabrielle Allen
    @desc
-              Utility routines which may be called by other IO thorns
+              Utility routines which may be called by other I/O thorns.
    @enddesc 
    @version   $Id$
  @@*/
@@ -15,6 +15,9 @@
 
 #include "cctk.h"
 #include "cctk_Parameters.h"
+#include "cctk_GNU.h"
+#include "util_String.h"
+#include "ioGH.h"
 #include "ioutil_Utils.h"
 #include "ioutil_CheckpointRecovery.h"
 
@@ -23,10 +26,109 @@ static const char *rcsid = "$Header$";
 CCTK_FILEVERSION(CactusBase_IOUtil_Utils_c)
 
 
+/********************************************************************
+ ********************    Macro Definitions   ************************
+ ********************************************************************/
 /* uncomment this if you want some debugging output */
 /* #define DEBUG_IOUTIL 1 */
 
 
+/********************************************************************
+ ********************    Internal Typedefs   ************************
+ ********************************************************************/
+typedef struct
+{
+  const cGH *GH;
+  ioRequest **request_list;
+} info_t;
+
+
+/********************************************************************
+ ********************    Internal Routines   ************************
+ ********************************************************************/
+static void SetOutputVar (int vindex, const char *optstring, void *arg);
+
+
+/********************************************************************
+ ********************    External Routines   ************************
+ ********************************************************************/
+int CCTK_RegexMatch (const char *string, const char *pattern, const int nmatch,
+                     regmatch_t *pmatch);
+
+
+ /*@@
+   @routine    IOUtil_ParseVarsForOutput
+   @date       Fri 26 April 2002
+   @author     Thomas Radke
+   @desc
+               Parses the given 'out_vars' string as a list of variable and/or
+               groupnames. If an option string is appended to a name this will
+               be parsed for I/O request options.
+   @enddesc
+
+   @calls      CCTK_TraverseString
+
+   @var        GH
+   @vdesc      pointer to CCTK grid hierarchy
+   @vtype      const cGH *
+   @vio        in
+   @endvar
+   @var        out_vars
+   @vdesc      string with list of variables and/or group names to parse
+   @vtype      const char *
+   @vio        in
+   @endvar
+   @var        request_list
+   @vdesc      list of I/O requests to fill out
+   @vtype      ioRequest *[]
+   @vio        out
+   @endvar
+@@*/
+void IOUtil_ParseVarsForOutput (const cGH *GH, const char *out_vars,
+                                ioRequest *request_list[])
+{
+  int i;
+  info_t info;
+
+
+  /* free current list of I/O requests */
+  for (i = CCTK_NumVars () - 1; i >= 0; i--)
+  {
+    if (request_list[i])
+    {
+      IOUtil_FreeIORequest (&request_list[i]);
+    }
+  }
+
+  /* generate new list of I/O requests */
+  info.GH = GH;
+  info.request_list = request_list;
+  CCTK_TraverseString (out_vars, SetOutputVar, &info, CCTK_GROUP_OR_VAR);
+}
+
+
+ /*@@
+   @routine    IOUtil_FreeIORequest
+   @date       Fri 26 April 2002
+   @author     Thomas Radke
+   @desc
+               Frees an I/O request description.
+   @enddesc
+
+   @var        request
+   @vdesc      pointer to the I/O request structure
+   @vtype      ioRequest **
+   @vio        inout
+   @endvar
+@@*/
+void IOUtil_FreeIORequest (ioRequest **request)
+{
+  free ((*request)->vectors);
+  free (*request);
+  *request = NULL;
+}
+
+
 /*@@
    @routine    IOUtil_1DLines
    @date       July 4 2000
@@ -474,3 +576,314 @@ int IOUtil_CreateDirectory (const cGH *GH, const char *dirname,
 
   return (retval);
 }
+
+
+/********************************************************************
+ ********************    Internal Routines   ************************
+ ********************************************************************/
+static void SetOutputVar (int vindex, const char *optstring, void *arg)
+{
+  info_t *info;
+  regmatch_t gmatch[6], *dmatch;
+  int i, j, bytes, matched;
+  char *token, *separator, *fullname;
+  char *substring, *parsestring, *regexstring;
+  ioRequest *request;
+  DECLARE_CCTK_PARAMETERS
+
+
+  info = (info_t *) arg;
+
+  /* allocate a new I/O request structure and initialize it with defaults */
+  request = IOUtil_DefaultIORequest (info->GH, vindex);
+
+  if (! optstring)
+  {
+    info->request_list[vindex] = request;
+    return;
+  }
+
+  fullname = CCTK_FullName (vindex);
+
+  /* parse the I/O request information */
+  matched = CCTK_RegexMatch (optstring,
+                             "\\{([0-9]*)\\}"            /* dimension  */
+                             "\\{([0-9,()]+)*\\}"        /* direction  */
+                             "\\{([0-9,]+)*\\}"          /* origin     */
+                             "\\{([-0-9,]+)*\\}"         /* extent     */
+                             "\\{([0-9,]+)*\\}",         /* downsample */
+                             6, gmatch);
+  if (matched <= 0)
+  {
+    CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
+                "Couldn't parse I/O request options '%s' for variable '%s'",
+                optstring, fullname);
+    free (fullname); free (request);
+    return;
+  }
+
+  /* SLAB DIMENSION */
+  bytes = (int) (gmatch[1].rm_eo - gmatch[1].rm_so);
+  if (gmatch[1].rm_so != -1 && bytes > 0)
+  {
+    request->hdim = atoi (optstring + gmatch[1].rm_so);
+    if (request->hdim <= 0 || request->hdim > request->vdim)
+    {
+      CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
+                  "Invalid dimension given %d in I/O request options '%s' "
+                  "for variable '%s'", request->hdim, optstring, fullname);
+      free (fullname); free (request);
+      return;
+    }
+  }
+
+  /* DIRECTION */
+  bytes = (int) (gmatch[2].rm_eo - gmatch[2].rm_so);
+  if (gmatch[2].rm_so != -1 && bytes > 0)
+  {
+    substring = strdup (optstring + gmatch[2].rm_so);
+    substring[bytes] = 0;
+
+    dmatch = (regmatch_t *) malloc ((request->hdim + 1) *
+                                    sizeof (regmatch_t));
+    regexstring = (char *) malloc (request->hdim * sizeof ("\\(([0-9,]+)\\)"));
+    regexstring[0] = 0;
+    for (i = 0; i < request->hdim; i++)
+    {
+      strcat (regexstring, "\\(([0-9,]+)\\)");
+    }
+    matched = CCTK_RegexMatch (substring, regexstring, request->hdim + 1,
+                               dmatch);
+    free (regexstring);
+    if (matched <= 0)
+    {
+      CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
+                  "Couldn't parse direction vectors in I/O request options '%s' "
+                  "for variable '%s'.", optstring, fullname);
+      free (fullname); free (dmatch); free (request);
+      return;
+    }
+
+    for (j = 0; j < request->hdim; j++)
+    {
+      i = 0;
+      bytes = (int) (dmatch[j + 1].rm_eo - dmatch[j + 1].rm_so);
+      if (dmatch[j + 1].rm_so != -1 && bytes > 0)
+      {
+        parsestring = strdup (substring + dmatch[j + 1].rm_so);
+        parsestring[bytes] = 0;
+
+        token = parsestring;
+        while ((separator = strchr (token, ',')) != NULL)
+        {
+          *separator = 0;
+          request->direction[j * request->vdim + i] = atoi (token);
+          if (++i >= request->vdim)
+          {
+            break;
+          }
+          token = separator + 1;
+        }
+        request->direction[j * request->vdim + i++] = atoi (token);
+        free (parsestring);
+      }
+      free (substring);
+      if (i < request->vdim)
+      {
+        CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
+                    "Direction vectors are incomplete or missing in I/O request "
+                    "options '%s' for variable '%s'.", optstring, fullname);
+        free (fullname); free (request);
+        return;
+      }
+    }
+  }
+
+  /* ORIGIN */
+  bytes = (int) (gmatch[3].rm_eo - gmatch[3].rm_so);
+  if (gmatch[3].rm_so != -1 && bytes > 0)
+  {
+    substring = strdup (optstring + gmatch[3].rm_so);
+    substring[bytes] = 0;
+
+    i = 0;
+    token = substring;
+    while ((separator = strchr (token, ',')) != NULL)
+    {
+      *separator = 0;
+      request->origin[i] = atoi (token);
+      if (++i >= request->vdim)
+      {
+        break;
+      }
+      token = separator + 1;
+    }
+    request->origin[i++] = atoi (token);
+    free (substring);
+
+    if (i < request->vdim)
+    {
+      CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
+                  "Origin vector is incomplete or missing in I/O request "
+                  "options '%s' for variable '%s'.", optstring, fullname);
+      free (fullname); free (request);
+      return;
+    }
+  }
+
+  /* LENGTH */
+  bytes = (int) (gmatch[4].rm_eo - gmatch[4].rm_so);
+  if(gmatch[4].rm_so != -1 && bytes > 0)
+  {
+    substring = strdup (optstring + gmatch[4].rm_so);
+    substring[bytes] = 0;
+
+    i = 0;
+    token = substring;
+    while ((separator = strchr (token, ',')) != NULL)
+    {
+      *separator = 0;
+      request->extent[i] = atoi (token);
+      if (++i >= request->hdim)
+      {
+        break;
+      }
+      token = separator + 1;
+    }
+    request->extent[i++] = atoi (token);
+    free (substring);
+
+    if (i < request->hdim)
+    {
+      CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
+                  "Length vector is incomplete or missing in I/O request "
+                  "options '%s' for variable '%s'.", optstring, fullname);
+      free (fullname); free (request);
+      return;
+    }
+  }
+
+  /* DOWNSAMPLING */
+  bytes = (int) (gmatch[5].rm_eo - gmatch[5].rm_so);
+  if(gmatch[5].rm_so != -1 && bytes > 0)
+  {
+    substring = strdup (optstring + gmatch[5].rm_so);
+    substring[bytes] = 0;
+
+    i = 0;
+    token = substring;
+    while ((separator = strchr (token, ',')) != NULL)
+    {
+      *separator = 0;
+      request->downsample[i] = atoi (token);
+      if (++i >= request->hdim)
+      {
+        break;
+      }
+      token = separator + 1;
+    }
+    request->downsample[i++] = atoi (token);
+    free (substring);
+
+    if (i < request->hdim)
+    {
+      CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
+                  "Downsampling vector is incomplete or missing in I/O request "
+                  "options '%s' for variable '%s'.", optstring, fullname);
+      free (fullname); free (request);
+      return;
+    }
+  }
+
+  /* assign the new I/O request */
+  info->request_list[vindex] = request;
+
+  /* clean up */
+  free (fullname);
+}
+
+
+ioRequest *IOUtil_DefaultIORequest (const cGH *GH, int vindex)
+{
+  ioRequest *request;
+  int *extent_int;
+  const ioGH *myGH;
+  DECLARE_CCTK_PARAMETERS
+
+
+  myGH = (const ioGH *) CCTK_GHExtension (GH, "IO");
+
+  /* allocate a new I/O request structure */
+  request = (ioRequest *) malloc (sizeof (ioRequest));
+
+  /* fill out the basics */
+  request->vindex = vindex;
+  request->timelevel = 0;
+  request->check_exist = myGH->recovered;
+
+  /* get the I/O request datatype (will be single-precision if requested) */
+  request->hdatatype = CCTK_VarTypeI (vindex);
+  if (myGH->out_single)
+  {
+    if (request->hdatatype == CCTK_VARIABLE_REAL)
+    {
+      request->hdatatype = CCTK_VARIABLE_REAL4;
+    }
+    else if (request->hdatatype == CCTK_VARIABLE_COMPLEX)
+    {
+      request->hdatatype = CCTK_VARIABLE_COMPLEX8;
+    }
+#ifdef CCTK_INT2
+    else if (request->hdatatype == CCTK_VARIABLE_INT)
+    {
+      request->hdatatype = CCTK_VARIABLE_INT2;
+    }
+#endif
+  }
+
+  /* get the variable's dimension and extents */
+  request->vdim = CCTK_GroupDimFromVarI (vindex);
+  extent_int = (int *) malloc (request->vdim * sizeof (int));
+  CCTK_GroupgshVI (GH, request->vdim, extent_int, vindex);
+
+  /* allocate the arrays all in one go
+     only initialize those which are mandatory for the Hyperslab API */
+  request->vectors = (CCTK_INT *) calloc ((request->vdim + 6) * request->vdim + 1,
+                                       sizeof (CCTK_INT));
+  request->hoffset      = request->vectors + 0*request->vdim;
+  request->hsize        = request->vectors + 1*request->vdim;
+  request->hsize_chunk  = request->vectors + 2*request->vdim;
+  request->origin       = request->vectors + 3*request->vdim + 1;
+  request->extent       = request->vectors + 4*request->vdim + 1;
+  request->downsample   = request->vectors + 5*request->vdim + 1;
+  request->direction    = request->vectors + 6*request->vdim + 1;
+
+  for (request->hdim = 0; request->hdim < request->vdim; request->hdim++)
+  {
+    request->extent[request->hdim] = extent_int[request->hdim];
+    request->direction[request->hdim * (request->vdim + 1)] = 1;
+
+    /* take the downsampling parameters from IOUtil */
+    if (request->hdim == 0)
+    {
+      request->downsample[request->hdim] = out3D_downsample_x;
+    }
+    else if (request->hdim == 1)
+    {
+      request->downsample[request->hdim] = out3D_downsample_y;
+    }
+    else if (request->hdim == 2)
+    {
+      request->downsample[request->hdim] = out3D_downsample_z;
+    }
+    else
+    {
+      request->downsample[request->hdim] = 1;
+    }
+  }
+
+  /* clean up */
+  free (extent_int);
+
+  return (request);
+}
diff --git a/src/ioGH.h b/src/ioGH.h
index c77c7b9..150e4da 100644
--- a/src/ioGH.h
+++ b/src/ioGH.h
@@ -2,22 +2,14 @@
    @header    ioGH.h
    @date      Tue 9th Jan 1999
    @author    Gabrielle Allen
-   @desc 
-   The extensions to the GH structure from IOUtil.
-   @history
-   @hauthor Thomas Radke @hdate 16 Mar 1999
-   @hdesc Added parameters for 2D and 3D output
-   @hauthor Thomas Radke @hdate 17 Mar 1999
-   @hdesc Changed naming: IEEEIO -> FlexIO
-   @hauthor Thomas Radke @hdate 30 Mar 1999
-   @hdesc Undefined DI macro
-   @endhistory
-   @version $Header$
+   @desc
+              The extensions to the GH structure from IOUtil.
+   @enddesc
+   @version   $Header$
  @@*/
 
-#ifndef _IOGH_H_
-#define _IOGH_H_ 1
-
+#ifndef _IOUTIL_IOGH_H_
+#define _IOUTIL_IOGH_H_ 1
 
 #ifdef __cplusplus
 extern "C"
@@ -26,34 +18,11 @@ extern "C"
 
 
 /* IOUtil's GH extension structure */
-typedef struct IOGH
+typedef struct
 {
-
-#if 0
-  /* TR: commented these things out because they were moved into the other
-         IO thorns' GH extensions
-         But maybe someday we want them back here, eg. if the user 
-         wants to say how often to do 3D output in general for all IO thorns
-         that can produce 3D output; of course they should still be able
-         override this with their own parameters.
-   */
-  /* How often to output */
-  int  infoevery;
-  int  IO_0Devery;
-  int  IO_1Devery;
-  int  IO_2Devery;
-  int  IO_3Devery;
-
-  /* Directory in which to output */
-  char  *outpfx_0D;
-  char  *outpfx_1D;
-  char  *outpfx_2D;
-  char  *outpfx_3D;
-#endif
-
   /* for 3D output */
-  int ioproc;       /* the IO processor each proc belongs to */
-  int nioprocs;     /* total number of IO processors */
+  int ioproc;       /* the I/O processor each proc belongs to */
+  int nioprocs;     /* total number of I/O processors */
   int ioproc_every; /* output by every N'th processor */
   int unchunked;    /* if true generate unchunked output file */
   int *downsample;  /* downsampling parameters array of size cctk_maxdim */
@@ -72,5 +41,4 @@ typedef struct IOGH
 }
 #endif
 
-#endif /* _IOGH_H_ */
-
+#endif /* _IOUTIL_IOGH_H_ */
diff --git a/src/ioutil_Utils.h b/src/ioutil_Utils.h
index 519f6ee..83831dc 100644
--- a/src/ioutil_Utils.h
+++ b/src/ioutil_Utils.h
@@ -4,13 +4,12 @@
    @author    Thomas Radke
    @desc 
               Function prototypes for setting up slice centers.
-   @history
-   @endhistory
-   @version $Header$
+   @enddesc
+   @version   $Header$
  @@*/
 
-#ifndef _IOUTIL_UTILS_H_
-#define _IOUTIL_UTILS_H_
+#ifndef _IOUTIL_IOUTIL_UTILS_H_
+#define _IOUTIL_IOUTIL_UTILS_H_ 1
 
 #ifdef __cplusplus
 extern "C"
@@ -18,6 +17,44 @@ extern "C"
 #endif
 
 
+/* structure describing an I/O request (including hyperslab parameters) */
+typedef struct
+{
+  /* index and timelevel of the variable */
+  int vindex, timelevel;
+
+  /* dimensionality of the variable and the hyperslab */
+  int vdim, hdim;
+
+  /* CCTK datatype for the hyperslab */
+  int hdatatype;
+
+  /* flag indicating wheter check whether an object to be written already
+     exists (and remove it in that case) */
+  int check_exist;
+
+  /* pointer to allocated buffers */
+  CCTK_INT *vectors;
+
+  /* hyperslab mapping parameters */
+  CCTK_INT *origin, *direction, *extent, *downsample;
+
+  /* offset and sizes of hyperslab into the variable's dataspace */
+  CCTK_INT *hoffset, *hsize, *hsize_chunk;
+
+} ioRequest;
+
+
+/* parse a given 'out_vars' parameter string */
+void IOUtil_ParseVarsForOutput (const cGH *GH, const char *out_vars,
+                                ioRequest *request_list[]);
+
+/* return the default I/O request description structure for a variable */
+ioRequest *IOUtil_DefaultIORequest (const cGH *GH, int vindex);
+
+/* free an I/O request description */
+void IOUtil_FreeIORequest (ioRequest **request);
+
 /* set the slice center for 1D lines */
 int IOUtil_1DLines (const cGH *GH,
                     int num_dims,
@@ -32,6 +69,7 @@ int IOUtil_2DPlanes (const cGH *GH,
                      const CCTK_REAL *origin_phys,
                      int *slice_center);
 
+/* create an output directory on all I/O processors */
 int IOUtil_CreateDirectory (const cGH *GH,
                             const char *dirname,
                             int multiple_io_procs,
@@ -41,4 +79,4 @@ int IOUtil_CreateDirectory (const cGH *GH,
 }
 #endif
 
-#endif  /* _IOUTIL_UTILS_H_ */
+#endif  /* _IOUTIL_IOUTIL_UTILS_H_ */