replace linked list with hash lookup

rfiorella · Mar 11, 2019 · 23d71d3 · 23d71d3
1 parent ebd44d3
commit 23d71d3
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Showing 5 changed files with 1,251 additions and 29 deletions.
diff --git a/src/clib/pio.h b/src/clib/pio.h
@@ -14,6 +14,7 @@
 #include <stdbool.h>
 #include <string.h> /* memcpy */
 #include <mpi.h>
+#include <uthash.h>
 
 #ifdef _NETCDF
 #include <netcdf.h>
@@ -528,8 +529,9 @@ typedef struct wmulti_buffer
     /** Pointer to the data. */
     void *data;
 
-    /** Pointer to the next multi-buffer in the list. */
-    struct wmulti_buffer *next;
+  /** uthash handle for hash of buffers **/
+  int htid;
+  UT_hash_handle hh;
 } wmulti_buffer;
 
 /**
@@ -563,7 +565,7 @@ typedef struct file_desc_t
 
     /** The wmulti_buffer is used to aggregate multiple variables with
      * the same communication pattern prior to a write. */
-    struct wmulti_buffer buffer;
+    struct wmulti_buffer *buffer;
 
     /** Data buffer for this file. */
     void *iobuf;

diff --git a/src/clib/pio_darray.c b/src/clib/pio_darray.c
@@ -11,7 +11,7 @@
 #include <config.h>
 #include <pio.h>
 #include <pio_internal.h>
-
+#include <uthash.h>
 /* 10MB default limit. */
 PIO_Offset pio_buffer_size_limit = PIO_BUFFER_SIZE;
 
@@ -619,6 +619,7 @@ int PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *
     bufsize totfree;       /* Amount of free space in the buffer. */
     bufsize maxfree;       /* Max amount of free space in buffer. */
 #endif
+    int hashid;
     int mpierr = MPI_SUCCESS;  /* Return code from MPI functions. */
     int ierr = PIO_NOERR;      /* Return code. */
     size_t io_data_size;          /* potential size of data on io task */
@@ -673,29 +674,29 @@ int PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *
             return pio_err(ios, file, PIO_EINVAL, __FILE__, __LINE__);
 
     /* Move to end of list or the entry that matches this ioid. */
-    for (wmb = &file->buffer; wmb->next; wmb = wmb->next)
-        if (wmb->ioid == ioid && wmb->recordvar == vdesc->rec_var)
-            break;
-    LOG((3, "wmb->ioid = %d wmb->recordvar = %d", wmb->ioid, wmb->recordvar));
+    hashid = ioid*10 + vdesc->rec_var;
+    HASH_FIND_INT( file->buffer, &hashid, wmb);
+    if (wmb)
+      LOG((3, "wmb->ioid = %d wmb->recordvar = %d", wmb->ioid, wmb->recordvar));
 
     /* If we did not find an existing wmb entry, create a new wmb. */
-    if (wmb->ioid != ioid || wmb->recordvar != vdesc->rec_var)
+    if (!wmb)
     {
         /* Allocate a buffer. */
-        if (!(wmb->next = bget((bufsize)sizeof(wmulti_buffer))))
+        if (!(wmb = bget((bufsize)sizeof(wmulti_buffer))))
             return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
 
         /* Set pointer to newly allocated buffer and initialize.*/
-        wmb = wmb->next;
         wmb->recordvar = vdesc->rec_var;
-        wmb->next = NULL;
         wmb->ioid = ioid;
         wmb->num_arrays = 0;
         wmb->arraylen = arraylen;
         wmb->vid = NULL;
         wmb->data = NULL;
         wmb->frame = NULL;
         wmb->fillvalue = NULL;
+	wmb->htid = hashid;
+	HASH_ADD_INT( file->buffer, htid, wmb );
     }
     LOG((2, "wmb->num_arrays = %d arraylen = %d iodesc->mpitype_size = %d\n",
          wmb->num_arrays, arraylen, iodesc->mpitype_size));

diff --git a/src/clib/pio_file.c b/src/clib/pio_file.c
@@ -5,7 +5,7 @@
 #include <config.h>
 #include <pio.h>
 #include <pio_internal.h>
-
+#include <uthash.h>
 /* This is the next ncid that will be used when a file is opened or
    created. We start at 16 so that it will be easy for us to notice
    that it's not netcdf (starts at 4), pnetcdf (starts at 0) or
@@ -386,25 +386,17 @@ int PIOc_sync(int ncid)
             wmulti_buffer *wmb, *twmb;
 
             LOG((3, "PIOc_sync checking buffers"));
-            wmb = &file->buffer;
-            while (wmb)
-            {
+	    HASH_ITER(hh, file->buffer, wmb, twmb)
+	      {  
                 /* If there are any data arrays waiting in the
                  * multibuffer, flush it. */
                 if (wmb->num_arrays > 0)
                     flush_buffer(ncid, wmb, true);
-                twmb = wmb;
-                wmb = wmb->next;
-                if (twmb == &file->buffer)
-                {
-                    twmb->ioid = -1;
-                    twmb->next = NULL;
-                }
-                else
-                {
-                    brel(twmb);
-                }
-            }
+		HASH_DEL(file->buffer, wmb);
+		brel(wmb);
+
+	      }
+	    file->buffer = NULL;
         }
     }
 

diff --git a/src/clib/pioc_support.c b/src/clib/pioc_support.c
@@ -1755,7 +1755,7 @@ int PIOc_createfile_int(int iosysid, int *ncidp, int *iotype, const char *filena
     file->fh = -1;
     file->iosystem = ios;
     file->iotype = *iotype;
-    file->buffer.ioid = -1;
+    file->buffer = NULL;
     file->writable = 1;
 
     /* Set to true if this task should participate in IO (only true for