Improved TNG compression speed.

Change-Id: I71c66c6b534cb402048dcd75e008d3db4bd3fb71

1 files changed, 72 insertions, 48 deletions

diff --git a/src/compression/xtc2.c b/src/compression/xtc2.c
index bbd45e9..e5b688a 100644
--- a/src/compression/xtc2.c
+++ b/src/compression/xtc2.c
@@ -1,7 +1,7 @@
 /* This code is part of the tng compression routines.
  *
- * Written by Daniel Spangberg
- * Copyright (c) 2010, 2013, The GROMACS development team.
+ * Written by Daniel Spangberg and Magnus Lundborg
+ * Copyright (c) 2010, 2013-2014 The GROMACS development team.
  *
  *
  * This program is free software; you can redistribute it and/or
@@ -26,6 +26,12 @@
 /* Generated by gen_magic.py */
 #define MAX_MAGIC  92
 
+#ifdef USE_WINDOWS
+#define TNG_INLINE __inline
+#else
+#define TNG_INLINE inline
+#endif
+
 static unsigned int magic[MAX_MAGIC]={
 2U,  3U,  4U,  5U,
 6U,  8U,  10U,  12U,
@@ -159,20 +165,43 @@ static const double iflipgaincheck=0.89089871814033927; /*  1./(2**(1./6)) */
 #define SHOWIT
 #endif
 
+#ifdef USE_WINDOWS
+#define TNG_INLINE __inline
+#else
+#define TNG_INLINE inline
+#endif
+
 int Ptngc_magic(unsigned int i)
 {
   return magic[i];
 }
 
-int Ptngc_find_magic_index(unsigned int maxval)
+TNG_INLINE int Ptngc_find_magic_index(const unsigned int maxval)
 {
-  int i=0;
+  int i;
+
+  if(maxval > magic[MAX_MAGIC/4])
+  {
+      if(maxval > magic[MAX_MAGIC/2])
+      {
+          i = MAX_MAGIC/2 + 1;
+      }
+      else
+      {
+          i = MAX_MAGIC/4 + 1;
+      }
+  }
+  else
+  {
+      i = 0;
+  }
+
   while (magic[i]<=maxval)
     i++;
   return i;
 }
 
-static unsigned int positive_int(int item)
+TNG_INLINE static unsigned int positive_int(const int item)
 {
   int s=0;
   if (item>0)
@@ -182,7 +211,7 @@ static unsigned int positive_int(int item)
   return s;
 }
 
-static int unpositive_int(int val)
+TNG_INLINE static int unpositive_int(const int val)
 {
   int s=(val+1)/2;
   if ((val%2)==0)
@@ -438,23 +467,26 @@ static int compute_magic_bits(int *index)
 /* Convert a sequence of (hopefully) small positive integers
    using the base pointed to by index (x base, y base and z base can be different).
    The largest number of integers supported is 18 (29 to handle/detect overflow) */
-static void trajcoder_base_compress(int *input, int n, int *index, unsigned char *result)
+static void trajcoder_base_compress(int *input, const int n, int *index, unsigned char *result)
 {
   unsigned int largeint[19];
   unsigned int largeint_tmp[19];
-  int i,j;
-  for (i=0; i<19; i++)
-    largeint[i]=0U;
+  int i, j;
+
+  memset(largeint, 0U, sizeof(unsigned int) * 19);
 
-  for (i=0; i<n; i++)
+  if(n > 0)
     {
-      if (i!=0)
-        {
-          /* We must do the multiplication of the largeint with the integer base */
-          Ptngc_largeint_mul(magic[index[i%3]],largeint,largeint_tmp,19);
-          for (j=0; j<19; j++)
-            largeint[j]=largeint_tmp[j];
-        }
+      Ptngc_largeint_add(input[0],largeint,19);
+    }
+
+  for (i=1; i<n; i++)
+    {
+      /* We must do the multiplication of the largeint with the integer base */
+      Ptngc_largeint_mul(magic[index[i%3]],largeint,largeint_tmp,19);
+
+      memcpy(largeint,largeint_tmp,19*sizeof *largeint);
+
       Ptngc_largeint_add(input[i],largeint,19);
     }
   if (largeint[18])
@@ -481,7 +513,7 @@ static void trajcoder_base_compress(int *input, int n, int *index, unsigned char
 }
 
 /* The opposite of base_compress. */
-static void trajcoder_base_decompress(unsigned char *input, int n, int *index, int *output)
+static void trajcoder_base_decompress(unsigned char *input, const int n, int *index, int *output)
 {
   unsigned int largeint[19];
   unsigned int largeint_tmp[19];
@@ -524,7 +556,7 @@ static void trajcoder_base_decompress(unsigned char *input, int n, int *index, i
 /* It is "large" if we have to increase the small index quite a
    bit. Not so much to be rejected by the not very large check
    later. */
-static int is_quite_large(int *input, int small_index, int max_large_index)
+static int is_quite_large(int *input, const int small_index, const int max_large_index)
 {
   int is=0;
   int i;
@@ -547,7 +579,7 @@ int nbits_sum;
 int nvalues_sum;
 #endif
 
-static void write_three_large(struct coder *coder, int *encode_ints, int *large_index, int nbits, unsigned char *compress_buffer, unsigned char **output_ptr)
+static void write_three_large(struct coder *coder, int *encode_ints, int *large_index, const int nbits, unsigned char *compress_buffer, unsigned char **output_ptr)
 {
   trajcoder_base_compress(encode_ints,3,large_index,compress_buffer);
   Ptngc_writemanybits(coder,compress_buffer,nbits,output_ptr);
@@ -559,7 +591,7 @@ static void write_three_large(struct coder *coder, int *encode_ints, int *large_
 #endif
 }
 
-static void insert_batch(int *input_ptr, int ntriplets_left, int *prevcoord,int *minint, int *encode_ints, int startenc, int *nenc)
+static void insert_batch(int *input_ptr, int ntriplets_left, const int *prevcoord,int *minint, int *encode_ints, const int startenc, int *nenc)
 {
   int nencode=startenc*3;
   int tmp_prevcoord[3];
@@ -617,8 +649,8 @@ static void insert_batch(int *input_ptr, int ntriplets_left, int *prevcoord,int
   *nenc=nencode;
 }
 
-static void flush_large(struct coder *coder, int *has_large, int *has_large_ints, int n,
-                        int *large_index, int large_nbits, unsigned char *compress_buffer,
+static void flush_large(struct coder *coder, int *has_large, int *has_large_ints, const int n,
+                        int *large_index, const int large_nbits, unsigned char *compress_buffer,
                         unsigned char **output_ptr)
 {
   int i;
@@ -651,7 +683,7 @@ static void flush_large(struct coder *coder, int *has_large, int *has_large_ints
 }
 
 static void buffer_large(struct coder *coder, int *has_large, int *has_large_ints, int *new_large_ints,
-                        int *large_index, int large_nbits, unsigned char *compress_buffer,
+                        int *large_index, const int large_nbits, unsigned char *compress_buffer,
                         unsigned char **output_ptr)
 {
   /* If it is full we must write them all. */
@@ -669,7 +701,7 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length
 {
   unsigned char *output=NULL;
   unsigned char *output_ptr=NULL;
-  int i,ienc,j;
+  int i,ienc,j,imult;
   int output_length=0;
   /* Pack triplets. */
   int ntriplets=*length/3;
@@ -709,13 +741,15 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length
   maxint[2]=minint[2]=input[2];
 
   for (i=1; i<ntriplets; i++)
-    for (j=0; j<3; j++)
-      {
-        if (input[i*3+j]>maxint[j])
-          maxint[j]=input[i*3+j];
-        if (input[i*3+j]<minint[j])
-          minint[j]=input[i*3+j];
-      }
+    {
+      for (j=0; j<3; j++)
+        {
+          if (input[i*3+j]>maxint[j])
+            maxint[j]=input[i*3+j];
+          if (input[i*3+j]<minint[j])
+            minint[j]=input[i*3+j];
+        }
+    }
 
   large_index[0]=Ptngc_find_magic_index(maxint[0]-minint[0]+1);
   large_index[1]=Ptngc_find_magic_index(maxint[1]-minint[1]+1);
@@ -794,9 +828,7 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length
 #endif
 
   /* Initial prevcoord is the minimum integers. */
-  prevcoord[0]=minint[0];
-  prevcoord[1]=minint[1];
-  prevcoord[2]=minint[2];
+  memcpy(prevcoord, minint, 3*sizeof *prevcoord);
 
   while (ntriplets_left)
     {
@@ -1304,9 +1336,7 @@ int Ptngc_unpack_array_xtc2(struct coder *coder,unsigned char *packed,int *outpu
 #endif
 
   /* Initial prevcoord is the minimum integers. */
-  prevcoord[0]=minint[0];
-  prevcoord[1]=minint[1];
-  prevcoord[2]=minint[2];
+  memcpy(prevcoord, minint, 3*sizeof *prevcoord);
 
   while (ntriplets_left)
     {
@@ -1329,9 +1359,7 @@ int Ptngc_unpack_array_xtc2(struct coder *coder,unsigned char *packed,int *outpu
               /* Get the large value. */
               readmanybits(&ptr,&bitptr,large_nbits,compress_buffer);
               trajcoder_base_decompress(compress_buffer,3,large_index,encode_ints);
-              large_ints[0]=encode_ints[0];
-              large_ints[1]=encode_ints[1];
-              large_ints[2]=encode_ints[2];
+              memcpy(large_ints, encode_ints, 3*sizeof *large_ints);
 #ifdef SHOWIT
               fprintf(stderr,"large ints: %d %d %d\n",large_ints[0],large_ints[1],large_ints[2]);
 #endif
@@ -1444,16 +1472,12 @@ int Ptngc_unpack_array_xtc2(struct coder *coder,unsigned char *packed,int *outpu
               /* Get the large value. */
               readmanybits(&ptr,&bitptr,large_nbits,compress_buffer);
               trajcoder_base_decompress(compress_buffer,3,large_index,encode_ints);
-              large_ints[0]=encode_ints[0];
-              large_ints[1]=encode_ints[1];
-              large_ints[2]=encode_ints[2];
+              memcpy(large_ints, encode_ints, 3*sizeof *large_ints);
               /* Output large value */
               *output++=large_ints[0]+minint[0];
               *output++=large_ints[1]+minint[1];
               *output++=large_ints[2]+minint[2];
-              prevcoord[0]=large_ints[0];
-              prevcoord[1]=large_ints[1];
-              prevcoord[2]=large_ints[2];
+              memcpy(prevcoord, large_ints, 3*sizeof *prevcoord);
             }
           ntriplets_left-=n;
         }