cd $AMBERHOME
patch -p0 -N < ptraj_2010-07-16-fixFilesize.patch 

Author: Daniel R. Roe
Date: 2010-07-16
Description:
Fixes reading of hex values on big endian machines which prevented
correct identification of files and/or reading incorrect number of
frames in gzipped trajectory files. Use unsigned char instead of
uint8_t for compatibility with obsolete compilers.
Also fix calculation of # frames in Amber Trajectories by switching to 
long long int (to be consistent with the stat struct) and clean up
the bitwise arithmetic in gzipFileSize().
-----------------------------------------------------------------------------
--- AmberTools/src/ptraj/ptraj.c	2010-07-16 20:27:16.000000000 -0400
+++ AmberTools/src/ptraj/ptraj.c	2010-07-16 20:56:55.000000000 -0400
@@ -2058,7 +2058,8 @@
   int lines_per_set;
   int start = 1;
   int stop = 1;
-  int frame_lines, frame_size, title_size, seekable, file_size;
+  int frame_lines, title_size, seekable;
+  long long int file_size, frame_size;
   long int endoffset;
   float *binposScratch;
   FILE *fp;
@@ -2417,20 +2418,29 @@
 
       // Determine Uncompressed File Size for Nframes calculation
       file_size=0;
-      if (trajInfo->compressType==1) // Gzip
+      if (trajInfo->compressType==1)      // Gzip
         file_size=gzipFileSize(filename);
       else if (trajInfo->compressType==2) // Bzip2
         file_size=bzip2FileSize(filename);
       else if (trajInfo->compressType==3) // Zip
         file_size=zipFileSize(filename);
-      if (file_size<0) return NULL;
+      if (file_size<0) {
+        fprintf(stdout,
+                "ERROR in %s: Could not calculate uncompressed file size for %s\n",
+                ROUTINE, filename);
+        return NULL;
+      }
       if (file_size==0) file_size=frame_stat.st_size;
 
       if (prnlev>0)
-        fprintf(stdout,"[%i] Title offset %u   Frame Size %u    File size %lu\n",
+        fprintf(stdout,"[%i] Title offset %u   Frame Size %u    File size %lli\n",
                 worldrank,trajInfo->titleSize,trajInfo->frameSize,file_size);
-      trajInfo->Nframes = (int) ((file_size - trajInfo->titleSize) / trajInfo->frameSize);
-      if (((file_size - trajInfo->titleSize) % (trajInfo->frameSize)) == 0) {
+      frame_size = (long long int) trajInfo->titleSize;
+      file_size = file_size - frame_size; // Subtract title size from file total size.
+      frame_size = (long long int) trajInfo->frameSize;
+      trajInfo->Nframes = (int) (file_size / frame_size);
+      if (prnlev>0) fprintf(stdout,"    File has %i frames.\n",trajInfo->Nframes);
+      if ( (file_size % frame_size) == 0 ) {
 	seekable = 1;
 	stop = trajInfo->Nframes;
       } else {
--- AmberTools/src/ptraj/io.c	2010-07-01 00:41:40.000000000 -0400
+++ AmberTools/src/ptraj/io.c	2010-07-16 21:51:04.000000000 -0400
@@ -673,14 +673,15 @@
   }
 }
 
-/* DAN ROE:
- * gzipFileSize()
- * Return the uncompressed size in bytes of gzipped file by peeking at the 
- * last 4 bytes.
+/* gzipFileSize()
+ * DRR: Return the uncompressed size in bytes of gzipped file by peeking 
+ * at the last 4 bytes.
+ * NOTE: long long int should be equivalent to off_t. 
  */
-int gzipFileSize(char *filename) {
+long long int gzipFileSize(char *filename) {
   FILE *infile;
-  int b1,b2,b3,b4,val;
+  unsigned char b1,b2,b3,b4;
+  long long int val,temp;
 
   if (filename==NULL) return -1;
   if ( (infile = fopen(filename,"rb"))==NULL ) {
@@ -697,21 +698,35 @@
   fread(&b2,1,1,infile);
   fread(&b1,1,1,infile);
 
-  val = (b1 << 24) | (b2 << 16) + (b3 << 8) + b4;
+  val = 0;
+  temp = (long long int) b1;
+  temp <<= 24;
+  val = val | temp;
+  temp = (long long int) b2;
+  temp <<= 16;
+  val = val | temp;
+  temp = (long long int) b3;
+  temp <<= 8;
+  val = val | temp;
+  temp = (long long int) b4;
+  val = val | temp;
+
+  //val = (b1 << 24) | (b2 << 16) + (b3 << 8) + b4;
 
   fclose(infile);
 
-  if (prnlev>0) fprintf(stdout,"gzipFileSize: Uncompressed size of %s: %i\n",filename,val);
+  if (prnlev>0) fprintf(stdout,"gzipFileSize: Uncompressed size of %s: %lli\n",filename,val);
 
   return val;
 }
-/* DAN ROE: 
+
+/* 
  * bzip2FileSize()
- * Return the uncompressed size of bzip2 file in bytes by counting all 
- * characters using bzcat and wc.
+ * DRR: Return the uncompressed size of bzip2 file in bytes by counting 
+ * all characters using bzcat and wc.
  */
-int bzip2FileSize(char *filename) {
-  int val;
+long long int bzip2FileSize(char *filename) {
+  long long int val;
   char *command;
   FILE *pipe;
 
@@ -724,20 +739,21 @@
     fprintf(stdout,"       Check that bzcat and wc are present on your system.\n");
     return -1;
   }
-  fscanf(pipe,"%i",&val);
+  fscanf(pipe,"%lli",&val);
   pclose(pipe);
 
-  if (prnlev>0) fprintf(stdout,"bzip2FileSize: Uncompressed size of %s: %i\n",filename,val);
+  if (prnlev>0) fprintf(stdout,"bzip2FileSize: Uncompressed size of %s: %lli\n",filename,val);
 
   return val;
 }
-/* DAN ROE: 
+
+/* 
  * zipFileSize()
- * Return the uncompressed size of zip file in bytes by counting all 
- * characters using unzip and wc.
+ * DRR: Return the uncompressed size of zip file in bytes by counting 
+ * all characters using unzip and wc.
  */
-int zipFileSize(char *filename) {
-  int val;
+long long int zipFileSize(char *filename) {
+  long long int val;
   char *command;
   FILE *pipe;
 
@@ -750,10 +766,10 @@
     fprintf(stdout,"       Check that unzip and wc are present on your system.\n");
     return -1;
   }
-  fscanf(pipe,"%i",&val);
+  fscanf(pipe,"%lli",&val);
   pclose(pipe);
 
-  if (prnlev>0) fprintf(stdout,"zipFileSize: Uncompressed size of %s: %i\n",filename,val);
+  if (prnlev>0) fprintf(stdout,"zipFileSize: Uncompressed size of %s: %lli\n",filename,val);
 
   return val;
 }
@@ -774,7 +790,7 @@
  *  -2: Internal error
  */
 int id_Filesig(char *filename, FILE *infile) {
-  int *h;
+  unsigned char *h;
   int i, type;
 
   /* Check that either filename or infile is specified, but not both */
@@ -797,7 +813,7 @@
     rewind(infile);
 
   /* Read first 3 bytes from file */
-  h=(int*) calloc(3,sizeof(int));
+  h=(unsigned char*) calloc(3,sizeof(unsigned char));
   fread(h,1,1,infile);
   fread(h+1,1,1,infile);
   fread(h+2,1,1,infile);
--- AmberTools/src/ptraj/io.h	2010-07-16 20:26:17.000000000 -0400
+++ AmberTools/src/ptraj/io.h	2010-07-16 20:26:56.000000000 -0400
@@ -76,9 +76,9 @@
 
 extern void doSystem(char *);
 extern char * promptToOpenFile( FILE **, char *, char *, char *);
-extern int gzipFileSize(char *);
-extern int bzip2FileSize(char *);
-extern int zipFileSize(char *);
+extern long long int gzipFileSize(char *);
+extern long long int bzip2FileSize(char *);
+extern long long int zipFileSize(char *);
 extern int id_Filesig(char *,FILE *);
 extern int openFile( FILE **, char *, char *);
 extern int  promptUserResponse(FILE *, FILE *, char *, char *, int);
@@ -97,9 +97,9 @@
 
 extern void doSystem();
 extern char * promptToOpenFile();
-extern int gzipFileSize();
-extern int bzip2FileSize();
-extern int zipFileSize();
+extern long long int gzipFileSize();
+extern long long int bzip2FileSize();
+extern long long int zipFileSize();
 extern int id_Filesig();
 extern int openFile();
 extern int  promptUserResponse();