.

3dhit_asynch/3dhit.h

@@ -0,0 +1,228 @@
+/*
+ * 3dhit.h
+ *
+ * autor: Łukasz Bieniasz-Krzywiec
+ *
+ */
+
+#ifndef _3DHIT_H_
+#define _3DHIT_H_
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <string.h>
+#include <time.h>
+#include <math.h>
+
+#include "modules/err.h"
+
+/*
+ * DEKLARACJE STAŁYCH:
+ */
+
+#define LEN         13
+#define RMSD        2.0   /* max rmsd */
+#define ENDS        2.0   /* max distance of ends */
+#define RMSDSEQ     3.0   /* 3.0 max rmsd */
+#define ENDSSEQ     3.0   /* 3.0 max distance of ends */
+#define SEGSIZE     99    /* superimposed segment */
+#define SEGSIZE2    259   /* superimposed segment */
+#define INCREMENT
+
+#define DISTCUTOFF  8.0   /* cutoff for contact analysis, not used */
+#define DISTSIGMA   3.0   /* distanse scaling factor */
+#define MINSEQDIFF  6     /* min sequence separation */
+#define MOVEMINSEG  4     /* initial segment to calculate superposition */
+#define MOVEMINHIT  8.0   /* minimum superposition score to continue */
+#define MOVESTEPS   4     /* minimum superposition score to continue */
+
+#define MINCOS      0.707 /* acos(0.707)=45 => dAngle=90 */
+#define SEGSIGMA    3.0
+#define MVGSIGMA    9.0
+#define MVGALIGN    10
+#define MVGPRGAP    1.02
+#define MVGPREXT    0.02
+
+                          /* FAST - OK  */
+#define SEGHITS1    18    /* 25     18  */
+#define SEGRMSD1    3.0   /* 2.5    3.0 */
+#define SEGHITS2    25    /* 30     25  */
+#define SEGRMSD2    8.0   /* 8.0    8.0 */
+#define SEGRMSD0    3.0   /* 2.5    3.0 */
+#define MOVEW
+#define TWOSTEP
+#define OPTIMIZE    2     /* optimization steps */
+#ifdef PAIR
+#endif
+#define ALIGNMENT
+#define ALIMIN      0.0   /* min score for a position in final alignment */
+
+#define ALIGLOB_NO
+#define paraZero    0.0
+#define paraGap     1.02
+#define paraExt     0.02
+
+#define PAIRSTEP    1
+
+/* Maksymalna długość linii w pliku wejściowym. */
+#define MAX_LINE_LENGTH 1000
+
+/* Kody zleceń: */
+#define MSG_STOP    0     /* zakończ pracę */
+
+
+/*
+ * DEKLARACJE TYPÓW:
+ */
+
+/* unsigned char */
+typedef unsigned char uchar;
+
+/* unsigned int */
+typedef unsigned int uint;
+
+/* unsigned long int */
+typedef unsigned long int luint;
+
+/* long long */
+typedef long long LL;
+
+/* unsigned long long */
+typedef unsigned long long ULL;
+
+/* Współrzędne. */
+typedef float coor_t[3];
+
+/* Białko. */
+typedef struct prot_t_ {
+  int     len;
+  char    *name;
+  short   *num;
+  char    *seq;
+  coor_t  *coor;
+  coor_t  *c;
+} prot_t;
+
+/* Kontakty. */
+typedef struct contacts_t_ {
+  float   *map;
+} contacts_t;
+
+/* Wyjście wątku obliczeniowego. */
+typedef struct spe_worker_output_t_ {
+  int           result;
+  int           hitn, hitn1, hitn2, hitn3;
+  float         alibest;
+  float         Ubest[3][3], xbest[3], ybest[3];
+  int           pathn2, pathn3;
+  int           s, t, pbest[SEGSIZE2], pfull[SEGSIZE2];
+  uchar         pad[4 + 0 * 8];
+} spe_worker_output_t __attribute__((aligned(128)));
+
+/* Parametry wątku obliczeniowego. */
+typedef struct spe_worker_parameters_t_ {
+  prot_t              protein1;
+  prot_t              protein2;
+  spe_worker_output_t *output;
+  volatile uint32_t   *output_status;
+  uint                from;
+  uint                to;
+} spe_worker_parameters_t __attribute__((aligned(64)));
+
+
+/*
+ * DEKLARACJE ZMIENNYCH GLOBALNYCH:
+ */
+
+
+/*
+ * DEKLARACJE PODPROGRAMÓW:
+ */
+
+/*
+ * Funkcje z pliku modules/alignment.c
+ */
+
+float align2_f(float*, const int, const int, int*);
+void calcvect(coor_t*, const coor_t*, int);
+int calc_within(int*, float, int*, float, int*, int, coor_t*, coor_t*, float[3][3], float[3], float[3]);
+float mvg_3Dscore(int*, float[3][3], coor_t*, int, float[3], coor_t*, int, float[3]);
+void print_alin1(FILE*, int, int, char*, char*, int*);
+void ascending_sort(float*, int*, int*, int, int);
+void print_alin(FILE*, const int, const int, const char*, const char*, const int*, const int, const int, int);
+void print_whole_pdb1(FILE*, char**, char**, float[3][3], float[3], float[3]);
+void print_whole_pdb2(FILE*, char**, char**, float[3][3], float[3], float[3]);
+
+/*
+ * Funkcje z pliku modules/contacts.c
+ */
+
+void setcontacts(contacts_t*, coor_t*, int, short*);
+void contactoverlap(contacts_t*, contacts_t*, int, float*, float*);
+
+/*
+ * Funkcje z pliku modules/input.c
+ */
+
+prot_t *readpdb(char*, char ***xpdb);
+
+/*
+ * Funkcje z pliku modules/memory.c
+ */
+
+void *mem(void*, size_t);
+
+
+/*
+ * PRZYDATNE MAKRA
+ */
+
+/* MODULO(a,w) = a mod 2^w */
+#define MODULO(a, w) ((a) & ((1 << (w)) - 1))
+
+/*
+ * Macros for rounding input value to the next lower multiple of either
+ * 16, 32 or 128.
+ */
+#define floor16(value)  ((value) - ((value) & ~15))
+#define floor32(value)  ((value) - ((value) & ~31))
+#define floor128(value) ((value) - ((value) & ~127))
+
+/*
+ * Macros for rounding input value to the next higher multiple of either
+ * 16, 32 or 128.
+ */
+#define ceil16(value)   (((value) + 15) & ~15)
+#define ceil32(value)   (((value) + 31) & ~31)
+#define ceil128(value)  (((value) + 127) & ~127)
+
+
+/*
+ * MACROS TO HELP DEBUGGING:
+ */
+
+#undef PDEBUG
+#undef ASSERT
+
+#ifdef DEBUG
+# ifdef __KERNEL__
+    /* This one if debugging is on, and kernel space */
+#   define PDEBUG(fmt, args...) printk(KERN_CRIT ": " fmt, ## args)
+# else
+    /* This one for user space */
+#   define PDEBUG(fmt, args...) fprintf(stderr, fmt, ## args)
+# endif
+
+# define ASSERT(x) do {\
+    if (!(x)) {\
+      PDEBUG("Assertion failed at line %d in file %s: " #x "\n", __LINE__, __FILE__);\
+      exit(1);\
+    }\
+  } while(0)
+#else
+# define PDEBUG(fmt, args...) /* not debugging: nothing */
+# define ASSERT(x)
+#endif
+
+#endif /* _3DHIT_H_ */

3dhit_asynch/Makefile

@@ -0,0 +1,13 @@
+include make.debug
+
+DIRS = spe
+
+PROGRAM_ppu = 3dhit
+PPU_COMPILER = gcc
+CPPFLAGS = $(DEBFLAGS)
+CFLAGS = -ffast-math
+CC_OPT_LEVEL = -O3
+VPATH = modules:.
+IMPORTS = spe/worker_spe.a -lm -lmisc -lspe2 -lpthread 
+
+include $(CELL_TOP)/buildutils/make.footer

3dhit_asynch/make.debug

@@ -0,0 +1,25 @@
+# Zakomentuj/Odkomentuj nastepna linie, aby wylaczyc/wlaczyc debuggowanie
+#DEBUG = y
+#PROF = y
+#TIMER = y
+
+# Dodajemy flagi debuggera (lub nie) do CFLAGS
+ifeq ($(DEBUG),y)
+  DEBFLAGS = -DDEBUG
+else
+  DEBFLAGS = -DNODEBUG
+endif
+
+# Dodajemy flagi profilera (lub nie) do CFLAGS
+ifeq ($(PROF),y)
+  DEBFLAGS += -DPROF
+else
+  DEBFLAGS += -DNOPROF
+endif
+
+# Dodajemy flagi timera (lub nie) do CFLAGS
+ifeq ($(TIMER),y)
+  DEBFLAGS += -DTIMER
+else
+  DEBFLAGS += -DNOTIMER
+endif