+++ /dev/null
-/* copyright (c) 1996, 1997, 1998, 1999 William R. Pearson and the
- U. of Virginia */
-
-/* $Name: fa_34_26_5 $ - $Id: p2_complib.c,v 1.96 2007/01/12 20:15:16 wrp Exp $ */
-
-/*
- * pcomplib.c : Parallel library search
- *
- * #define FIRSTNODE 0/1 (in msg.h) can be used to reserve one node
- * for collecting results
- *
- * Parallel specific options (from doinit.c):
- * -J # jump to query #
- * -I self-comparison, do (N choose 2) comparisons
- * -T # number of workers
- */
-
-/* This version is modifed to read all files, query and database,
- through the manager process. Workers will now receive their
- database from the manager, rather than reading it themselves. This
- cuts down considerably on NFS traffic, simplifies searches of
- multiple files, and allows use of clusters of slave nodes that do
- not have NFS access
-*/
-
-/* modified 5-November-2004 to ensure 15 byte (SEQ_PAD) NULL
- padding
-
- modified 12-December-2006 to ensure n0>0 before SEQ_PAD padding.
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
-#include <time.h>
-
-#include <limits.h>
-#include <float.h>
-#include <math.h>
-
-#include <unistd.h>
-#include <sys/types.h>
-#include <signal.h>
-#include <sys/stat.h>
-
-#ifdef PVM_SRC
-#include "pvm3.h"
-char *mp_verstr="34.26, January 12, 2007 PVM";
-#endif
-
-#ifdef MPI_SRC
-#include "mpi.h"
-char *mp_verstr="34.26, January 12, 2007 MPI";
-#endif
-
-#include "msg.h"
-#include "defs.h"
-#include "mm_file.h"
-
-#include "structs.h"
-#include "param.h"
-#include "p_mw.h"
-
-#define XTERNAL
-#include "uascii.h"
-
-char pgmdir[MAX_FN];
-char workerpgm[MAX_FN];
-char managepgm[MAX_FN];
-
-#define XTERNAL
-#include "upam.h"
-#undef XTERNAL
-
-/********************************/
-/* global variable declarations */
-/********************************/
-char gstring2[MAX_STR]; /* string for label */
-char gstring3[MAX_STR]; /* string for label */
-char hstring1[MAX_STR];
-
-int nsfnum; /* number of superfamily numbers */
-int sfnum[10]; /* superfamily number from types 0 and 5 */
-int nsfnum_n;
-int sfnum_n[10];
-
-/********************************/
-/* extern variable declarations */
-/********************************/
-extern char *prog_func; /* function label */
-extern char *verstr, *iprompt0, *iprompt1, *iprompt2, *refstr;
-
-/********************************/
-/*extern function declarations */
-/********************************/
-
-void libchoice(char *lname, int, struct mngmsg *); /* lib_sel.c */
-void libselect(char *lname, struct mngmsg *); /* lib_sel.c */
-
-extern void closelib();
-/* check for DNA sequence (nxgetaa.c) */
-extern int scanseq(unsigned char *seq, int n, char *str);
-extern void re_ascii(int *qascii, int *sascii);
-extern int recode(unsigned char *seq, int n, int *qascii, int nsq);
-
-/* 1d to 2d pam (initxx.c) */
-extern void initpam2 (struct pstruct *ppst);
-/* initialize environment (doinit.c) */
-extern void h_init (struct pstruct *ppst, struct mngmsg *, char *);
-extern void s_abort (char *p, char *p1);
-extern void query_parm (struct mngmsg *m_msp, struct pstruct *ppst);
-extern void last_init (struct mngmsg *, struct pstruct *, int);
-
-extern void initenv (int argc, char **argv, struct mngmsg *m_msg,
- struct pstruct *ppst, unsigned char **aa0);
-
-/* print hist, summaries, timing information */
-void prhist(FILE *, struct mngmsg, struct pstruct, struct hist_str, int nstats, struct db_str, char *);
-void printsum(FILE *);
-extern void ptime (FILE *, time_t);
-
-/* reset parameters if DNA sequence (initxx.c) */
-extern void resetp (struct mngmsg *, struct pstruct *);
-
-/* read a sequence (nmgetlib.c) */
-struct lmf_str *openlib(char *, int, int *, int, struct lmf_str *);
-
-#define QGETLIB (q_file_p->getlib)
-#define LGETLIB (l_file_p->getlib)
-
-/* these functions are in scaleswn.c */
-extern int process_hist(struct stat_str *sptr, int nstat,
- struct mngmsg m_msg, struct pstruct pst,
- struct hist_str *hist, void **pstat_void, int);
-extern double zs_to_E(double zs, int n1, int isdna, long, struct db_str ntt);
-extern double (*find_zp)(int score, double escore, int length, double comp, void *);
-void addhistz(double zscore, struct hist_str *); /* scaleswn.c */
-void last_stats(const unsigned char *aa0, int n0,
- struct stat_str *sptr, int nstats,
- struct beststr **bestp_arr, int nbest,
- struct mngmsg m_msg, struct pstruct pst,
- struct hist_str *histp, void *rs);
-
-void selectbestz(struct beststr **, int, int);
-void sortbest(struct beststr **, int, int);
-
-void showbest (FILE *fp, struct beststr **bptr, int nbest,
- int qlib, struct mngmsg *m_msg, struct pstruct pst,
- struct db_str ntt, char *gstring2);
-
-void showalign (FILE *fp,
- struct beststr **bptr, int nbest,int qlib, struct mngmsg m_msg,
- struct pstruct pst, char *gstring2);
-
-#ifdef PVM_SRC
-char worknode[120];
-int pinums[MAXNOD],hosttid;
-int narch;
-struct pvmhostinfo *hostp;
-#endif
-
-FILE *outfd; /* Output file */
-
-extern time_t s_time (); /* fetches time for timing */
-
-/* this information is global for fsigint() */
-time_t tstart, tscan, tprev, tdone; /* Timing */
-time_t tdstart, tddone, time();
-int max_nodes, nnodes; /* number of nodes */
-int node_map[MAXWRKR], node_id[MAXWRKR];
-int tot_speed,h_speed;
-int qlib = 0; /* number of sequences scanned */
-struct db_str ntt, qtt;
-
-extern int max_workers, worker_1, worker_n;
-int wlsn [MAXWRKR + 1]; /* number of library sequences in worker */
-int clsn [MAXWRKR + 1]; /* number of 1st library sequence in worker */
-
-int max_buf_cnt;
-
-#ifdef PVM_SRC
-#ifndef WORKERPGM
-#define WORKERPGM "c34.work"
-#endif
-#endif
-
-main (int argc, char *argv[])
-{
- unsigned char *aa00, *aa01, *aa0p0, *aa0p1;
- unsigned char *aa1, *aa1ptr, *aa1prev;
- int aa1i, *aa1i_arr; /* integer offset of sequence in buffer */
-
- int n1;
- int *n1tot_ptr=NULL, *n1tot_cur;
- int n1tot_cnt=0;
- int n1tot_v;
-
- long l_off;
- char nodefile[240];
- struct pstruct pst;
- int i_score;
- struct lmf_str *q_file_p;
- struct lmf_str *l_file_p;
-
- /* from manage code */
- struct mngmsg m_msg0, m_msg1; /* Message from host to manager */
- struct mngmsg *m_msp0, *m_msp1; /* alternating pointers */
- struct qmng_str qm_msg0, qm_msg1; /* stuff updated for each query */
- char q_sqnam[4];
- int sstart, sstop;
-
- struct qmng_str *qm_msp0, *qm_msp1; /* pointer to stuff updated */
- int last_msg_b[10]; /* last set of numbers */
- long curtype = ONETYPE; /* current message type */
- int nclib;
- struct beststr *best, /* array of best scores */
- **bptr; /* array of pointers */
- struct comstr bestr[BFR+1]; /* temporary structure array */
- struct comstr2 bestr2[BFR2+1]; /* temporary structure array */
- struct a_struct *aln_d_base=NULL; /* alignment info for -m 9 */
- int qres_bufsize; /* buffer size for results */
- struct stat_str *stats=NULL, *qstats=NULL;
- int best_flag = 1; /* bptr[] must be re-initialized */
- int fast_flag = 0; /* send new sequences before old displayed */
- int nstats, nqstats, kstats, jstats;
- int nbest, nres; /* number of best scores */
- double zbestcut = -BIGNUM; /* z-value cutoff */
- int lcnt; /* counters */
- int nopt;
- int i, j, k, is, id, iw, ires, naa0 = 0;
-
- FILE *fdata=NULL; /* file for full results */
- struct sql *desptr;
- struct sql *ldes; /* descriptive lines for all lib sequences */
- char *bline_buf, *bline_bufp;
- char *bline_buf_mx; /* buffer for blines */
- char q_bline[256];
- char t_bline[256];
- int max_bline_b, bline_inc;
- int *n1_arr, *m_seqnm_arr;
- unsigned char *aa1_buf;
-
- char tlibstr[11]; /* used only for fdata *.res files */
-
- int node, snode, zero; /* Number of nodes */
- int bufid, numt, tid;
-
- int ave_seq_len;
- int max_sql;
- int ntbuff, nseq, m_seqnm;
- int iln, ocont, maxt;
- long loffset;
-
- int leng; /* leng is length of the descriptive line */
- fseek_t qseek,lseek; /* seek into library of current sequence */
- int qlcont,lcont; /* continued sequence */
- int n_proc, n_tmp;
- char errstr[120];
- int stats_done =0; /* flag for z-value processing */
- int tm_best, t_rbest, t_qrbest, t_best, t_n1;
- double e_score, tm_escore, t_rescore, t_qrescore;
- double zscore; /* tmp value */
- double k_H, k_comp;
- char tmp_str[MAX_FN];
- char pgm_abbr[MAX_SSTR];
- char *bp;
-#ifdef MPI_SRC
- MPI_Status mpi_status;
-#endif
-
- void fsigint();
-
- signal(SIGHUP,SIG_IGN);
- if (signal(SIGINT,SIG_IGN) != SIG_IGN) signal(SIGINT,fsigint);
- if (signal(SIGQUIT,SIG_IGN) != SIG_IGN) signal(SIGQUIT,fsigint);
-/* if (signal(SIGSEGV,SIG_IGN) != SIG_IGN) signal(SIGSEGV,fsigint); */
-
- /* Initialization */
-
-
-#if defined(UNIX)
- m_msg0.quiet = !isatty(1);
-#endif
-
- /* BFR must be %6 = 0 for TFASTA */
- if ((BFR%6) != 0) {
- fprintf(stderr," BFR size %d not %%6=0 - recompile\n",BFR);
- exit(1);
- }
-
-#ifdef MPI_SRC
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(MPI_COMM_WORLD,&tid);
- if (tid > 0) {
- workcomp(tid);
- MPI_Finalize();
- exit(0);
- }
-#endif
-
- printf("#");
- for (i=0; i<argc; i++) {
- if (strchr(argv[i],' ')) printf(" \"%s\"",argv[i]);
- else printf(" %s",argv[i]);
- }
- printf("\n");
-
-#ifdef MPI_SRC
- MPI_Comm_size(MPI_COMM_WORLD,&nnodes);
- if (nnodes <= 1) {
- fprintf(stderr," nnodes = %d; no workers available\n",nnodes);
- exit(1);
- }
- else fprintf(stderr," have %d nodes\n",nnodes);
-
- tot_speed = nnodes*100;
-#endif
-
- h_init (&pst,&m_msg0, pgm_abbr);
-
- initenv (argc, argv, &m_msg0, &pst, &aa00);
-
-#ifdef PVM_SRC
- strncpy (workerpgm, WORKERPGM,sizeof(workerpgm)-1);
- strncat(workerpgm, pgm_abbr, sizeof(workerpgm)-strlen(workerpgm)-1);
- workerpgm[sizeof(workerpgm)-1] = '\0';
-#endif
-
- strncpy(q_sqnam,"aa",sizeof(q_sqnam));
- m_msg0.quiet = 1;
- if (m_msg0.qdnaseq != SEQT_UNK &&
- (m_msg0.qdnaseq == SEQT_DNA || m_msg0.qdnaseq == SEQT_RNA))
- strncpy(q_sqnam,"nt",sizeof(q_sqnam));
-
- m_msg0.pstat_void = NULL;
- m_msg0.hist.hist_a = NULL;
-
- fprintf (stderr, "Pcomp library processor\n");
- fprintf (stderr, "Using %s\n", prog_func);
-
- tstart = tscan = s_time();
- tdstart = time(NULL);
-
-
-#ifdef PVM_SRC
- if ((hosttid=pvm_mytid())<0) {
- pvm_perror("initialization");
- fprintf(stderr,"can't initialize %s\n", argv[0]);
- pvm_exit();
- exit(1);
- }
-
- pvm_config(&nnodes,&narch,&hostp);
- fprintf(stderr,"nnodes: %d, narch: %d\n",nnodes, narch);
- max_nodes = nnodes;
-
-#ifdef DEBUG
- pvm_catchout(stderr);
-#endif
-
-/* if (nnodes < 2 ) nnodes = 4; */
- if (max_workers > 0 && nnodes > max_workers) {
- nnodes = max_workers+FIRSTNODE;
- fprintf(stderr," workers reset from %d to %d\n",
- max_nodes,nnodes-FIRSTNODE);
- }
- else max_workers = nnodes;
-
- strncpy(nodefile,pgmdir,sizeof(nodefile)-1);
- strncat(nodefile,workerpgm,sizeof(nodefile)-strlen(nodefile)-1);
- nodefile[sizeof(nodefile)-1] = '\0';
-
- if (worker_1 > 0) {
- /* remap configuration to specific nodes */
- for (i=FIRSTNODE, j=worker_1; i<nnodes && j<=worker_n; i++,j++)
- node_id[i]=j;
- nnodes = i;
- max_workers = i-FIRSTNODE;
- fprintf(stderr," workers remapped from %d to %d\n",
- max_nodes,nnodes-FIRSTNODE);
- max_nodes = nnodes;
- }
- else {
- for (i=0; i< nnodes; i++) node_map[i]=node_id[i] = i;
- }
-
- if (nnodes < max_nodes) {
- hostp++; /* bump over host name for spawn */
- rand_nodes(node_map,nnodes,max_nodes-1);
- for (i=FIRSTNODE; i<nnodes; i++) {
- numt+=pvm_spawn(nodefile,NULL,PvmTaskHost,hostp[node_map[i]].hi_name,
- 1,&pinums[i]);
- }
- }
- else {
- /* i counts through nodes (machines) */
- /* j counts through processes (multiple processes/node) */
- /* node map maps the process (virtual node) to a physical node (machine) */
-
- for (i=j=FIRSTNODE; i<nnodes && j < MAXWRKR; i++) {
- n_proc = hostp[node_id[i]].hi_speed%100;
- if (n_proc == 0) n_proc = 1;
- if (n_proc > max_workers) n_proc = max_workers;
-
- n_tmp =pvm_spawn(nodefile,NULL,PvmTaskHost,hostp[node_id[i]].hi_name,
- n_proc,&pinums[j]);
- if (n_tmp < n_proc)
- fprintf(stderr," spawn problem: %d\n", pinums[j]);
- if (n_tmp > 0) {
- for (k=j; k < j+n_tmp; k++) node_map[k]=node_id[i];
- j += n_tmp;
- }
- }
- nnodes = numt = j;
- }
-
- if (numt < nnodes) {
- if (numt <= 0) {
- pvm_perror("");
- pvm_exit();
- exit(1);
- }
- nnodes = numt;
- }
-
- for (tot_speed=0,i=FIRSTNODE; i<nnodes; i++) {
- if (pinums[i]<0) {
- fprintf(stderr," tids %d %8o\n",i,pinums[i]);
- pvm_perror("");
- pvm_exit();
- exit(1);
- }
- else {
- h_speed = hostp[node_map[tidtonode(pinums[i])]].hi_speed;
- if (h_speed <= 0) h_speed = 100;
- fprintf(stderr," tids %d %8o %s %5d\n",i,pinums[i],
- hostp[node_map[tidtonode(pinums[i])]].hi_name,
- h_speed);
- tot_speed +=(hostp[node_map[tidtonode(pinums[i])]].hi_speed);
- }
- }
-
- strncpy(worknode,nodefile,sizeof(worknode));
- fprintf (stderr, "%3d worker programs loaded from %s\n",
- nnodes-FIRSTNODE,worknode);
-#endif
-
- /* need to allocate two aa0 arrays so that the old is saved for alignments */
-
- /* Allocate space for the query sequence */
- if ((aa00 = (unsigned char *) malloc ((MAXTST + SEQ_PAD + 1)* sizeof (char))) == NULL)
- s_abort ("Unable to allocate query sequence", "");
-
- if ((aa01 = (unsigned char *) malloc ((MAXTST + SEQ_PAD + 1) * sizeof (char))) == NULL)
- s_abort ("Unable to allocate query sequence", "");
-
- fputs(iprompt0,stdout);
- fprintf(stdout," %s%s\n",verstr,refstr);
-
- /* Query library */
- if (m_msg0.tname[0] == '\0') {
- if (m_msg0.quiet == 1) s_abort("query sequence undefined","");
-
- fprintf(stderr, "Pvcomplib [%s]\n",mp_verstr);
- l1: fputs (iprompt1, stdout);
- fflush (stdout);
- if (fgets (m_msg0.tname, 80, stdin) == NULL)
- s_abort ("Unable to read query library name","");
- if ((bp=strchr(m_msg0.tname,'\n'))!=NULL) *bp='\0';
- if (m_msg0.tname[0] == '\0') goto l1;
- }
-
- /* Open query library */
- if ((q_file_p=
- openlib(m_msg0.tname, m_msg0.qdnaseq,qascii,!m_msg0.quiet,NULL))==NULL) {
- s_abort(" cannot open library ",m_msg0.tname);
- }
- /*
- else {
- printf ("searching %s library\n",m_msg0.tname);
- }
- */
-
- ntt.entries = qtt.entries = 0;
- ntt.carry = qtt.carry = 0;
- ntt.length = qtt.length = 0l;
-
- /* Fetch first sequence */
- qlcont = 0;
- while (qlib < m_msg0.ql_start) { /* skip through query sequences */
- pst.n0 = qm_msg0.n0 = m_msg0.n0 =
- QGETLIB (aa00, MAXTST, q_bline, sizeof(q_bline), &qseek, &qlcont,
- q_file_p,&m_msg0.sq0off);
-
- strncpy(qm_msg0.libstr,q_bline,sizeof(qm_msg0.libstr)-20);
- qm_msg0.libstr[sizeof(qm_msg0.libstr)-21]='\0';
- if ((bp=strchr(qm_msg0.libstr,' '))!=NULL) *bp='\0';
-
- /* if annotations are included in sequence, remove them */
- if (m_msg0.ann_flg) {
- pst.n0 = qm_msg0.n0 = m_msg0.n0 =
- ann_scan(aa00, m_msg0.n0, &m_msg0, m_msg0.qdnaseq);
-#ifdef DEBUG
- fprintf(stderr,"m_msp0->/aa0a is: %o/%o\n",&m_msg0,m_msg0.aa0a);
-#endif
- }
-
- if (m_msg0.term_code &&
- !(m_msg0.qdnaseq == SEQT_DNA || m_msg0.qdnaseq==SEQT_RNA) &&
- aa00[m_msg0.n0-1]!='*') {
- aa00[m_msg0.n0++]='*';
- aa00[m_msg0.n0]=0;
- pst.n0 = qm_msg0.n0 = m_msg0.n0;
- }
-
- /* check for subset */
- if (q_file_p->opt_text[0]!='\0') {
- if (q_file_p->opt_text[0]=='-') {
- sstart=0; sscanf(&q_file_p->opt_text[1],"%d",&sstop);
- }
- else {
- sscanf(&q_file_p->opt_text[0],"%d-%d",&sstart,&sstop);
- sstart--;
- if (sstop <= 0 ) sstop = BIGNUM;
- }
- for (id=0,is=sstart; is<min(m_msg0.n0,sstop); ) aa00[id++]=aa00[is++];
- aa00[id]=0;
- pst.n0 = qm_msg0.n0 = m_msg0.n0 = min(m_msg0.n0,sstop)-sstart;
- if (m_msg0.sq0off==1) m_msg0.sq0off = sstart+1;
- }
-
- qlib++;
-
- if (m_msg0.n0 <= 0)
- s_abort ("Unable to fetch sequence from library: ", m_msg0.tname);
- }
- qtt.entries=1;
- qm_msg0.slist = 0;
-
- /* now have correct query sequence - check sequence type and reset */
- if (m_msg0.qdnaseq == SEQT_UNK) { /* check for DNA sequence */
- if (m_msg0.n0 > 20 &&
- (float)scanseq(aa00,m_msg0.n0,"ACGTUNacgtun")/(float)m_msg0.n0>0.85) {
- pascii = nascii;
- m_msg0.qdnaseq = SEQT_DNA;
- }
- else { /* its protein */
- pascii = aascii;
- m_msg0.qdnaseq = SEQT_PROT;
- }
-
- re_ascii(qascii,pascii);
- init_ascii(pst.ext_sq_set,qascii,m_msg0.qdnaseq);
- m_msg0.n0 = recode(aa00,m_msg0.n0,qascii,pst.nsqx);
- }
-
- /* for ALTIVEC, must pad with 15 NULL's */
- for (i=0; i<SEQ_PAD+1; i++) {aa00[m_msg0.n0+i]=0;}
-
- qtt.length = m_msg0.n0;
-
- if (qlib <= 0) {
- fprintf(stderr," no sequences found in query library\n");
- exit(1);
- }
-
- resetp (&m_msg0, &pst);
-
- sprintf(tmp_str," %d %s", qm_msg0.n0, q_sqnam);
- leng = strlen (qm_msg0.libstr);
- if (leng + strlen(tmp_str) >= sizeof(qm_msg0.libstr))
- qm_msg0.libstr[sizeof(qm_msg0.libstr)-strlen(tmp_str)-2] = '\0';
- strncat(&qm_msg0.libstr[0],tmp_str,
- sizeof(qm_msg0.libstr)-strlen(qm_msg0.libstr)-1);
- qm_msg0.libstr[sizeof(qm_msg0.libstr)-1]='\0';
-
- qm_msg0.seqnm = qlib-1;
-
- /* Library */
-
- if (strlen (m_msg0.lname) == 0) {
- if (m_msg0.quiet == 1) s_abort("library name undefined","");
- libchoice(m_msg0.lname, sizeof(m_msg0.lname), &m_msg0);
- }
-
- libselect(m_msg0.lname, &m_msg0);
-
- /* Get additional parameters here */
- if (!m_msg0.quiet) query_parm (&m_msg0, &pst);
-
- last_init(&m_msg0, &pst,nnodes-FIRSTNODE);
- memcpy(&m_msg1, &m_msg0, sizeof(m_msg0));
-
- /* m_msg0.maxn needs to be set to MAXLIB or MAXTRN, depending on the
- function - max_tot has the MAXTST + (MAXLIB|MAXTRN) */
- if (m_msg0.maxn <= 0) m_msg0.maxn = m_msg0.max_tot - MAXTST;
-
- if (m_msg0.maxn < 2 * m_msg0.dupn) m_msg0.maxn = 5*m_msg0.dupn;
- pst.maxlen = m_msg0.maxn;
-
- m_msg0.loff = m_msg0.dupn;
- m_msg0.maxt3 = m_msg0.maxn-m_msg0.loff;
-
-
- /* ******************** */
- /* initial manager code */
- /* ******************** */
-
- outfd = stdout;
- if (m_msg0.outfile[0]!='\0') {
- if ((outfd = fopen(m_msg0.outfile,"w"))==NULL) {
- fprintf(stderr, "cannot open %s for output\n", m_msg0.outfile);
- outfd = stdout;
- }
- }
-
- /* Label the output */
- printf("Query library %s vs %s library\n", m_msg0.tname, m_msg0.lname);
-
- /* Allocate space for saved scores */
- if ((best =
- (struct beststr *)malloc((MAXBEST+1)*sizeof(struct beststr)))==NULL)
- s_abort ("Cannot allocate best struct","");
- if ((bptr =
- (struct beststr **)malloc((MAXBEST+1)*sizeof(struct beststr *)))==NULL)
- s_abort ("Cannot allocate bptr","");
-
- /* Initialize bptr */
- for (nbest = 0; nbest < MAXBEST+1; nbest++)
- bptr[nbest] = &best[nbest];
-
- best++; bptr++;
- best[-1].score[0]=best[-1].score[1]=best[-1].score[2]=INT_MAX;
- best[-1].zscore = FLT_MAX;
- best[-1].escore = FLT_MIN;
- best_flag = 0;
-
- if ((stats =
- (struct stat_str *)calloc((size_t)MAXSTATS,sizeof(struct stat_str)))
- ==NULL)
- s_abort ("Cannot allocate stats struct","");
- nstats = 0;
-
- /* Now open the second library, divide it, send sequences to all workers */
- /* Set up buffer for reading the library:
-
- We will start by using a 2 Mbyte buffer for each worker. For
- proteins, that means 5,000 sequences of length 400 (average).
- For DNA, that means 2,000 sequences of length 1000. At the moment,
- those are good averages.
- */
-
- if (max_buf_cnt <= 0) {
- if (m_msg0.ldnaseq==SEQT_DNA) max_buf_cnt = MAX_NT_BUF;
- else max_buf_cnt = MAX_AA_BUF;
- }
-
- if (m_msg0.ldnaseq==SEQT_DNA) ave_seq_len = AVE_NT_LEN;
- else ave_seq_len = AVE_AA_LEN;
-
- /* however - buffer sizes should be a function of the number of
- workers so that all the workers are kept busy. Assuming a 10,000
- entry library is the smallest we want to schedule, then
- */
-
- if (max_buf_cnt > 10000/(nnodes-FIRSTNODE))
- max_buf_cnt = 10000/(2*(nnodes-FIRSTNODE));
-
- /* allocate space for sequence buffers */
-
- m_msg0.pbuf_siz=max_buf_cnt*ave_seq_len;
- if (m_msg0.pbuf_siz < 5*m_msg0.maxn)
- m_msg0.pbuf_siz = 5*m_msg0.maxn;
-
-#ifdef PVM_SRC
-#ifdef ROUTE_DIRECT
- pvm_setopt(PvmRoute,PvmRouteDirect);
-#endif
- pvm_initsend(PvmDataRaw);
- pvm_pkint(&nnodes,1,1);
- pvm_pkint(pinums,nnodes,1);
- pvm_pkbyte((char *)&m_msg0,(int)sizeof(m_msg0),1);
- for (node = FIRSTNODE; node<nnodes; node++)
- if (pvm_send(pinums[node],STARTTYPE0)<0) {
- pvm_perror("pvm_send1");
- pvm_exit();
- exit(1);
- }
-#endif
-#ifdef MPI_SRC
- for (node = FIRSTNODE; node<nnodes; node++) {
- MPI_Send(&m_msg0,(int)sizeof(m_msg0),MPI_BYTE,node,STARTTYPE0,
- MPI_COMM_WORLD);
- }
-#endif
-
- /* now send pst, sascii */
-#ifdef PVM_SRC
- pvm_initsend(PvmDataRaw);
- pvm_pkbyte((char *)&pst,(int)sizeof(pst),1);
- pvm_pkbyte((char *)pascii,(int)sizeof(aascii),1);
-
- for (node = FIRSTNODE; node< nnodes; node++)
- pvm_send(pinums[node],STARTTYPE1);
-
- /* send pam12 */
- pvm_initsend(PvmDataRaw);
- pvm_pkint(pam12,m_msg0.pamd1*m_msg0.pamd2,1);
- for (node = FIRSTNODE; node< nnodes; node++)
- pvm_send(pinums[node],STARTTYPE2);
-
- /* send pam12x */
- pvm_initsend(PvmDataRaw);
- pvm_pkint(pam12x,m_msg0.pamd1*m_msg0.pamd2,1);
- for (node = FIRSTNODE; node< nnodes; node++)
- pvm_send(pinums[node],STARTTYPE3);
-
-#endif
-#ifdef MPI_SRC
- for (node=FIRSTNODE; node < nnodes; node++) {
- MPI_Send(&pst,(int)sizeof(pst),MPI_BYTE,node,STARTTYPE1,
- MPI_COMM_WORLD);
- MPI_Send(pascii,(int)sizeof(aascii),MPI_BYTE,node,STARTTYPE1,
- MPI_COMM_WORLD);
- MPI_Send(pam12,m_msg0.pamd1*m_msg0.pamd2,MPI_INT,node,STARTTYPE2,
- MPI_COMM_WORLD);
- MPI_Send(pam12x,m_msg0.pamd1*m_msg0.pamd2,MPI_INT,node,STARTTYPE3,
- MPI_COMM_WORLD);
- }
-#endif
-
- if ((n1_arr =
- (int *)calloc((size_t)(max_buf_cnt+1),sizeof(int)))
- ==NULL) {
- fprintf(stderr," cannot allocate n1_arr %d\n",max_buf_cnt+1);
- s_abort(" cannot allocate n1_arr","");
- exit(1);
- }
-
- if ((aa1i_arr =
- (int *)calloc((size_t)(max_buf_cnt+1),sizeof(int)))
- ==NULL) {
- fprintf(stderr," cannot allocate aa1i_arr %d\n",max_buf_cnt+1);
- s_abort(" cannot allocate aa1i_arr","");
- exit(1);
- }
-
- if ((m_seqnm_arr=
- (int *)calloc((size_t)(max_buf_cnt+1),sizeof(int)))
- ==NULL) {
- fprintf(stderr," cannot allocate m_seqnm_arr %d\n",max_buf_cnt+1);
- s_abort(" cannot allocate m_seqnm_arr","");
- exit(1);
- }
-
- if ((aa1_buf =
- (unsigned char *)calloc((size_t)(m_msg0.pbuf_siz),sizeof(unsigned char)))
- ==NULL) {
- s_abort(" cannot allocate library buffer %d","");
- exit(1);
- }
-
-
- /* also allocate space for descriptions. Assume max of 250,000 sequences/
- worker for now
- */
-
- /* max_sql is the maxinum number of library sequences that can be stored */
- max_sql = MAXSQL;
-
- if ((ldes=(struct sql *)calloc(max_sql,sizeof(struct sql)))==NULL) {
- fprintf(stderr," failure to allocate ldes(%d) %ld\n",
- max_sql,max_sql*sizeof(struct sql));
- s_abort("cannot allocate ldes","");
- exit(1);
- }
-
- max_bline_b = MAXSQL * (m_msg0.aln.llen+1)/4;
- bline_inc = m_msg0.aln.llen;
- if (m_msg0.markx & MX_M9SUMM) bline_inc += 40;
-
- i = 4;
- while (i-- > 0) {
- if ((bline_buf=(char *)calloc(max_bline_b,sizeof(char)))!=NULL) break;
- max_bline_b /= 2;
- bline_inc /= 2;
- }
- if (bline_buf == NULL) {
- fprintf(stderr," failure to allocate bline_buf(%d) %d\n",
- max_sql,max_bline_b);
- s_abort(" cannot allocate bline_buf","");
- }
-
- bline_bufp = bline_buf;
- bline_buf_mx = bline_buf+max_bline_b;
-
- /* the code for filling the buffers is copied from comp_thr.c */
- /* the major differences reflect the fact that all library descriptions
- will be kept in memory, indexed by sequence number.
-
- As a result, one buffer is filled by this loop -
- ldes[] has the descriptive information for every sequence
- this array could potentially be quite large
- */
-
- /* now open the library and start reading */
- /* get a buffer and fill it up */
-
- ntbuff = 0;
- m_seqnm = 0; /* m_seqnm is the number of this library sequence */
- nseq = 0;
-
- node = FIRSTNODE;
-
- /* sqs2_buf[0].aa1 = aa1_buf; */
- aa1 = aa1_buf;
-
- /* iln counts through each library */
- for (iln = 0; iln < m_msg0.nln; iln++) {
- if ((l_file_p=
- openlib(m_msg0.lbnames[iln], m_msg0.ldnaseq,lascii,!m_msg0.quiet,NULL))==NULL) {
- fprintf(stderr," cannot open library %s\n",m_msg0.lbnames[iln]);
- continue;
- }
- else {
- printf ("searching %s library\n",m_msg0.lbnames[iln]);
- }
-
- lcont = ocont = 0;
- n1tot_v = n1tot_cnt = 0;
- n1tot_ptr = n1tot_cur = NULL;
- maxt = m_msg0.maxn;
- loffset = 0l;
-
- /* read sequence directly into buffer */
- aa1ptr = aa1; /* = sqs2_buf[0].aa1; */
-
- while ((n1= LGETLIB(aa1ptr,maxt,t_bline,sizeof(t_bline),&lseek,&lcont,
- l_file_p,&l_off))>=0) {
-
- /* skip sequences outside range */
- if (n1 < m_msg0.n1_low || n1 > m_msg0.n1_high) goto loop1;
-
- /* add termination code for proteins, if asked */
- if (m_msg0.term_code && !lcont &&
- m_msg0.ldnaseq==SEQT_PROT && aa1ptr[n1-1]!=m_msg0.term_code) {
- aa1ptr[n1++]=m_msg0.term_code;
- aa1ptr[n1]=0;
- }
-
- /* check for a continued sequence and provide a pointer to
- the n1_tot array if lcont || ocont */
- n1tot_v += n1;
- if (lcont && !ocont) { /* get a new pointer */
- if (n1tot_cnt <= 0) {
- if ((n1tot_ptr=calloc(1000,sizeof(int)))==NULL) {
- fprintf(stderr," cannot allocate n1tot_ptr\n");
- exit(1);
- }
- else {n1tot_cnt=1000;}
- }
- n1tot_cnt--;
- n1tot_cur = n1tot_ptr++;
- }
-
- if (bline_bufp + bline_inc > bline_buf_mx) {
- i = 4;
- while (i-- > 0) {
- if ((bline_buf=(char *)calloc(max_bline_b,sizeof(char)))!=NULL)
- break;
- fprintf(stderr," failure to allocate bline_buf(%d) %d\n",
- max_sql,max_bline_b);
- max_bline_b /= 2;
- bline_inc /= 2;
- }
- if (bline_buf != NULL) {
- bline_bufp = bline_buf;
- bline_buf_mx = bline_buf+max_bline_b;
- }
- else {
- s_abort("cannot allocate bline_buf ","");
- exit(1);
- }
- }
-
- if (bline_bufp+bline_inc < bline_buf_mx ) {
- strncpy(bline_bufp,t_bline,bline_inc);
- ldes[m_seqnm].bline = bline_bufp;
- bline_bufp[bline_inc]= '\0';
- bline_bufp += bline_inc+1;
- }
- else {
- fprintf(stderr," bline_buf overrun\n");
- }
-
- ntt.entries++; /* inc number of sequences */
- ntt.length += n1; /* update total library length */
- if (ntt.length > LONG_MAX) {ntt.length -= LONG_MAX; ntt.carry++;}
-
-#ifdef DEBUG
- /* This discovers most reasons for core dumps */
- if (pst.debug_lib)
- for (i=0; i<n1; i++)
- if (aa1[i]>pst.nsq) {
- fprintf(stderr,
- "%s residue[%d/%d] %d range (%d) lcont/ocont: %d/%d\n%s\n",
- qm_msg0.libstr,i,n1,aa1[i],pst.nsq,lcont,ocont,aa1ptr+i);
- aa1[i]=0;
- n1=i-1;
- break;
- }
-#endif
-
- /* for ALTIVEC, must pad with 15 NULL's */
- for (i=0; i<SEQ_PAD+1; i++) {aa1ptr[n1+i]=0;}
-
- /* don't count long sequences more than once */
- if (aa1!=aa1ptr) {
- n1 += m_msg0.loff; m_msg0.db.entries--; ntt.entries--;
- }
-
- if (n1>1) {
-
- desptr = &ldes[m_seqnm];
-
- aa1i_arr[nseq] = (int)(aa1-aa1_buf);
- m_seqnm_arr[nseq] = m_seqnm;
- desptr->n1 = n1_arr[nseq] = n1;
- desptr->n1tot_p = n1tot_cur;
- desptr->lseek = lseek;
- desptr->loffset = loffset+l_off;
- desptr->cont = ocont;
- desptr->wrkr = node;
- desptr->nsfnum = nsfnum;
-#ifdef SUPERFAMNUM
- if ((desptr->sfnum[0]=sfnum[0])>0 &&
- (desptr->sfnum[1]=sfnum[1])>0 &&
- (desptr->sfnum[2]=sfnum[2])>0 &&
- (desptr->sfnum[3]=sfnum[3])>0 &&
- (desptr->sfnum[4]=sfnum[4])>0 &&
- (desptr->sfnum[5]=sfnum[5])>0 &&
- (desptr->sfnum[6]=sfnum[6])>0 &&
- (desptr->sfnum[7]=sfnum[7])>0 &&
- (desptr->sfnum[8]=sfnum[8])>0 &&
- (desptr->sfnum[9]=sfnum[9])>0) ;
-#endif
- m_seqnm++;
- nseq++;
-
- if (m_seqnm >= max_sql) {
- max_sql += MAXSQL;
- if ((ldes=(struct sql *)realloc(ldes,max_sql*sizeof(struct sql)))
- ==NULL) {
- fprintf(stderr," failure to realloc ldes(%d) %ld\n",
- max_sql,max_sql*sizeof(struct sql));
- s_abort("cannot allocate ldes","");
- exit(1);
- }
- }
-
- /* increment ptrs */
- aa1prev = aa1;
-
- aa1 += n1+1+SEQ_PAD;
- ntbuff += n1+1+SEQ_PAD;
-
- /* if the buffer is filled */
- if (nseq >= max_buf_cnt || ntbuff >= m_msg0.pbuf_siz - m_msg0.maxn) {
- /* provide filled buffer to workers */
-#ifdef PVM_SRC
- pvm_initsend(PvmDataRaw);
- pvm_pkint(&nseq,1,1);
- pvm_pkint(&ntbuff,1,1);
- pvm_pkint(n1_arr,nseq,1);
- pvm_pkint(aa1i_arr,nseq,1);
- pvm_pkint(m_seqnm_arr,nseq,1);
- pvm_send(pinums[node],STARTTYPE4);
-
- pvm_initsend(PvmDataRaw);
- pvm_pkbyte((char *)aa1_buf,ntbuff,1);
- pvm_send(pinums[node],STARTTYPE5);
-#endif
-#ifdef MPI_SRC
- MPI_Send(&nseq,1,MPI_INT,node,STARTTYPE4, MPI_COMM_WORLD);
- MPI_Send(&ntbuff,1,MPI_INT,node,STARTTYPE4, MPI_COMM_WORLD);
- MPI_Send(n1_arr,nseq,MPI_INT,node,STARTTYPE4, MPI_COMM_WORLD);
- MPI_Send(aa1i_arr,nseq,MPI_INT,node,STARTTYPE4, MPI_COMM_WORLD);
- MPI_Send(m_seqnm_arr,nseq,MPI_INT,node,STARTTYPE4, MPI_COMM_WORLD);
-
- MPI_Send(aa1_buf,ntbuff,MPI_BYTE,node,STARTTYPE5,MPI_COMM_WORLD);
-#endif
- nseq = 0;
-
- aa1 = aa1_buf;
- ntbuff = 0;
- if (++node >= nnodes) node = FIRSTNODE;
- }
-
- loop1:
- if (lcont) {
- memcpy(aa1,&aa1prev[n1-m_msg0.loff],m_msg0.loff);
- aa1ptr = &aa1[m_msg0.loff];
- ocont = lcont;
- maxt = m_msg0.maxt3;
- loffset += n1 - m_msg0.loff;
- }
- else {
- if (ocont) *n1tot_cur = n1tot_v;
- n1tot_v = 0;
- n1tot_cur = NULL;
-
- ocont = 0;
- aa1ptr = aa1;
- maxt = m_msg0.maxn;
- loffset = 0l;
- }
- }
- }
- } /* for (iln < nln) */
-
- if (nseq > 0) {
-#ifdef PVM_SRC
- pvm_initsend(PvmDataRaw);
- pvm_pkint(&nseq,1,1);
- pvm_pkint(&ntbuff,1,1);
- pvm_pkint(n1_arr,nseq,1);
- pvm_pkint(aa1i_arr,nseq,1);
- pvm_pkint(m_seqnm_arr,nseq,1);
- pvm_send(pinums[node],STARTTYPE4);
-
- pvm_initsend(PvmDataRaw);
- pvm_pkbyte((char *)aa1_buf,ntbuff,1);
- pvm_send(pinums[node],STARTTYPE5);
-#endif
-#ifdef MPI_SRC
- MPI_Send(&nseq,1,MPI_INT,node,STARTTYPE4, MPI_COMM_WORLD);
- MPI_Send(&ntbuff,1,MPI_INT,node,STARTTYPE4, MPI_COMM_WORLD);
- MPI_Send(n1_arr,nseq,MPI_INT,node,STARTTYPE4, MPI_COMM_WORLD);
- MPI_Send(aa1i_arr,nseq,MPI_INT,node,STARTTYPE4, MPI_COMM_WORLD);
- MPI_Send(m_seqnm_arr,nseq,MPI_INT,node,STARTTYPE4, MPI_COMM_WORLD);
-
- MPI_Send(aa1_buf,ntbuff,MPI_BYTE,node,STARTTYPE5,MPI_COMM_WORLD);
-#endif
- }
-
- /* fprintf(stderr," all sequences sent\n"); */
-
- if (ntt.entries <= 0) {
- s_abort("no reference library sequences found\n","");
- }
-
- zero = 0;
- for (node=FIRSTNODE; node < nnodes; node++) {
-#ifdef PVM_SRC
- pvm_initsend(PvmDataRaw);
- pvm_pkint(&zero,1,1);
- pvm_pkint(&zero,1,1);
- pvm_pkint(n1_arr,1,1);
- pvm_pkint(aa1i_arr,1,1);
- pvm_pkint(m_seqnm_arr,1,1);
- pvm_send(pinums[node],STARTTYPE4);
-#endif
-#ifdef MPI_SRC
- MPI_Send(&zero,1,MPI_INT,node,STARTTYPE4, MPI_COMM_WORLD);
- MPI_Send(&zero,1,MPI_INT,node,STARTTYPE4, MPI_COMM_WORLD);
- MPI_Send(n1_arr,0,MPI_INT,node,STARTTYPE4, MPI_COMM_WORLD);
- MPI_Send(aa1i_arr,0,MPI_INT,node,STARTTYPE4, MPI_COMM_WORLD);
- MPI_Send(m_seqnm_arr,0,MPI_INT,node,STARTTYPE4, MPI_COMM_WORLD);
-#endif
- }
-
- for (node = FIRSTNODE; node < nnodes; node++) {
-#ifdef PVM_SRC
- bufid = pvm_recv(-1,STARTTYPE0);
- pvm_bufinfo(bufid,NULL,NULL,&tid);
- snode = tidtonode(tid);
- pvm_upkint(&lcnt,1,1);
- pvm_freebuf(bufid);
-#endif
-#ifdef MPI_SRC
- MPI_Recv(&lcnt,1,MPI_INT,MPI_ANY_SOURCE,STARTTYPE0,
- MPI_COMM_WORLD,&mpi_status);
- snode= mpi_status.MPI_SOURCE;
-#endif
- wlsn [snode-FIRSTNODE] = lcnt;
- fprintf(stderr," %d sequences at %d\n",lcnt,snode);
- }
-
- /* print out all descriptions */
- /*
- for (node = FIRSTNODE; node < nnodes; node++)
- for (lcnt = 0; lcnt < wlsn[node-FIRSTNODE]; lcnt ++)
- printf("%2d:%3d\t%s\n",node,lcnt,ldes[lcnt].bline);
- */
-
- /* Calculate cumulative totals and send to workers for a self search */
-
- clsn [0] = nclib= 0;
- for (node = FIRSTNODE; node < nnodes-1; node++) {
- /* clsn[] is for the next node */
- clsn[node-FIRSTNODE+1] = nclib += wlsn[node-FIRSTNODE];
- }
-
- if (m_msg0.self)
- for (node = FIRSTNODE; node < nnodes; node++) {
-#ifdef PVM_SRC
- pvm_initsend(PvmDataRaw);
- pvm_pkint(&clsn[node-FIRSTNODE],1,1);
- pvm_send(pinums[node],STARTTYPE1);
-#endif
-#ifdef MPI_SRC
- MPI_Send(&clsn[node-FIRSTNODE],1,MPI_INT,node,STARTTYPE1,MPI_COMM_WORLD);
-#endif
- fprintf(stderr,"sending lend: %d to worker %d\n",clsn[node-FIRSTNODE],node);
- }
-
- last_msg_b[0] = m_msg0.nbr_seq = m_msg1.nbr_seq = ntt.entries;
-
- qres_bufsize = BFR;
- /* if BFR is too big for this library, reduce it */
- while ( ntt.entries*(m_msg0.nitt1+1)/(2*nnodes) < qres_bufsize) {
- qres_bufsize /= 2;
- if ((qres_bufsize%(m_msg0.nitt1+1))!= 0) {
- qres_bufsize *= (m_msg0.nitt1+1);
- break;
- }
- if (qres_bufsize < 50) break;
- }
- last_msg_b[1] = qres_bufsize;
-
- fprintf(stderr," using BFR=%d/%d\n",qres_bufsize,BFR);
-
-#ifdef PVM_SRC
- pvm_initsend(PvmDataRaw);
- pvm_pkint(last_msg_b,2,1);
- for (node=FIRSTNODE; node < nnodes; node++)
- pvm_send(pinums[node],STARTTYPE0);
-#endif
-#ifdef MPI_SRC
- for (node=FIRSTNODE; node < nnodes; node++)
- MPI_Send(last_msg_b,2,MPI_INT,node,STARTTYPE0,MPI_COMM_WORLD);
-#endif
-
- tscan = tprev = s_time();
-
-/**************************************
- The logic of this section has been simplified to allow multistage
- comparison functions to be used and alignments to be generated.
-
- send 1st query to workers
- get next query sequence from host (m_msp1)
- L1: get results from next-1 search (m_msp0)
- sort the results of the next-1 search
- (possibly) do additional stages of search
- (possibly produce alignments for search
- send next query to workers (m_msp1)
- display result of next-1 search (m_msp0)
- get next query sequence from host (m_msp1)
- goto L1;
-
-As a result of the interleaving, there must be two qm_msg structures,
-one for the next-1 sequence (which is required for labeling the
-output), and one for the next sequence (which is sent to the workers
-while the results are being displayed. qm_msp0 and qm_msp1 alternate
-between these two structures.
-***************************************/
-
-/*
- qm_msp0 points to the older qm_msg
- qm_msp1 points to the newer qm_msg
- the assignment below goes with curtype==ONETYPE
-*/
- m_msp0 = &m_msg0;
- m_msp1 = &m_msg1;
-
- qm_msp0 = &qm_msg0;
- qm_msp1 = &qm_msg1;
-
- aa0p0 = aa00; /* aa0p0 is the "old" sequence */
- aa0p1 = aa01; /* aa0p1 is the "new" sequence */
-
- last_params(aa00,m_msp0->n0,m_msp0,&pst,qm_msp0);
-
- /* process_hist() is called here to get find_zp(), and some other
- structures initialized that would otherwise not be initialized
- because z-scores are not being calculated */
-
- if (m_msp0->escore_flg) {
- pst.zsflag_f = process_hist(stats,nstats,*m_msp0,pst,
- &m_msp0->hist,&m_msp0->pstat_void,0);
- stats_done=1;
- }
-
- if (m_msp0->qshuffle && qstats==NULL) {
- if ((qstats =
- (struct stat_str *)calloc(m_msg0.shuff_max+1,sizeof(struct stat_str)))==NULL)
- s_abort ("Cannot allocate qstats struct","");
- }
- nqstats = 0;
-
-/* Send first query sequence to each worker */
-
- if (m_msg0.dfile[0] && (fdata=fopen(m_msg0.dfile,"w"))!=NULL)
- fprintf(fdata,"%3d>%-50s\n",qlib,qm_msp0->libstr);
-
-#ifdef PVM_SRC
- pvm_initsend(PvmDataRaw);
- pvm_pkbyte((char *)qm_msp0,sizeof(qm_msg0),1);
- if (qm_msp0->n0 > 0) {
- pvm_pkbyte((char *)aa0p0,qm_msp0->n0+1+SEQ_PAD,1);
- if (m_msg0.ann_flg) pvm_pkbyte((char *)m_msp0->aa0a,qm_msp0->n0+1,1);
- }
- for (node = FIRSTNODE; node < nnodes; node++)
- pvm_send(pinums[node],MSEQTYPE);
-#endif
-#ifdef MPI_SRC
- for (node = FIRSTNODE; node < nnodes; node++) {
- MPI_Send(qm_msp0,sizeof(qm_msg0),MPI_BYTE,node,MSEQTYPE,MPI_COMM_WORLD);
- if (qm_msp0->n0 > 0) {
- MPI_Send(aa0p0,qm_msp0->n0+1+SEQ_PAD,MPI_BYTE,node,
- MSEQTYPE1,MPI_COMM_WORLD);
- if (m_msg0.ann_flg) {
- if (m_msp0->aa0a == NULL) {
- fprintf(stderr," m_msp0: %o/%oaa0a is null\n",m_msp0,m_msp0->aa0a);
- }
- MPI_Send(m_msp0->aa0a,qm_msp0->n0+1,MPI_BYTE,node, MSEQTYPE2,MPI_COMM_WORLD);
- }
- }
- }
-#endif
-
- /* Get second query sequence (additional query sequences are read in
- the main loop */
-
- m_msp1->n0 = qm_msp1->n0 =
- QGETLIB(aa0p1,MAXTST,q_bline, sizeof(q_bline),&qseek, &qlcont,q_file_p,&m_msp1->sq0off);
- strncpy(qm_msp1->libstr,q_bline,sizeof(qm_msg0.libstr)-20);
- qm_msp1->libstr[sizeof(qm_msg0.libstr)-21]='\0';
- if ((bp=strchr(qm_msp1->libstr,' '))!=NULL) *bp='\0';
-
- /* if annotations are included in sequence, remove them */
- if (m_msg0.ann_flg) {
- m_msp1->n0 = qm_msp1->n0 =
- ann_scan(aa0p1,qm_msp1->n0,m_msp1,m_msp1->qdnaseq);
-#ifdef DEBUG
- fprintf(stderr,"m_msp1->/aa0a is: %o/%o\n",m_msp1,m_msp1->aa0a);
-#endif
- }
-
- if (qm_msp1->n0 > 0 && m_msg0.term_code && !qlcont &&
- m_msg0.qdnaseq == SEQT_PROT &&
- aa0p1[m_msp1->n0-1]!=m_msg0.term_code) {
- aa0p1[m_msp1->n0++]=m_msg0.term_code;
- aa0p1[m_msp1->n0]=0;
- qm_msp1->n0 = m_msp1->n0;
- }
-
- /* for ALTIVEC, must pad with 15 NULL's */
- if (m_msp1->n0 > 0) {
- for (i=0; i<SEQ_PAD+1; i++) {aa0p1[m_msp1->n0+i]=0;}
- }
-
- qm_msp1->slist = 0;
- qm_msp1->seqnm = qlib;
-
- last_params(aa0p1,m_msp1->n0,m_msp1,&pst,qm_msp1);
-
- sprintf(tmp_str," - %d %s", qm_msp1->n0, q_sqnam);
- if (strlen(qm_msp1->libstr) + strlen(tmp_str) >= sizeof(qm_msg0.libstr))
- qm_msp1->libstr[sizeof(qm_msg0.libstr)-strlen(tmp_str)-2] = '\0';
- strncat(qm_msp1->libstr,tmp_str,
- sizeof(qm_msg0.libstr)-strlen(qm_msp1->libstr)-1);
- qm_msp1->libstr[sizeof(qm_msg0.libstr)-1]='\0';
-
- naa0 = 0; /* reset node counter */
-
- /* sit in loop and collect results */
- nbest = nopt = 0;
- zbestcut = -BIGNUM;
-
-
- while (1) {
-
-#ifdef PVM_SRC
- bufid = pvm_recv(-1,curtype);
- pvm_bufinfo(bufid,NULL,NULL,&tid);
- pvm_upkbyte((char *)&bestr[0],sizeof(struct comstr)*(qres_bufsize+1),1);
- snode = tidtonode(tid);
- pvm_freebuf(bufid);
-#endif
-#ifdef MPI_SRC
- MPI_Recv(bestr,sizeof(struct comstr)*(qres_bufsize+1),
- MPI_BYTE,MPI_ANY_SOURCE,curtype,MPI_COMM_WORLD,&mpi_status);
- snode = mpi_status.MPI_SOURCE;
-#endif
-
- nres = bestr[qres_bufsize].seqnm & ~FINISHED;
-
-#ifdef DEBUG
- fprintf(stderr,"%d results from %d\n",nres,snode);
-#endif
-
- if (bestr[qres_bufsize].seqnm&FINISHED) { /* a worker is finished */
- naa0++;
-
- /* fast_flag == 1 => send new sequences immediately */
- fast_flag = ((m_msp0->stages==1) && !(m_msp0->markx & MX_M9SUMM) &&
- (m_msp0->ashow == 0) && (m_msp0->last_calc_flg==0));
- /* send a new query sequence if no more processing required */
- if (fast_flag) {
-#ifdef PVM_SRC
- pvm_initsend(PvmDataRaw);
- pvm_pkbyte((char *)qm_msp1,sizeof(qm_msg1),1);
- if (qm_msp1->n0 != -1) {
- pvm_pkbyte((char *)aa0p1,qm_msp1->n0+1+SEQ_PAD,1);
- if (m_msp1->ann_flg) pvm_pkbyte((char *)m_msp1->aa0a,qm_msp1->n0+1,1);
- }
- pvm_send(tid,MSEQTYPE);
-#endif
-#ifdef MPI_SRC
- MPI_Send(qm_msp1,sizeof(qm_msg1),MPI_BYTE,snode,MSEQTYPE,MPI_COMM_WORLD);
- if (qm_msp1->n0 != -1) {
- MPI_Send(aa0p1,qm_msp1->n0+1+SEQ_PAD,MPI_BYTE,snode,MSEQTYPE1,MPI_COMM_WORLD);
- if (m_msp1->ann_flg)
- MPI_Send(m_msp1->aa0a,qm_msp1->n0+1,MPI_BYTE,snode,MSEQTYPE2,MPI_COMM_WORLD);
- }
-#endif
- }
- }
-
-#ifdef DEBUG
- if (pst.debug_lib)
- fprintf(stderr," unpacking %d from %d; nbest %d\n",nres,snode,nbest);
-#endif
-
- /* this section is now more complex because can get groups of
- sequence results; e.g. forward and reverse frame */
-
- t_best = t_rbest = t_qrbest = -1;
- tm_escore = t_rescore = t_qrescore = FLT_MAX;
- for (ires = 0; ires < nres; ires++) {
- desptr = &ldes[bestr[ires].m_seqnm];
-
- /* save raw results */
- if (fdata) {
- strncpy(tlibstr,desptr->bline,10);
- if ((bp=strchr(tlibstr,' '))!=NULL) *bp='\0';
- fprintf(fdata,"%-10s\t%4d\t%4d\t%d\t%4d\t%4d\t%4d\t%8ld\n",
- tlibstr,desptr->sfnum[0],desptr->n1,bestr[ires].frame,
- bestr[ires].score[0],bestr[ires].score[1],bestr[ires].score[2],
- desptr->lseek);
- }
-
- i_score = bestr[ires].score[pst.score_ix];
- e_score = bestr[ires].escore;
- k_comp = bestr[ires].comp;
- k_H = bestr[ires].H;
-
- t_n1 = desptr->n1;
- if (i_score > t_best) {tm_best = t_best = i_score;}
- if (e_score < tm_escore) tm_escore = e_score;
-
- if (m_msp0->qshuffle) {
- if (bestr[ires].qr_score > t_qrbest)
- t_qrbest = bestr[ires].qr_score;
- if (bestr[ires].qr_escore < t_qrescore)
- t_qrescore = bestr[ires].qr_escore;
-
- if (bestr[ires].frame==m_msp0->nitt1 &&
- nqstats < m_msp0->shuff_max &&
- bestr[ires].qr_score >= 0) {
- qstats[nqstats].n1 = t_n1; /* save the best score */
- qstats[nqstats].comp = bestr[ires].comp;
- qstats[nqstats].H = bestr[ires].H;
- qstats[nqstats].escore = t_qrescore;
- qstats[nqstats++].score = t_qrbest;
- t_qrbest = -1; /* reset t_qrbest, t_qrescore */
- t_qrescore = FLT_MAX;
- }
- }
-
- if (pst.zsflag >= 10 && bestr[ires].r_score > t_rbest) {
- t_rbest = bestr[ires].r_score;
- t_rescore = bestr[ires].r_escore;
- }
-
- if (nstats < MAXSTATS) {
- if (bestr[ires].frame == m_msg0.nitt1) {
- stats[nstats].n1 = t_n1;
- stats[nstats].comp = k_comp;
- stats[nstats].H = k_H;
-
- if (pst.zsflag > 10) {
- tm_best = t_rbest;
- tm_escore = t_rescore;
- t_rbest = -1;
- t_rescore = FLT_MAX;
- }
- stats[nstats].escore = tm_escore;
- stats[nstats++].score = tm_best;
- tm_escore = FLT_MAX;
- t_best = -1;
- }
- }
- else if (pst.zsflag >=0) { /* nstats >= MAXSTATS, zsflag >=0 */
- if (!stats_done ) {
- pst.n0 = qm_msp0->n0;
- pst.zsflag_f = process_hist(stats,nstats,*m_msp0,pst,
- &m_msp0->hist, &m_msp0->pstat_void,0);
- stats_done = 1;
- kstats = nstats;
- for (i=0; i<nbest; i++) {
- bptr[i]->zscore = (*find_zp)(bptr[i]->score[pst.score_ix],
- bptr[i]->escore,bptr[i]->n1,
- bptr[i]->comp, m_msp0->pstat_void);
- }
- }
-#ifdef SAMP_STATS
- if (!m_msp0->escore_flg) {
- jstats = nrand(kstats++);
- if (jstats < MAXSTATS) {
- stats[jstats].n1 = t_n1; /* save the best score */
- stats[jstats].comp = k_comp;
- stats[jstats].H = k_H;
- if (pst.zsflag >=10) t_best = t_rbest;
- stats[jstats].score = t_best;
- }
- }
-#endif
- }
-
- if (stats_done) {
- zscore=(*find_zp)(i_score,e_score,desptr->n1,k_comp,
- m_msp0->pstat_void);
- if (bestr[ires].frame == m_msg0.nitt1) {
- addhistz((*find_zp)(tm_best,tm_escore,t_n1,k_comp,
- m_msp0->pstat_void),
- &(m_msp0->hist));
- t_best = t_rbest = -1;
- }
-
- }
- else zscore = (double) i_score;
-
- if (zscore > zbestcut) {
- if (nbest>=MAXBEST) {
- selectbestz(bptr, nbest-MAXBEST/4-1, nbest);
- nbest -= MAXBEST/4;
- zbestcut = bptr[nbest-1]->zscore;
- best_flag = 0;
- }
- /* if zbestcut == -BIGNUM, bptr[] has not been reinitialized */
- else if (best_flag) bptr[nbest]=&best[nbest];
-
- bptr[nbest]->m_seqnm = bestr[ires].m_seqnm ;
- bptr[nbest]->seqnm = bestr[ires].seqnm;
- bptr[nbest]->score[0] = bestr[ires].score[0];
- bptr[nbest]->score[1] = bestr[ires].score[1];
- bptr[nbest]->score[2] = bestr[ires].score[2];
- bptr[nbest]->escore = bestr[ires].escore;
- bptr[nbest]->segnum = bestr[ires].segnum;
- bptr[nbest]->seglen = bestr[ires].seglen;
- bptr[nbest]->comp = bestr[ires].comp;
- bptr[nbest]->H = bestr[ires].H;
- bptr[nbest]->zscore = zscore;
- bptr[nbest]->wrkr = snode;
- bptr[nbest]->desptr = desptr;
- bptr[nbest]->lseek = desptr->lseek; /* needed for identifying alternate
- strand scores from same sequence */
- bptr[nbest]->n1 = desptr->n1;
- bptr[nbest]->frame = bestr[ires].frame;
-
- /* this was used when -m 9 info was calculated in 1st scan */
- /*
- bptr[nbest]->sw_score = bestr[ires].sw_score;
- if (bestr[ires].sw_score > -1) {
- nopt++;
- bptr[nbest]->a_len = bestr[ires].a_len;
- bptr[nbest]->percent = bestr[ires].percent;
- bptr[nbest]->gpercent = bestr[ires].gpercent;
- bptr[nbest]->min0 = bestr[ires].min0;
- bptr[nbest]->min1 = bestr[ires].min1;
- bptr[nbest]->max0 = bestr[ires].max0;
- bptr[nbest]->max1 = bestr[ires].max1;
- bptr[nbest]->ngap_q = bestr[ires].ngap_q;
- bptr[nbest]->ngap_l = bestr[ires].ngap_l;
- }
- else {
- bptr[nbest]->percent = -1.0;
- bptr[nbest]->min0 = bptr[nbest]->min1 = bptr[nbest]->max0 =
- bptr[nbest]->max1 = 0;
- }
- */
-
- nbest++;
- }
- } /* for loop */
- if (naa0 < nnodes-FIRSTNODE) continue;
-
- gstring2[0]='\0';
-
- /* get gstring2,3 - algorithm/parameter description */
-#ifdef PVM_SRC
- bufid = pvm_recv(pinums[FIRSTNODE],PARAMTYPE);
- pvm_upkbyte(gstring2,sizeof(gstring2),1);
- pvm_upkbyte(gstring3,sizeof(gstring3),1);
- pvm_freebuf(bufid);
-#endif
-#ifdef MPI_SRC
- MPI_Recv(gstring2,sizeof(gstring2),MPI_BYTE,FIRSTNODE,PARAMTYPE,
- MPI_COMM_WORLD,&mpi_status);
- MPI_Recv(gstring3,sizeof(gstring3),MPI_BYTE,FIRSTNODE,PARAMTYPE,
- MPI_COMM_WORLD,&mpi_status);
-#endif
-
-/* ********************** */
-/* analyze the results */
-/* ********************** */
-
- if (!stats_done) {
- if (nbest < 20 || pst.zsflag <= 0) {
- pst.zsflag_f = -1;
- }
- else {
- pst.n0 = qm_msp0->n0;
- pst.zsflag_f = process_hist(stats,nstats,*m_msp0,pst,
- &m_msp0->hist, &m_msp0->pstat_void,stats_done);
-
- for (i=0; i<nbest; i++)
- bptr[i]->zscore = (*find_zp)(bptr[i]->score[pst.score_ix],
- bptr[i]->escore, bptr[i]->n1,
- bptr[i]->comp, m_msp0->pstat_void);
- }
- }
-
- m_msp0->db.entries = ntt.entries;
- m_msp0->db.length = ntt.length;
- m_msp0->db.carry = ntt.carry;
-
- if (pst.zdb_size < 1) pst.zdb_size = ntt.entries;
-
- if (!qm_msp0->qshuffle) {
- last_stats(aa0p0, m_msp0->n0,
- stats,nstats, bptr,nbest, *m_msp0, pst,
- &m_msp0->hist, &m_msp0->pstat_void);
- }
- else {
- last_stats(aa0p0, m_msp0->n0,
- qstats,nqstats, bptr,nbest, *m_msp0, pst,
- &m_msp0->hist, &m_msp0->pstat_void);
- }
-
- if (m_msp0->last_calc_flg) {
- nbest = last_calc(bptr,nbest, *m_msp0, &pst,qm_msp0,
- m_msp0->pstat_void);
- }
-
- sortbeste(bptr,nbest);
- scale_scores(bptr,nbest,m_msp0->db,pst,m_msp0->pstat_void);
-
- if (pst.zsflag >= 0 && bptr[0]->escore >= m_msg0.e_cut) goto no_results;
-
- /* else sortorder(bptr,nbest,wlsn,nnodes); */
-
-/* if more than one stage or markx==9, calculate opt scores or do alignment */
-/* send results to workers as available */
-
- if (m_msg0.stages > 1 || m_msg0.markx & MX_M9SUMM) {
-
- /* to determine how many sequences to re-align (either for
- do_opt() or calc_id() we need to modify m_msg.mshow to get
- the correct number of alignments */
-
- if (m_msg0.mshow_flg != 1 && pst.zsflag >= 0) {
- for (i=0; i<nbest && bptr[i]->escore< m_msg0.e_cut; i++) {}
- m_msg0.mshow = i;
- }
-
- /* allocate space for a_struct info */
- if (m_msg0.markx & MX_M9SUMM && m_msg0.mshow > 0) {
- if ((aln_d_base=(struct a_struct *)
- calloc((size_t)m_msg0.mshow,sizeof(struct a_struct)))==NULL) {
- fprintf(stderr," cannot allocate a_struct %d\n", m_msg0.mshow);
- exit(1);
- }
-
- for (is = 0; is < m_msg0.mshow; is++ ) {
- bptr[is]->aln_d = &aln_d_base[is];
- }
- }
-
- do_stage2(bptr,m_msg0.mshow, *m_msp0, DO_OPT_FLG, qm_msp0);
- }
-
- no_results:
- tdone = s_time();
- tddone = time(NULL);
-
- /* changed from >> to >>> because qm_msp0->libstr is missing '>' */
- fprintf (outfd, "%3d>>>%s\n", qlib,qm_msp0->libstr);
-
- /* make certain that m_msp0->n0, libstr are current */
- m_msp0->n0 = qm_msp0->n0;
- /* strncpy(m_msp0->libstr,qm_msp0->libstr,sizeof(m_msg0.libstr)); */
-
- prhist (outfd,*m_msp0,pst,m_msp0->hist,nstats,m_msp0->db,gstring2);
-
- if (bptr[0]->escore < m_msg0.e_cut) {
-
- showbest (outfd, bptr, nbest, qlib, m_msp0,pst,ntt,gstring2);
-
- if (m_msg0.markx & MX_M9SUMM) {
- fprintf(outfd,"\n>>>%s#%d %s%s, %d %s vs %s library\n",
- m_msg0.tname,qlib,qm_msp0->libstr,
- (m_msg0.revcomp ? "-":"\0"), qm_msp0->n0, m_msg0.sqnam,
- m_msg0.lname);
- }
- else if (m_msg0.markx & MX_M10FORM) {
- if ((bp=strchr(qm_msp0->libstr,' '))!=NULL) *bp = '\0';
- fprintf(outfd,"\n>>>%s#%d %s%s, %d %s vs %s library\n",
- m_msg0.tname,qlib,qm_msp0->libstr,
- (m_msg0.revcomp ? "-":"\0"), qm_msp0->n0, m_msg0.sqnam,
- m_msg0.lname);
- if (bp!=NULL) *bp=' ';
- fprintf(outfd,"; mp_name: %s\n",argv[0]);
- fprintf(outfd,"; mp_ver: %s\n",mp_verstr);
- fprintf(outfd,"; mp_argv:");
- for (i=0; i<argc; i++)
- fprintf(outfd," %s",argv[i]);
- fputc('\n',outfd);
- fputs(gstring3,outfd);
- fputs(hstring1,outfd);
- }
-
- /* ashow is -1 if not set, -d 0 indicates no alignments, > 0 if set */
- /* if ashow is -1, m_msg.nshow (set by e_cut above) sets limit
- in showalign */
-
- if (m_msp0->ashow != 0) {
- /* showalign needs m_msp->qtitle, so fill it in */
- strncpy(m_msp0->qtitle,qm_msp0->libstr,MAX_FN-1);
- m_msp0->qtitle[MAX_FN-1]='\0';
- showalign (outfd, bptr, nbest, qlib, *m_msp0, pst, gstring2);
- }
- }
- else {
- if (m_msg0.markx & (MX_M9SUMM + MX_M10FORM)) {
- fprintf(outfd,"\n>>>%s#%d %s%s, %d %s vs %s library\n",
- m_msg0.tname,qlib,qm_msp0->libstr,(m_msg0.revcomp ? "-":"\0"), qm_msg0.n0, m_msg0.sqnam,
- m_msg0.lname);
- fprintf(outfd,">>>!!! No sequences with E() < %f\n",m_msg0.e_cut);
- }
- else fprintf(outfd,"!! No sequences with E() < %f\n",m_msg0.e_cut);
- }
-
- if (! (m_msg0.markx & (MX_M9SUMM + MX_M10FORM))) {
- fprintf(outfd,"/** search time: ");
- ptime(outfd,tdone-tprev);
- fprintf(outfd," **/\n");
- tprev = tdone;
- }
- else if (m_msg0.markx & MX_M9SUMM) {
- if (aln_d_base != NULL) {
- free((void *)aln_d_base);
- aln_d_base = NULL;
- }
- fprintf(outfd,">>>***\n");
- fprintf(outfd,"/** %s **/\n",gstring2);
- fprintf(outfd,"/** %s **/\n",m_msp0->hist.stat_info);
- fprintf(outfd,">>><<<\n");
- }
- else if (m_msg0.markx & MX_M10FORM) {
- fprintf(outfd,">>><<<\n");
- }
- fflush(outfd);
-
-/* *********************** */
-/* end of analysis/display */
-/* *********************** */
-
-
-/* *********************** */
-/* start the next search */
-/* *********************** */
-
- if (fdata) { /* label the results file */
- fprintf(fdata,"/** %s **/\n",gstring2);
- fprintf(fdata,"%3d>%-50s\n",qlib-1,qm_msp1->libstr);
- fflush(fdata);
- }
-
- if (m_msp1->escore_flg) { /* re-initialize some stats stuff before search */
- pst.zsflag_f = process_hist(stats,nstats,*m_msp1,pst,
- &m_msp1->hist,&m_msp1->pstat_void,0);
- stats_done=1;
- }
- else stats_done = 0;
-
- /* set up qstats if necessary - different queries have different qshuffle */
- if (m_msp1->qshuffle && qstats==NULL) {
- if ((qstats =
- (struct stat_str *)calloc(m_msg0.shuff_max+1,sizeof(struct stat_str)))==NULL)
- s_abort ("Cannot allocate qstats struct","");
- }
-
- nqstats = nstats = 0;
-
- /* send new qm_msp, sequence */
- if (!fast_flag) {
-#ifdef PVM_SRC
- pvm_initsend(PvmDataRaw);
- pvm_pkbyte((char *)qm_msp1,sizeof(qm_msg1),1);
- if (qm_msp1->n0 != -1) {
- pvm_pkbyte((char *)aa0p1,qm_msp1->n0+1+SEQ_PAD,1);
- if (m_msp1->ann_flg) {
- pvm_pkbyte((char *)m_msp1->aa0a,qm_msp1->n0+1,1);
- }
- }
- for (node = FIRSTNODE; node < nnodes; node++)
- pvm_send(pinums[node],MSEQTYPE);
-#endif
-#ifdef MPI_SRC
- for (node=FIRSTNODE; node < nnodes; node++) {
- MPI_Send(qm_msp1,sizeof(qm_msg1),MPI_BYTE,node,MSEQTYPE,
- MPI_COMM_WORLD);
- if (qm_msp1->n0 != -1) {
- MPI_Send(aa0p1,qm_msp1->n0+1+SEQ_PAD,MPI_BYTE,node,MSEQTYPE1,MPI_COMM_WORLD);
- if (m_msp1->ann_flg)
- MPI_Send(m_msp1->aa0a,qm_msp1->n0+1,MPI_BYTE,snode,MSEQTYPE2,MPI_COMM_WORLD);
- }
- }
-#endif
- }
-
- qlib++;
- if (qm_msp1->n0 != -1) {
- qtt.entries++;
- qtt.length += qm_msp1->n0;
- }
- else goto done;
-
-/* ******************************** */
-/* flip m_msg, qm_msg, aa0 pointers */
-/* ******************************** */
-
- naa0 = 0;
- best_flag = 1;
- nbest = nopt = 0;
- zbestcut = -BIGNUM;
- if (curtype == ONETYPE) {
- curtype = TWOTYPE;
- qm_msp0 = &qm_msg1;
- qm_msp1 = &qm_msg0;
- m_msp0 = &m_msg1;
- m_msp1 = &m_msg0;
- aa0p0 = aa01;
- aa0p1 = aa00;
- }
- else {
- curtype = ONETYPE;
- qm_msp0 = &qm_msg0;
- qm_msp1 = &qm_msg1;
- m_msp0 = &m_msg0;
- m_msp1 = &m_msg1;
- aa0p0 = aa00;
- aa0p1 = aa01;
- }
-
-
-/* **********************************************************/
-/* all library sequences are done get next library sequence */
-/* **********************************************************/
-
- m_msp1->n0 = qm_msp1->n0 =
- QGETLIB(aa0p1,MAXTST,q_bline, sizeof(q_bline),&qseek, &qlcont,q_file_p,&m_msp1->sq0off);
- strncpy(qm_msp1->libstr,q_bline,sizeof(qm_msg0.libstr)-20);
- qm_msp1->libstr[sizeof(qm_msg0.libstr)-21]='\0';
-
- if ((qlib+1) >= m_msg0.ql_stop) { qm_msp1->n0 = m_msp1->n0 = -1;}
-
- if (qm_msp1->n0 > 0 && m_msg0.term_code && !qlcont &&
- m_msg0.qdnaseq==SEQT_PROT &&
- aa0p1[m_msp1->n0-1]!=m_msg0.term_code) {
- aa0p1[m_msp1->n0++]=m_msg0.term_code;
- aa0p1[m_msp1->n0]=0;
- qm_msp1->n0 = m_msp1->n0;
- }
-
- /* for ALTIVEC, must pad with 15 NULL's */
- if (m_msg0.n0 > 0) {
- for (i=0; i<SEQ_PAD+1; i++) {aa00[m_msg0.n0+i]=0;}
- }
-
- qm_msp1->slist = 0;
- /*
- leng = strlen (qm_msp1->libstr);
- sprintf (&(qm_msp1->libstr[leng]), " %d %s", qm_msp1->n0, q_sqnam);
- */
- sprintf(tmp_str," %d %s", qm_msp1->n0, q_sqnam);
- if (strlen(qm_msp1->libstr) + strlen(tmp_str) >= sizeof(qm_msg0.libstr))
- qm_msp1->libstr[sizeof(qm_msg0.libstr)-strlen(tmp_str)-2] = '\0';
- strncat(qm_msp1->libstr,tmp_str,
- sizeof(qm_msg0.libstr)-strlen(qm_msp1->libstr)-1);
- qm_msp1->libstr[sizeof(qm_msg0.libstr)-1]='\0';
-
- qm_msp1->seqnm = qlib;
-
- last_params(aa0p1,m_msp1->n0,m_msp1,&pst,qm_msp1);
-
- } /* while loop */
-
- /* ******************** */
- /* end of library while */
- /* ******************** */
-
- done:
- tdone = s_time();
- if (m_msg0.markx & (MX_M9SUMM + MX_M10FORM)) fputs(">>>///\n",outfd);
- printsum(outfd);
- if (outfd!=stdout) printsum(stdout);
- printsum(stderr);
-#ifdef PVM_SRC
- pvm_exit();
-#endif
-#ifdef MPI_SRC
- MPI_Finalize();
-#endif
-
- exit(0);
-} /* End of main program */
-
-void
-printsum(FILE *fd)
-{
- double db_tt;
- char tstr1[26], tstr2[26];
-
- strncpy(tstr1,ctime(&tdstart),sizeof(tstr1));
- strncpy(tstr2,ctime(&tddone),sizeof(tstr1));
- tstr1[24]=tstr2[24]='\0';
-
- /* Print timing to output file as well */
- if (qtt.carry==0) {
- fprintf(fd, "\n%ld residues in %d query sequences\n", qtt.length, qtt.entries);
- }
- else {
- db_tt = (double)qtt.carry*(double)LONG_MAX + (double)qtt.length;
- fprintf(fd, "\n%.0g residues in %d query sequences\n", db_tt, qtt.entries);
- }
-
- if (ntt.carry==0) {
- fprintf(fd, "%ld residues in %ld library sequences\n", ntt.length, ntt.entries);
- }
- else {
- db_tt = (double)ntt.carry*(double)LONG_MAX + (double)ntt.length;
- fprintf(fd, "%.6f residues in %ld library sequences\n", db_tt, ntt.entries);
- }
-
- fprintf(fd," %d processors (%d workers) were used\n",
- nnodes+-FIRSTNODE+1,nnodes-FIRSTNODE);
- fprintf(fd," Pvcomplib [%s]\n start: %s done: %s\n",mp_verstr,tstr1,tstr2);
- fprintf(fd," Loading time: ");
- ptime(fd, tscan - tstart);
- fprintf (fd," Scan time: ");
- ptime (fd, tdone - tscan);
- fprintf (fd,"\n");
- fprintf (fd, "\nFunction used was %s [%s]\n", prog_func,verstr);
-}
-
-void fsigint()
-{
- int i;
-
- tdone = s_time();
- tddone = time(NULL);
-
- if (outfd!=stdout) fprintf(outfd,"/*** interrupted ***/\n");
- fprintf(stderr,"/*** interrupted ***/\n");
-
- printsum(stdout);
- if (outfd!=stdout) printsum(outfd);
-
-#ifdef PVM_SRC
- for (i=FIRSTNODE; i<nnodes; i++) pvm_kill(pinums[i]);
- pvm_exit();
-#endif
-#ifdef MPI_SRC
- MPI_Abort(MPI_COMM_WORLD,1);
- MPI_Finalize();
-#endif
- exit(1);
-}
git://source.jalview.org / jabaws.git / blobdiff