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HPC.daligner.c
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/*********************************************************************************************\
*
* Produce a script to compute overlaps for all block pairs of a DB, and then sort and merge
* them into as many .las files as their are blocks.
*
* Author: Gene Myers
* Date : June 1, 2014
*
*********************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <ctype.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>
#include "DB.h"
#include "filter.h"
#undef LSF // define if want a directly executable LSF script
static char *Usage[] =
{ "[-vbad] [-t<int>] [-w<int(6)>] [-l<int(1000)>] [-s<int(100)]",
" [-M<int>] [-B<int(4)>] [-D<int( 250)>] [-T<int(4)>] [-f<name>]",
" ( [-k<int(14)>] [-h<int(35)>] [-e<double(.70)>] [-AI] [-H<int>] |",
" [-k<int(20)>] [-h<int(50)>] [-e<double(.85)>] <ref:db|dam> )",
" [-m<track>]+ <reads:db|dam> [<first:int>[-<last:int>]"
};
// Command Options
static int DUNIT, BUNIT;
static int VON, BON, AON, ION, CON, DON;
static int WINT, TINT, HGAP, HINT, KINT, SINT, LINT, MINT;
static int NTHREADS;
static double EREL;
static int MMAX, MTOP;
static char **MASK;
static char *ONAME;
#define LSF_ALIGN "bsub -q medium -n 4 -o DALIGNER.out -e DALIGNER.err -R span[hosts=1] -J align#%d"
#define LSF_SORT "bsub -q short -n 12 -o SORT.DAL.out -e SORT.DAL.err -R span[hosts=1] -J sort#%d"
#define LSF_MERGE \
"bsub -q short -n 12 -o MERGE%d.DAL.out -e MERGE%d.DAL.err -R span[hosts=1] -J merge#%d"
#define LSF_CHECK \
"bsub -q short -n 12 -o CHECK%d.DAL.out -e CHECK%d.DAL.err -R span[hosts=1] -J check#%d"
void daligner_script(int argc, char *argv[])
{ int nblocks;
int usepath;
int useblock;
int fblock, lblock;
#ifdef LSF
int jobid;
#endif
FILE *out;
char name[100];
char *pwd, *root;
// Make sure DB exists and is partitioned, get number of blocks in partition
pwd = PathTo(argv[1]);
if (strcmp(argv[1]+(strlen(argv[1])-4),".dam") == 0)
root = Root(argv[1],".dam");
else
root = Root(argv[1],".db");
{ int i, nfiles;
FILE *dbvis;
dbvis = fopen(Catenate(pwd,"/",root,".dam"),"r");
if (dbvis == NULL)
{ dbvis = Fopen(Catenate(pwd,"/",root,".db"),"r");
if (dbvis == NULL)
exit (1);
}
if (fscanf(dbvis,"files = %d\n",&nfiles) != 1)
SYSTEM_ERROR
for (i = 0; i < nfiles; i++)
{ char buffer[30001];
if (fgets(buffer,30000,dbvis) == NULL)
SYSTEM_ERROR
}
useblock = 1;
if (fscanf(dbvis,"blocks = %d\n",&nblocks) != 1 || nblocks == 1)
{ useblock = 0;
nblocks = 1;
}
usepath = (strcmp(pwd,".") != 0);
}
// Set range fblock-lblock checking that DB.<fblock-1>.las exists & DB.<fblock>.las does not
{ char *eptr, *fptr;
FILE *file;
if (argc == 3)
{ fblock = strtol(argv[2],&eptr,10);
if (*eptr != '\0' && *eptr != '-')
{ fprintf(stderr,"%s: final argument '%s' does not start with an integer\n",
Prog_Name,argv[2]);
exit (1);
}
useblock = 1;
if (*eptr == '-')
{ lblock = strtol(eptr+1,&fptr,10);
if (*fptr != '\0')
{ fprintf(stderr,"%s: second part of range '%s' is not an integer\n",
Prog_Name,eptr+1);
exit (1);
}
}
else
lblock = fblock;
if (fblock < 1 || lblock > nblocks || fblock > lblock)
{ fprintf(stderr,"%s: range %d-%d is empty or out of bounds\n",Prog_Name,fblock,lblock);
exit (1);
}
}
else
{ fblock = 1;
lblock = nblocks;
}
if (fblock > 1)
{ file = fopen(Catenate(pwd,"/",root,Numbered_Suffix(".",fblock-1,".las")),"r");
if (file == NULL)
{ if (usepath)
fprintf(stderr,"%s: File %s/%s.%d.las should already be present!\n",
Prog_Name,pwd,root,fblock-1);
else
fprintf(stderr,"%s: File %s.%d.las should already be present!\n",
Prog_Name,root,fblock-1);
exit (1);
}
else
fclose(file);
}
if (useblock)
file = fopen(Catenate(pwd,"/",root,Numbered_Suffix(".",fblock,".las")),"r");
else
file = fopen(Catenate(pwd,"/",root,".las"),"r");
if (file != NULL)
{ if (usepath)
if (useblock)
fprintf(stderr,"%s: File %s/%s.%d.las should not yet exist!\n",
Prog_Name,pwd,root,fblock);
else
fprintf(stderr,"%s: File %s/%s.las should not yet exist!\n",Prog_Name,pwd,root);
else
if (useblock)
fprintf(stderr,"%s: File %s.%d.las should not yet exist!\n",Prog_Name,root,fblock);
else
fprintf(stderr,"%s: File %s.las should not yet exist!\n",Prog_Name,root);
exit (1);
}
DON = (DON && useblock);
out = stdout;
}
{ int level, njobs;
int i, j, k, p;
// Create all work subdirectories if DON
if (DON)
{ if (ONAME != NULL)
{ sprintf(name,"%s.00.MKDIR",ONAME);
out = fopen(name,"w");
}
fprintf(out,"# Create work subdirectories\n");
for (i = fblock; i <= lblock; i++)
fprintf(out,"mkdir work%d\n",i);
}
// Produce all necessary daligner jobs ...
if (ONAME != NULL)
{ sprintf(name,"%s.01.OVL",ONAME);
out = fopen(name,"w");
}
njobs = 0;
for (i = fblock; i <= lblock; i++)
njobs += (i-1)/BUNIT+1;
fprintf(out,"# Daligner jobs (%d)\n",njobs);
#ifdef LSF
jobid = 1;
#endif
for (i = fblock; i <= lblock; i++)
{ int bits;
int low, hgh;
bits = (i-1)/BUNIT+1;
low = 1;
for (j = 1; j <= bits; j++)
{
#ifdef LSF
fprintf(out,LSF_ALIGN,jobid++);
fprintf(out," \"");
#endif
fprintf(out,"daligner");
if (VON)
fprintf(out," -v");
if (BON)
fprintf(out," -b");
if (AON)
fprintf(out," -A");
if (ION)
fprintf(out," -I");
if (KINT != 14)
fprintf(out," -k%d",KINT);
if (WINT != 6)
fprintf(out," -w%d",WINT);
if (HINT != 35)
fprintf(out," -h%d",HINT);
if (TINT > 0)
fprintf(out," -t%d",TINT);
if (HGAP > 0)
fprintf(out," -H%d",HGAP);
if (EREL > 0.)
fprintf(out," -e%g",EREL);
if (LINT != 1000)
fprintf(out," -l%d",LINT);
if (SINT != 100)
fprintf(out," -s%d",SINT);
if (MINT >= 0)
fprintf(out," -M%d",MINT);
if (NTHREADS != 4)
fprintf(out," -T%d",NTHREADS);
for (k = 0; k < MTOP; k++)
fprintf(out," -m%s",MASK[k]);
if (useblock)
if (usepath)
fprintf(out," %s/%s.%d",pwd,root,i);
else
fprintf(out," %s.%d",root,i);
else
if (usepath)
fprintf(out," %s/%s",pwd,root);
else
fprintf(out," %s",root);
hgh = (i*j)/bits + 1;
for (k = low; k < hgh; k++)
if (useblock)
if (usepath)
fprintf(out," %s/%s.%d",pwd,root,k);
else
fprintf(out," %s.%d",root,k);
else
if (usepath)
fprintf(out," %s/%s",pwd,root);
else
fprintf(out," %s",root);
if (DON)
for (k = low; k < hgh; k++)
{ fprintf(out," && mv");
for (p = 0; p < NTHREADS; p++)
{ fprintf(out," %s.%d.%s.%d.C%d.las",root,i,root,k,p);
fprintf(out," %s.%d.%s.%d.N%d.las",root,i,root,k,p);
}
fprintf(out," work%d",i);
if (k != i)
{ fprintf(out," && mv");
for (p = 0; p < NTHREADS; p++)
{ fprintf(out," %s.%d.%s.%d.C%d.las",root,k,root,i,p);
fprintf(out," %s.%d.%s.%d.N%d.las",root,k,root,i,p);
}
fprintf(out," work%d",k);
}
}
#ifdef LSF
fprintf(out,"\"");
#endif
fprintf(out,"\n");
low = hgh;
}
}
// ... and then all the initial sort & merge jobs for each block pair
if (ONAME != NULL)
{ fclose(out);
sprintf(name,"%s.02.SORT",ONAME);
out = fopen(name,"w");
}
fprintf(out,"# Initial sort jobs (%d)\n", lblock*lblock - (fblock-1)*(fblock-1) );
#ifdef LSF
jobid = 1;
#endif
for (i = 1; i <= lblock; i++)
for (j = (i < fblock ? fblock : 1); j <= lblock; j++)
{
#ifdef LSF
fprintf(out,LSF_SORT,jobid++);
fprintf(out," \"");
#endif
fprintf(out,"LAsort");
if (VON)
fprintf(out," -v");
if (CON)
fprintf(out," -a");
for (k = 0; k < NTHREADS; k++)
if (useblock)
if (DON)
{ fprintf(out," work%d/%s.%d.%s.%d.C%d",i,root,i,root,j,k);
fprintf(out," work%d/%s.%d.%s.%d.N%d",i,root,i,root,j,k);
}
else
{ fprintf(out," %s.%d.%s.%d.C%d",root,i,root,j,k);
fprintf(out," %s.%d.%s.%d.N%d",root,i,root,j,k);
}
else
{ fprintf(out," %s.%s.C%d",root,root,k);
fprintf(out," %s.%s.N%d",root,root,k);
}
fprintf(out," && LAmerge");
if (VON)
fprintf(out," -v");
if (CON)
fprintf(out," -a");
if (lblock == 1)
{ if (usepath)
if (useblock)
fprintf(out," %s/%s.1",pwd,root);
else
fprintf(out," %s/%s",pwd,root);
else
if (useblock)
fprintf(out," %s.1",root);
else
fprintf(out," %s",root);
}
else if (i < fblock)
{ if (DON)
fprintf(out," work%d/L1.%d.%d",i,i,(j-fblock)+1);
else
fprintf(out," L1.%d.%d",i,(j-fblock)+1);
}
else
{ if (DON)
fprintf(out," work%d/L1.%d.%d",i,i,j);
else
fprintf(out," L1.%d.%d",i,j);
}
for (k = 0; k < NTHREADS; k++)
if (useblock)
if (DON)
{ fprintf(out," work%d/%s.%d.%s.%d.C%d.S",i,root,i,root,j,k);
fprintf(out," work%d/%s.%d.%s.%d.N%d.S",i,root,i,root,j,k);
}
else
{ fprintf(out," %s.%d.%s.%d.C%d.S",root,i,root,j,k);
fprintf(out," %s.%d.%s.%d.N%d.S",root,i,root,j,k);
}
else
{ fprintf(out," %s.%s.C%d.S",root,root,k);
fprintf(out," %s.%s.N%d.S",root,root,k);
}
#ifdef LSF
fprintf(out,"\"");
#endif
fprintf(out,"\n");
}
// Check .las files (optional)
if (ONAME != NULL)
{ fclose(out);
sprintf(name,"%s.03.CHECK.OPT",ONAME);
out = fopen(name,"w");
}
fprintf(out,"# Check initial .las files jobs (%d) (optional but recommended)\n",
(fblock-1) * ((lblock-fblock)/(BUNIT+1) + 1) +
(lblock-fblock+1) * ((lblock-1)/(BUNIT+1) + 1) );
#ifdef LSF
jobid = 1;
#endif
for (i = 1; i <= lblock; i++)
for (j = (i < fblock ? fblock : 1); j <= lblock; )
{ k = j+BUNIT;
if (k > lblock)
k = lblock;
#ifdef LSF
fprintf(out,LSF_CHECK,0,0,jobid++);
fprintf(out," \"");
#endif
fprintf(out,"LAcheck -vS");
if (usepath)
fprintf(out," %s/%s",pwd,root);
else
fprintf(out," %s",root);
while (j <= k)
{ if (lblock == 1)
{ if (usepath)
if (useblock)
fprintf(out," %s/%s.1",pwd,root);
else
fprintf(out," %s/%s",pwd,root);
else
if (useblock)
fprintf(out," %s.1",root);
else
fprintf(out," %s",root);
}
else if (i < fblock)
{ if (DON)
fprintf(out," work%d/L1.%d.%d",i,i,(j-fblock)+1);
else
fprintf(out," L1.%d.%d",i,(j-fblock)+1);
}
else
{ if (DON)
fprintf(out," work%d/L1.%d.%d",i,i,j);
else
fprintf(out," L1.%d.%d",i,j);
}
j += 1;
}
#ifdef LSF
fprintf(out,"\"");
#endif
fprintf(out,"\n");
}
// Clean up
if (ONAME != NULL)
{ fclose(out);
sprintf(name,"%s.04.RM",ONAME);
out = fopen(name,"w");
}
fprintf(out,"# Remove initial .las files\n");
for (i = 1; i <= lblock; i++)
{ if (DON)
fprintf(out,"cd work%d\n",i);
for (j = (i < fblock ? fblock : 1); j <= lblock; j++)
{ fprintf(out,"rm");
for (k = 0; k < NTHREADS; k++)
if (useblock)
{ fprintf(out," %s.%d.%s.%d.C%d.las",root,i,root,j,k);
fprintf(out," %s.%d.%s.%d.N%d.las",root,i,root,j,k);
}
else
{ fprintf(out," %s.%s.C%d.las",root,root,k);
fprintf(out," %s.%s.N%d.las",root,root,k);
}
fprintf(out,"\n");
fprintf(out,"rm");
for (k = 0; k < NTHREADS; k++)
if (useblock)
{ fprintf(out," %s.%d.%s.%d.C%d.S.las",root,i,root,j,k);
fprintf(out," %s.%d.%s.%d.N%d.S.las",root,i,root,j,k);
}
else
{ fprintf(out," %s.%s.C%d.S.las",root,root,k);
fprintf(out," %s.%s.N%d.S.las",root,root,k);
}
fprintf(out,"\n");
}
if (DON)
fprintf(out,"cd ..\n");
}
if (ONAME != NULL)
fclose(out);
// Higher level merges (if lblock > 1)
if (lblock > 1)
{ int pow, stage;
// Determine the number of merging levels
stage = 5;
pow = 1;
for (level = 0; pow < lblock; level++)
pow *= DUNIT;
// Issue the commands for each merge level
{ int p, cnt, dnt;
cnt = lblock;
dnt = (lblock-fblock)+1;
for (i = 1; i <= level; i++)
{ int bits, dits;
int low, hgh;
if (ONAME != NULL)
{ sprintf(name,"%s.%02d.MERGE",ONAME,stage++);
out = fopen(name,"w");
}
bits = (cnt-1)/DUNIT+1;
dits = (dnt-1)/DUNIT+1;
// Incremental update merges
#ifdef LSF
jobid = 1;
#endif
if (dnt >= 1)
{ int last;
last = (dnt == 1 || i == level);
fprintf(out,"# Level %d merge jobs (%d)\n",
i,bits*((lblock-fblock)+1) + dits*(fblock-1));
for (j = 1; j < fblock; j++)
{
#ifdef LSF
fprintf(out,LSF_MERGE,i,i,jobid++);
fprintf(out," \"");
#endif
if (last)
{ if (DON)
{ if (usepath)
fprintf(out,"mv %s/%s.%d.las work%d/L%d.%d.0.las && ",
pwd,root,j,j,i,j);
else
fprintf(out,"mv %s.%d.las work%d/L%d.%d.0.las && ",root,j,j,i,j);
}
else
{ if (usepath)
fprintf(out,"mv %s/%s.%d.las L%d.%d.0.las && ",pwd,root,j,i,j);
else
fprintf(out,"mv %s.%d.las L%d.%d.0.las && ",root,j,i,j);
}
}
low = 1;
for (p = 1; p <= dits; p++)
{ hgh = (dnt*p)/dits;
#ifdef LSF
if (p > 1)
{ fprintf(out,LSF_MERGE,i,i,jobid++);
fprintf(out," \"");
}
#endif
fprintf(out,"LAmerge");
if (VON)
fprintf(out," -v");
if (CON)
fprintf(out," -a");
if (last)
if (DON)
if (usepath)
fprintf(out," %s/%s.%d work%d/L%d.%d.0",pwd,root,j,j,i,j);
else
fprintf(out," %s.%d work%d/L%d.%d.0",root,j,j,i,j);
else
if (usepath)
fprintf(out," %s/%s.%d L%d.%d.0",pwd,root,j,i,j);
else
fprintf(out," %s.%d L%d.%d.0",root,j,i,j);
else
if (DON)
fprintf(out," work%d/L%d.%d.%d",j,i+1,j,p);
else
fprintf(out," L%d.%d.%d",i+1,j,p);
for (k = low; k <= hgh; k++)
if (DON)
fprintf(out," work%d/L%d.%d.%d",j,i,j,k);
else
fprintf(out," L%d.%d.%d",i,j,k);
#ifdef LSF
fprintf(out,"\"");
#endif
fprintf(out,"\n");
low = hgh+1;
}
}
}
else
fprintf(out,"# Level %d merge jobs (%d)\n",i,bits*((lblock-fblock)+1));
// New block merges
for (j = fblock; j <= lblock; j++)
{ low = 1;
for (p = 1; p <= bits; p++)
{ hgh = (cnt*p)/bits;
#ifdef LSF
fprintf(out,LSF_MERGE,i,i,jobid++);
fprintf(out," \"");
#endif
fprintf(out,"LAmerge");
if (VON)
fprintf(out," -v");
if (CON)
fprintf(out," -a");
if (i == level)
if (usepath)
fprintf(out," %s/%s.%d",pwd,root,j);
else
fprintf(out," %s.%d",root,j);
else
if (DON)
fprintf(out," work%d/L%d.%d.%d",j,i+1,j,p);
else
fprintf(out," L%d.%d.%d",i+1,j,p);
for (k = low; k <= hgh; k++)
if (DON)
fprintf(out," work%d/L%d.%d.%d",j,i,j,k);
else
fprintf(out," L%d.%d.%d",i,j,k);
#ifdef LSF
fprintf(out,"\"");
#endif
fprintf(out,"\n");
low = hgh+1;
}
}
// Check new .las (optional)
if (ONAME != NULL)
{ fclose(out);
sprintf(name,"%s.%02d.CHECK.OPT",ONAME,stage++);
out = fopen(name,"w");
}
fprintf(out,"# Check level %d .las files jobs (%d) (optional but recommended)\n",
i+1,(fblock-1)*((dits-1)/(BUNIT+1)+1) +
(lblock-fblock+1)*((bits-1)/(BUNIT+1)+1) );
#ifdef LSF
jobid = 1;
#endif
if (dnt >= 1)
{ int last;
last = (dnt == 1 || i == level);
for (j = 1; j < fblock; j++)
for (p = 1; p <= dits;)
{ k = p+BUNIT;
if (k > dits)
k = dits;
#ifdef LSF
fprintf(out,LSF_CHECK,i,i,jobid++);
fprintf(out," \"");
#endif
fprintf(out,"LAcheck -vS");
if (usepath)
fprintf(out," %s/%s",pwd,root);
else
fprintf(out," %s",root);
while (p <= k)
{ if (last)
if (usepath)
fprintf(out," %s/%s.%d",pwd,root,j);
else
fprintf(out," %s.%d",root,j);
else
if (DON)
fprintf(out," work%d/L%d.%d.%d",j,i+1,j,p);
else
fprintf(out," L%d.%d.%d",i+1,j,p);
p += 1;
}
#ifdef LSF
fprintf(out,"\"");
#endif
fprintf(out,"\n");
}
}
for (j = fblock; j <= lblock; j++)
for (p = 1; p <= bits;)
{ k = p+BUNIT;
if (k > bits)
k = bits;
#ifdef LSF
fprintf(out,LSF_CHECK,i,i,jobid++);
fprintf(out," \"");
#endif
fprintf(out,"LAcheck -vS");
if (usepath)
fprintf(out," %s/%s",pwd,root);
else
fprintf(out," %s",root);
while (p <= k)
{ if (i == level)
if (usepath)
fprintf(out," %s/%s.%d",pwd,root,j);
else
fprintf(out," %s.%d",root,j);
else
if (DON)
fprintf(out," work%d/L%d.%d.%d",j,i+1,j,p);
else
fprintf(out," L%d.%d.%d",i+1,j,p);
p += 1;
}
#ifdef LSF
fprintf(out,"\"");
#endif
fprintf(out,"\n");
}
// Cleanup (optional)
if (ONAME != NULL)
{ fclose(out);
if (i == 1)
sprintf(name,"%s.%02d.RM.OPT",ONAME,stage++);
else
sprintf(name,"%s.%02d.RM",ONAME,stage++);
out = fopen(name,"w");
}
if (i == 1)
fprintf(out,"# Remove level %d .las files (optional)\n",i);
else
fprintf(out,"# Remove level %d .las files\n",i);
if (dnt >= 1)
{ int last;
last = (dnt == 1 || i == level);
for (j = 1; j < fblock; j++)
{ low = 1;
if (DON)
fprintf(out,"cd work%d\n",j);
for (p = 1; p <= dits; p++)
{ hgh = (dnt*p)/dits;
fprintf(out,"rm");
if (last)
fprintf(out," L%d.%d.0.las",i,j);
for (k = low; k <= hgh; k++)
fprintf(out," L%d.%d.%d.las",i,j,k);
fprintf(out,"\n");
low = hgh+1;
}
if (DON)
fprintf(out,"cd ..\n");
}
}
for (j = fblock; j <= lblock; j++)
{ low = 1;
if (DON)
fprintf(out,"cd work%d\n",j);
for (p = 1; p <= bits; p++)
{ hgh = (cnt*p)/bits;
fprintf(out,"rm");
for (k = low; k <= hgh; k++)
fprintf(out," L%d.%d.%d.las",i,j,k);
fprintf(out,"\n");
low = hgh+1;
}
if (DON)
fprintf(out,"cd ..\n");
}
if (ONAME != NULL)
fclose(out);
if (dnt >= 1)
{ if (dnt > 1)
dnt = dits;
else
dnt = 0;
}
cnt = bits;
}
}
}
}
free(root);
free(pwd);
}
/*********************************************************************************************\
*
* Produce a script to compute overlaps for all block pairs between two DBs, and then sort
* and merge them into as many .las files as their are blocks of the 1st DB.
*
* Author: Gene Myers
* Date : December 31, 2014
*
*********************************************************************************************/
#define LSF_MALIGN "bsub -q medium -n 4 -o MAPALL.out -e MAPALL.err -R span[hosts=1] -J align#%d"
#define LSF_MSORT "bsub -q short -n 12 -o SORT.ALL.out -e SORT.ALL.err -R span[hosts=1] -J sort#%d"
#define LSF_MMERGE \
"bsub -q short -n 12 -o MERGE%d.ALL.out -e MERGE%d.ALL.err -R span[hosts=1] -J merge#%d"
void mapper_script(int argc, char *argv[])
{ int nblocks1, nblocks2;
int useblock1, useblock2;
int usepath1, usepath2;
int fblock, lblock;
#ifdef LSF
int jobid;
#endif
FILE *out;
char name[100];
char *pwd1, *root1;
char *pwd2, *root2;
// Make sure DAM and DB exist and the DB is partitioned, get number of blocks in partition
pwd1 = PathTo(argv[1]);
if (strcmp(argv[1]+(strlen(argv[1])-4),".dam") == 0)
root1 = Root(argv[1],".dam");
else
root1 = Root(argv[1],".db");
{ int i, nfiles;
FILE *dbvis;
dbvis = fopen(Catenate(pwd1,"/",root1,".dam"),"r");
if (dbvis == NULL)
{ dbvis = Fopen(Catenate(pwd1,"/",root1,".db"),"r");
if (dbvis == NULL)
exit (1);
}
if (fscanf(dbvis,"files = %d\n",&nfiles) != 1)
SYSTEM_ERROR
for (i = 0; i < nfiles; i++)
{ char buffer[30001];
if (fgets(buffer,30000,dbvis) == NULL)
SYSTEM_ERROR
}
useblock1 = 1;
if (fscanf(dbvis,"blocks = %d\n",&nblocks1) != 1 || nblocks1 == 1)
{ useblock1 = 0;
nblocks1 = 1;
}
usepath1 = (strcmp(pwd1,".") != 0);
fclose(dbvis);
}
pwd2 = PathTo(argv[2]);
if (strcmp(argv[2]+(strlen(argv[2])-4),".dam") == 0)
root2 = Root(argv[2],".dam");
else
root2 = Root(argv[2],".db");
if (strcmp(root2,root1) == 0 && strcmp(pwd1,pwd2) == 0)
{ fprintf(stderr,"%s: Comparing the same data base %s/%s against itself, use HPCdaligner\n",
Prog_Name,pwd1,root1);
exit (1);
}
{ int i, nfiles;
FILE *dbvis;
dbvis = fopen(Catenate(pwd2,"/",root2,".dam"),"r");
if (dbvis == NULL)
{ dbvis = Fopen(Catenate(pwd2,"/",root2,".db"),"r");
if (dbvis == NULL)
exit (1);
}
if (fscanf(dbvis,"files = %d\n",&nfiles) != 1)
SYSTEM_ERROR
for (i = 0; i < nfiles; i++)
{ char buffer[30001];
if (fgets(buffer,30000,dbvis) == NULL)
SYSTEM_ERROR
}
useblock2 = 1;
if (fscanf(dbvis,"blocks = %d\n",&nblocks2) != 1 || nblocks2 == 1)
{ useblock2 = 0;
nblocks2 = 1;
}
usepath2 = (strcmp(pwd2,".") != 0);
fclose(dbvis);
}
// Set range fblock-lblock checking that DB.<fblock-1>.las exists & DB.<fblock>.las does not
{ char *eptr, *fptr, *src2;
FILE *file;
if (argc == 4)
{ fblock = strtol(argv[3],&eptr,10);
if ((*eptr != '\0' && *eptr != '-') || eptr <= argv[3])
{ fprintf(stderr,"%s: final argument '%s' does not start with an integer\n",
Prog_Name,argv[3]);
exit (1);
}
useblock2 = 1;
if (*eptr == '-')
{ lblock = strtol(eptr+1,&fptr,10);
if (*fptr != '\0' || fptr <= eptr+1)
{ fprintf(stderr,"%s: second part of range '%s' is not an integer\n",
Prog_Name,eptr+1);
exit (1);
}
}
else
lblock = fblock;
if (fblock < 1 || lblock > nblocks2 || fblock > lblock)
{ fprintf(stderr,"%s: range %d-%d is empty or out of bounds\n",Prog_Name,fblock,lblock);
exit (1);
}
}
else
{ fblock = 1;
lblock = nblocks2;
}
if (usepath2)
src2 = Strdup(Catenate(pwd2,"/",root2,""),"Allocating small string!");
else
src2 = Strdup(root2,"Allocating small string!");
if (src2 == NULL)
exit (1);
if (fblock > 1)
{ file = fopen(Catenate(src2,".",root1,Numbered_Suffix(".",fblock-1,".las")),"r");
if (file == NULL)
{ fprintf(stderr,"%s: File %s.%s.%d.las should already be present!\n",
Prog_Name,src2,root1,fblock-1);
exit (1);
}
else
fclose(file);
}
if (useblock2)
{ file = fopen(Catenate(src2,".",root1,Numbered_Suffix(".",fblock,".las")),"r");
if (file != NULL)
{ fprintf(stderr,"%s: File %s.%s.%d.las should not yet exist!\n",
Prog_Name,src2,root1,fblock);
exit (1);
}
}
else
{ file = fopen(Catenate(src2,".",root1,".las"),"r");
if (file != NULL)
{ fprintf(stderr,"%s: File %s.%s.las should not yet exist!\n",
Prog_Name,src2,root1);
exit (1);
}
}
free(src2);
DON = (DON && useblock1 && useblock2);
out = stdout;
}
{ int level, njobs;
int i, j, k, t;
char orient[2] = { 'C', 'N' };
// Create all work subdirectories if DON
if (DON)
{ if (ONAME != NULL)
{ sprintf(name,"%s.00.MKDIR",ONAME);
out = fopen(name,"w");
}
fprintf(out,"# Create work subdirectories\n");
for (i = fblock; i <= lblock; i++)
fprintf(out,"mkdir work%d\n",i);
}
// Produce all necessary daligner jobs ...
if (ONAME != NULL)
{ sprintf(name,"%s.01.CMP",ONAME);
out = fopen(name,"w");
}