Commit 1d5a43ae authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 7.397

parent 20c547a7

MPI/Makefile

0 → 100644
+80 −0
Original line number Diff line number Diff line 
PREFIX = /usr/local

LIBDIR = $(PREFIX)/libexec/mafft

BINDIR = $(PREFIX)/bin

MANDIR = $(PREFIX)/share/man/man1

DESTDIR = 





#CC :=  mpicc -cc=gcc

CC :=  mpicc

#CC :=  /u33/app/openmpi/bin/mpicc

#CFLAGS := -O3 -ipo -no-prec-div -xHost -std=c99

#CFLAGS := -O3 -std=c99

CFLAGS := -O3

#CFLAGS =  -O0  -fPIC -pedantic -Wall -std=c99 -g -DMALLOC_CHECK_=3 # for shark, valgrind

# CFLAGS := -O0 -g -ipo -no-prec-div -xHost -std=c99

TARGET_ARCH := 

LDLIBS := -lm -lrt   # -lrt?





ENABLE_MULTITHREAD := -Denablemultithread

#ENABLE_ATOMIC := -Denableatomic

VPATH := ../core



ifdef ENABLE_ATOMIC

STDF = -std=c11

else

STDF = -std=c99

endif



CFLAGS := $(ENABLE_MULTITHREAD) $(ENABLE_ATOMIC) $(STDF) $(CFLAGS) -I../core -MMD -MP



OBJDIR := ./obj

ifeq "$(strip $(OBJDIR))" ""

  OBJDIR := .

endif



INSTALL = install



PROGS := nodepair_mpi

SCRIPTS := mpiscript

OBJNODPAIR := mtxutl.o io.o mltaln9_mpi.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \

		    Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o \

			nodepair_mpi.o defs.o fft.o fftFunctions.o addfunctions.o \

			pairlocalalign_mpi.o MSalign11.o

OBJNODPAIR := $(addprefix $(OBJDIR)/, $(OBJNODPAIR))

DEPSNODPAIR := $(OBJNODPAIR:%.o=%.d) 





all : $(PROGS) $(SCRIPTS)

	cp $(PROGS) $(SCRIPTS) ../binaries

	chmod 755 ../binaries/*

	@echo done.



install : all

	mkdir -p $(DESTDIR)$(LIBDIR)

	chmod 755 $(DESTDIR)$(LIBDIR)

	chmod 755 $(PROGS) ||:     # in MinGW, it's ok if this fails

	$(INSTALL) -s $(PROGS) $(DESTDIR)$(LIBDIR)

	$(INSTALL) $(SCRIPTS) $(DESTDIR)$(LIBDIR)

	@echo done.



nodepair_mpi : $(OBJNODPAIR)

	$(CC) $(LDFLAGS) $(TARGET_ARCH) $^ $(LOADLIBES) $(LDLIBS) -o $@



shmclear : shmclear.c

	$(CC) $(LDFLAGS) $(TARGET_ARCH) $^ $(LOADLIBES) $(LDLIBS) -o $@



mpiscript : mpiscript.tmpl

	cp mpiscript.tmpl mpiscript



$(OBJDIR)/%.o : %.c

	-@mkdir -p $(OBJDIR)

	@[ -d $(OBJDIR) ]

	$(CC) $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -o $@ -c $<



clean :

	rm -f $(OBJNODPAIR) $(DEPSNODPAIR) $(PROGS) $(SCRIPTS) *.o *.a *.exe *~

	rm -rf obj/



-include $(DEPSNODPAIR)

MPI/mltaln9_mpi.c

0 → 100644
+17080 −0

File added.

Preview size limit exceeded, changes collapsed.

MPI/mpiscript.tmpl

0 → 100644
+30 −0
Original line number Diff line number Diff line 
trap "echo 'Cancel' 1>&2" 0 15



if [ ! $MAFFT_N_THREADS_PER_PROCESS ]; then

	echo "set MAFFT_N_THREADS_PER_PROCESS, the number of cores to be used by a process." 1>&2

	exit 1

fi



if [ ! "$MAFFT_MPIRUN" ]; then

	MAFFT_MPIRUN="mpirun"

fi







command="$* -C $MAFFT_N_THREADS_PER_PROCESS"



#rm -rf hat3dir # To avoid cache, don't touch hat3dir here



$MAFFT_MPIRUN $command 1>&2

sync;



if [ -s hat3dir/tree ]; then

#if [ -s infile.tree ]; then

	val=0

else

	echo "error in MPI" 1>&2

	val=1

fi



trap - 0 15

exit $val

MPI/nodepair_mpi.c

0 → 100644
+561 −0
Original line number Diff line number Diff line 
#include "mltaln.h"

#include "mpi.h"

#include <errno.h>



#define DEBUG 0

#define IODEBUG 0

#define SCOREOUT 0

#define SHISHAGONYU 0 // for debug





// from tbfast

static int treein;

static int treeout;





// from pairlocalalign

static int stdout_dist;





static void arguments( int argc, char *argv[] )

{

    int c;



	nthread = 1;

	nadd = 0;

	inputfile = NULL;

	fftkeika = 0;

	pslocal = -1000.0;

	nblosum = 62;

	fmodel = 0;

	calledByXced = 0;

	devide = 0;

	use_fft = 0;

	fftscore = 1;

	fftRepeatStop = 0;

	fftNoAnchStop = 0;

    weight = 3;

    utree = 1;

	tbutree = 1;

    refine = 0;

    check = 1;

    cut = 0.0;

    disp = 0;

    outgap = 1;

    alg = 'A';

    mix = 0;

	tbitr = 0;

	scmtd = 5;

	tbweight = 0;

	tbrweight = 3;

	checkC = 0;

	treemethod = 'x';

	contin = 0;

	scoremtx = 1;

	kobetsubunkatsu = 0;

	divpairscore = 0;

	stdout_dist = 0;

//	dorp = NOTSPECIFIED;

	ppenalty = NOTSPECIFIED;

	ppenalty_OP = NOTSPECIFIED;

	ppenalty_ex = NOTSPECIFIED;

	ppenalty_EX = NOTSPECIFIED;

	penalty_shift_factor = 1000.0;

	poffset = NOTSPECIFIED;

	kimuraR = NOTSPECIFIED;

	pamN = NOTSPECIFIED;

	geta2 = GETA2;

	fftWinSize = NOTSPECIFIED;

	fftThreshold = NOTSPECIFIED;

	RNAppenalty = NOTSPECIFIED;

	RNApthr = NOTSPECIFIED;

	specificityconsideration = 0.0;

	usenaivescoreinsteadofalignmentscore = 0;

	specifictarget = 0;

	nwildcard = 0;

	compacttree = 2; // tsuneni!

	treein = 0;

	treeout = 0;

	fastathreshold = 2.7;

	constraint = 2;



//	localhomfile = 0; // tbfast.c no wo tsukaunode comment out



//	reporterr( "argc=%d\n", argc );

//	reporterr( "*argv=%s\n", *argv );

//	reporterr( "(*argv)[0]=%c\n", (*argv)[0] );

    while( --argc > 0 && (*++argv)[0] == '-' )

	{

//		reporterr( "(*argv)[0] in while loop = %s\n", (*argv) );

        while ( ( c = *++argv[0] ) )

		{

            switch( c )

            {

				case 'i':

					inputfile = *++argv;

//					fprintf( stderr, "inputfile = %s\n", inputfile );

					--argc;

					goto nextoption;

				case 'f':

					ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );

					--argc;

					goto nextoption;

				case 'g':

					ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );

					--argc;

					goto nextoption;

				case 'O':

					ppenalty_OP = (int)( atof( *++argv ) * 1000 - 0.5 );

					--argc;

					goto nextoption;

				case 'E':

					ppenalty_EX = (int)( atof( *++argv ) * 1000 - 0.5 );

					--argc;

					goto nextoption;

				case 'Q':

					penalty_shift_factor = atof( *++argv );

					--argc;

					goto nextoption;

				case 'h':

					poffset = (int)( atof( *++argv ) * 1000 - 0.5 );

					--argc;

					goto nextoption;

				case 'k':

					kimuraR = myatoi( *++argv );

//					fprintf( stderr, "kimuraR = %d\n", kimuraR );

					--argc;

					goto nextoption;

				case 'b':

					nblosum = myatoi( *++argv );

					scoremtx = 1;

//					fprintf( stderr, "blosum %d\n", nblosum );

					--argc;

					goto nextoption;

				case 'j':

					pamN = myatoi( *++argv );

					scoremtx = 0;

					TMorJTT = JTT;

//					fprintf( stderr, "jtt %d\n", pamN );

					--argc;

					goto nextoption;

				case 'm':

					pamN = myatoi( *++argv );

					scoremtx = 0;

					TMorJTT = TM;

//					fprintf( stderr, "TM %d\n", pamN );

					--argc;

					goto nextoption;

				case 'l':

					fastathreshold = atof( *++argv );

					constraint = 2;

					--argc;

					goto nextoption;

#if 0

				case 'l':

					ppslocal = (int)( atof( *++argv ) * 1000 + 0.5 );

					pslocal = (int)( 600.0 / 1000.0 * ppslocal + 0.5);

//					fprintf( stderr, "ppslocal = %d\n", ppslocal );

//					fprintf( stderr, "pslocal = %d\n", pslocal );

					--argc;

					goto nextoption;

#else

#endif

				case 'C':

					nthread = myatoi( *++argv );

					if( nthread == 0 ) nthread = 1;

//					fprintf( stderr, "nthread = %d\n", nthread );

					--argc; 

#ifndef enablemultithread

					nthread = 0;

#endif

					goto nextoption;

				case 'I':

					nadd = myatoi( *++argv );

//					fprintf( stderr, "nadd = %d\n", nadd );

					--argc;

					goto nextoption;

				case 'u':

					specificityconsideration = (double)myatof( *++argv );

//					fprintf( stderr, "specificityconsideration = %f\n", specificityconsideration );

					--argc; 

					goto nextoption;

				case 'c':

					stdout_dist = 1;

					break;

#if 1

				case 'a':

					fmodel = 1;

					break;

#endif

				case 'K':

					addprofile = 0;

					break;

#if 0

				case 'r':

					fmodel = -1;

					break;

#endif

				case 'D':

					dorp = 'd';

					break;

				case 'P':

					dorp = 'p';

					break;

#if 0

				case 'e':

					fftscore = 0;

					break;

				case 'O':

					fftNoAnchStop = 1;

					break;

#endif

#if 0

				case 'Q':

					calledByXced = 1;

					break;

				case 'x':

					disp = 1;

					break;

				case 'a':

					alg = 'a';

					break;

				case 'S':

					alg = 'S';

					break;

#endif

				case 'N':

					alg = 'N';

					break;

				case 'A':

					alg = 'A';

					break;

				case 'L':

					alg = 'L';

					break;

				case 'Z':

					usenaivescoreinsteadofalignmentscore = 1;

					break;

				case 'B': // hitsuyou! memopt -M -B no tame

					break;

#if 0

				case 'Y':

					alg = 'Y'; // nadd>0 no toki nomi. moto no hairetsu to atarashii hairetsuno alignmnt -> L;

					break;

				case 's':

					alg = 's';

					break;

				case 'G':

					alg = 'G';

					break;

				case 'B': // hitsuyou! memopt -M -B no tame

					break;

				case 'T':

					alg = 'T';

					break;

				case 'H':

					alg = 'H';

					break;

				case 'M':

					alg = 'M';

					break;

				case 'R':

					alg = 'R';

					break;

				case 'r':

					alg = 'r'; // nadd>0 no toki nomi. moto no hairetsu to atarashii hairetsuno alignmnt -> R, last

					break;

				case 'V':

					alg = 'V';

					break;

#endif

				case 'T': // tbfast.c no noalign ni taiou

					break;

				case 'F':

					use_fft = 1;

					break;

				case 'U':

					treein = 1;

					break;

				case 't':

					treeout = 1;

					break;

				case 'y':

					divpairscore = 1;

					break;

				case '=':

					specifictarget = 1;

					break;

				case ':':

					nwildcard = 1;

					break;

				case 'q':

					lhlimit = myatoi( *++argv );

					--argc; 

					goto nextoption;

/* Modified 01/08/27, default: user tree */

				case 'J':

					tbutree = 0;

					break;

/* modification end. */

                default:

                    fprintf( stderr, "illegal option %c\n", c );

                    argc = 0;

                    break;

            }

		}

		nextoption:

			;

	}

    if( argc == 1 )

    {

        cut = atof( (*argv) );

        argc--;

    }

    if( argc != 0 ) 

    {

        fprintf( stderr, "pairlocalalign options: Check source file !\n" );

        exit( 1 );

    }

	if( tbitr == 1 && outgap == 0 )

	{

		fprintf( stderr, "conflicting options : o, m or u\n" );

		exit( 1 );

	}

}



int main( int argc, char *argv[] )

{

	static int  *nlen = NULL;	

	static int *selfscore = NULL;

	static char **name = NULL, **seq = NULL;

	static double *eff = NULL;

	int i;

	static int ***topol = NULL;

	static Treedep *dep = NULL;

	static double **len = NULL;

	FILE *infp = NULL;



	char c;





#if 1

//	int required = MPI_THREAD_MULTIPLE;

	int required = MPI_THREAD_FUNNELED;

	int provided;

	MPI_Init_thread(&argc, &argv, required, &provided);

#else

	MPI_Init(&argc,&argv);

#endif



	int my_rank;

	int num_of_processes;

	MPI_Comm_rank(MPI_COMM_WORLD,&my_rank);

	MPI_Comm_size(MPI_COMM_WORLD,&num_of_processes);





	if (provided < required) {

#if 0

		if (my_rank == 0) {

			reporterr( "MPI_THREAD_MULTIPLE (mpi thread support level) is required\n");

			reporterr( "required level is %d and provided level is %d\n", required, provided );

		}

		MPI_Finalize();

		exit( 1 );

#else

		if (my_rank == 0) reporterr( "WARNING: mpi thread support level %d is required, but provided level is %d.\n", required, provided );

#endif

	} else {

		if (my_rank == 0) reporterr( "mpi thread support level : required level is %d and provided level is %d\n", required, provided );

	}





	arguments( argc, argv );



	if( alg != 'A' && alg != 'L' && alg != 'N' )

	{

		reporterr( "alg %c is not yet supported\n", alg );

		exit( 1 );

	}

	if( alg != 'N' && usenaivescoreinsteadofalignmentscore == 1 )

	{

		reporterr( "The combination of usenaivescoreinsteadofalignmentscore and alg %c is not yet supported\n", alg );

		exit( 1 );

	}



	if( fastathreshold < 0.0001 )

	{

		constraint = 0; 

		lhlimit = 0;

	}







	if(my_rank==0){

		if( inputfile )

		{

			infp = fopen( inputfile, "r" );

			if( !infp ) 

			{

				fprintf( stderr, "Cannot open %s\n", inputfile );

				exit( 1 );

			}

		}

		else    

			infp = stdin;



		getnumlen( infp );

		rewind( infp );

	}

	// getnumlen

	MPI_Bcast(&njob,1, MPI_INT, 0, MPI_COMM_WORLD);

	MPI_Bcast(&nlenmax,1, MPI_INT, 0, MPI_COMM_WORLD);

	MPI_Bcast(&dorp,1, MPI_INT, 0, MPI_COMM_WORLD);

	fprintf( stderr, "my_rank: %d, njob: %d, nlenmax: %d\n", my_rank, njob, nlenmax);







	if( njob < 2 )

	{

		fprintf( stderr, "At least 2 sequences should be input!\n"

						 "Only %d sequence found.\n", njob ); 

		exit( 1 );

	}





#ifndef mingw

	setstacksize( 200 * njob ); // topolorder() de ookime no stack wo shiyou.

#endif





	seq = AllocateCharMtx( njob, nlenmax+1 );



	name = AllocateCharMtx( njob, B+1 );

	nlen = AllocateIntVec( njob );

	selfscore = AllocateIntVec( njob );



	topol = AllocateIntCub( njob, 2, 0 );

	len = AllocateFloatMtx( njob, 2 );

	eff = AllocateDoubleVec( njob );





	dep = (Treedep *)calloc( njob, sizeof( Treedep ) );





	if(my_rank==0){

#if 0

		readData( infp, name, nlen, seq );

#else

		readData_pointer( infp, name, nlen, seq );

		fclose( infp );

#endif

	}

	for(i=0;i<njob;i++){

		MPI_Bcast(name[i], B+1, MPI_CHAR, 0, MPI_COMM_WORLD);

		MPI_Bcast(seq[i], nlenmax+1, MPI_CHAR, 0, MPI_COMM_WORLD);

	}

	MPI_Bcast(nlen, njob, MPI_INT, 0, MPI_COMM_WORLD);





	constants( njob, seq );



#if 0

	fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );

#endif



	initSignalSM();

	initFiles();



//	WriteOptions( trap_g );



	c = seqcheck( seq );

	if( c )

	{

		fprintf( stderr, "Illegal character %c\n", c );

		exit( 1 );

	}



//	writePre( njob, name, nlen, seq, 0 );



	if( treein ) loadtree( njob, topol, len, name, nlen, dep, treeout );

	pairalign_node( njob, nlenmax, name, seq, topol, len, dep, treein, treeout );





	FreeCharMtx( seq ); seq = NULL;



	FreeCharMtx( name ); name = NULL;

	free( nlen ); nlen = NULL;

	free( selfscore ); selfscore = NULL;



	for( i=0; i<njob; i++ ) 

	{

		free( topol[i][0] ); topol[i][0] = NULL;

		free( topol[i][1] ); topol[i][1] = NULL;

		free( topol[i] ); topol[i] = NULL;

		free( len[i] ); len[i] = NULL;

	}

	free( topol ); topol = NULL;

	free( len ); len = NULL;

	free( eff ); eff = NULL;

	free( dep ); dep = NULL;





	freeconstants();

	closeFiles();

	FreeCommonIP();



	MPI_Finalize();



//	reporterr( "nodepair_mpi used " );

//	use_getrusage();

	return( 0 );



#if 0 // gui mitaiou

chudan:

	if( seq ) FreeCharMtx( seq ); seq = NULL;



	if( name ) FreeCharMtx( name ); name = NULL;

	if( nlen ) free( nlen ); nlen = NULL;

	if( selfscore ) free( selfscore ); selfscore = NULL;







	if( topol ) FreeIntCub( topol ); topol = NULL;

	if( dep ) free( dep ); dep = NULL;



	freeconstants();

	closeFiles();

	FreeCommonIP();



	if( topol )

	{

		for( i=0; i<njob; i++ ) 

		{

			if( topol[i] )

			{

				if( topol[i][0] ) free( topol[i][0] ); topol[i][0] = NULL;

				if( topol[i][1] ) free( topol[i][1] ); topol[i][1] = NULL;

			}

			free( topol[i] ); topol[i] = NULL;

		}

		free( topol ); topol = NULL;

	}

	if( len ) 

	{

		for( i=0; i<njob; i++ ) 

		{

			if( len[i] ) free( len[i] ); len[i] = 0;

		}

		free( len ); len = NULL;

	}

	if( eff ) free( eff ); eff = NULL;

	if( dep ) free( dep ); dep = NULL;







	MPI_Finalize();





	return( 0 );

#endif



}

MPI/pairlocalalign_mpi.c

0 → 100644
+3552 −0

File added.

Preview size limit exceeded, changes collapsed.