int
main (
int argc,
char * argv[])
{
SCOTCH_Strat bipastrat; /* Bipartitioning strategy */
SCOTCH_Arch archdat; /* Target (terminal) architecture */
SCOTCH_Graph grafdat; /* Source graph to turn into architecture */
SCOTCH_Num vertnbr; /* Number of vertices in graph */
SCOTCH_Num * vlbltab; /* Pointer to vertex label array, if present */
SCOTCH_Num listnbr; /* Size of list array */
SCOTCH_Num * listtab; /* Pointer to list array */
C_VertSort * sorttab; /* Vertex label sort area */
SCOTCH_Num baseval;
int flagval; /* Process flags */
int i;
errorProg ("amk_grf");
if ((argc >= 2) && (argv[1][0] == '?')) { /* If need for help */
usagePrint (stdout, C_usageList);
return (0);
}
flagval = C_FLAGNONE;
SCOTCH_stratInit (&bipastrat);
fileBlockInit (C_fileTab, C_FILENBR); /* Set default stream pointers */
for (i = 1; i < argc; i ++) { /* Loop for all option codes */
if ((argv[i][0] != '-') || (argv[i][1] == '\0') || (argv[i][1] == '.')) { /* If found a file name */
if (C_fileNum < C_FILEARGNBR) /* File name has been given */
fileBlockName (C_fileTab, C_fileNum ++) = argv[i];
else {
errorPrint ("main: too many file names given");
return (1);
}
}
else { /* If found an option name */
switch (argv[i][1]) {
case 'B' : /* Bipartitioning strategy */
case 'b' :
SCOTCH_stratExit (&bipastrat);
SCOTCH_stratInit (&bipastrat);
if ((SCOTCH_stratGraphBipart (&bipastrat, &argv[i][2])) != 0) {
errorPrint ("main: invalid bipartitioning strategy");
return (1);
}
break;
case 'H' : /* Give the usage message */
case 'h' :
usagePrint (stdout, C_usageList);
return (0);
case 'L' : /* Input vertex list */
case 'l' :
flagval |= C_FLAGVRTINP;
if (argv[i][2] != '\0')
C_filenamevrtinp = &argv[i][2];
break;
case 'V' :
fprintf (stderr, "amk_grf, version " SCOTCH_VERSION_STRING "\n");
fprintf (stderr, "Copyright 2004,2007,2008,2010-2012,2014 IPB, Universite de Bordeaux, INRIA & CNRS, France\n");
fprintf (stderr, "This software is libre/free software under CeCILL-C -- see the user's manual for more information\n");
return (0);
default :
errorPrint ("main: unprocessed option '%s'", argv[i]);
return (1);
}
}
}
fileBlockOpen (C_fileTab, C_FILENBR); /* Open all files */
SCOTCH_graphInit (&grafdat); /* Create graph structure */
SCOTCH_graphLoad (&grafdat, C_filepntrgrfinp, -1, 0); /* Load source graph */
SCOTCH_graphData (&grafdat, &baseval, &vertnbr, NULL, NULL, NULL, /* Get graph data */
&vlbltab, NULL, NULL, NULL);
listnbr = 0; /* Initialize vertex list */
listtab = NULL;
if (flagval & C_FLAGVRTINP) { /* If list of vertices provided */
SCOTCH_Num listnum;
if ((intLoad (C_filepntrvrtinp, &listnbr) != 1) || /* Read list size */
(listnbr < 0) ||
(listnbr > vertnbr)) {
errorPrint ("main: bad list input (1)");
return (1);
}
if ((listtab = (SCOTCH_Num *) memAlloc (listnbr * sizeof (SCOTCH_Num) + 1)) == NULL) {
errorPrint ("main: out of memory (1)");
return (1);
}
for (listnum = 0; listnum < listnbr; listnum ++) { /* Read list data */
if (intLoad (C_filepntrvrtinp, &listtab[listnum]) != 1) {
errorPrint ("main: bad list input (2)");
return (1);
}
}
intSort1asc1 (listtab, listnbr);
for (listnum = 0; listnum < listnbr - 1; listnum ++) { /* Search for duplicates */
if (listtab[listnum] == listtab[listnum + 1]) {
errorPrint ("main: duplicate list labels");
memFree (listtab);
return (1);
}
}
if (vlbltab != NULL) { /* If graph has vertex labels */
SCOTCH_Num vertnum;
if ((sorttab = (C_VertSort *) memAlloc (vertnbr * sizeof (C_VertSort))) == NULL) {
errorPrint ("main: out of memory (2)");
memFree (listtab);
return (1);
}
for (vertnum = 0; vertnum < vertnbr; vertnum ++) { /* Initialize sort area */
sorttab[vertnum].vlblnum = vlbltab[vertnum];
sorttab[vertnum].vertnum = vertnum;
}
intSort2asc1 (sorttab, vertnbr); /* Sort by ascending labels */
for (listnum = 0, vertnum = 0; listnum < listnbr; listnum ++) { /* For all labels in list */
while ((vertnum < vertnbr) && (sorttab[vertnum].vlblnum < listtab[listnum]))
vertnum ++; /* Search vertex graph with corresponding label */
if ((vertnum >= vertnbr) || /* If label not found */
(sorttab[vertnum].vlblnum > listtab[listnum])) {
errorPrint ("main: list label '" SCOTCH_NUMSTRING "' not in graph", (SCOTCH_Num) listtab[listnum]);
memFree (sorttab);
memFree (listtab);
return (1);
}
listtab[listnum] = sorttab[vertnum ++].vertnum; /* Replace label by number */
}
memFree (sorttab); /* Free sort area */
}
}
SCOTCH_archInit (&archdat); /* Initialize target architecture */
SCOTCH_archBuild (&archdat, &grafdat, listnbr, listtab, &bipastrat); /* Compute architecture */
SCOTCH_archSave (&archdat, C_filepntrtgtout); /* Write target architecture */
fileBlockClose (C_fileTab, C_FILENBR); /* Always close explicitely to end potential (un)compression tasks */
SCOTCH_graphExit (&grafdat); /* Free target graph */
SCOTCH_archExit (&archdat); /* Free target architecture */
SCOTCH_stratExit (&bipastrat); /* Free strategy string */
if (listtab != NULL) /* If vertex list provided */
memFree (listtab); /* Free it */
#ifdef COMMON_PTHREAD
pthread_exit ((void *) 0); /* Allow potential (un)compression tasks to complete */
#endif /* COMMON_PTHREAD */
return (0);
}
static PetscErrorCode MatPartitioningApply_Scotch(MatPartitioning part, IS * partitioning)
{
PetscErrorCode ierr;
int *parttab, *locals = PETSC_NULL, rank, i, size;
size_t j;
Mat mat = part->adj, matMPI, matSeq;
int nb_locals = mat->rmap->n;
Mat_MPIAdj *adj = (Mat_MPIAdj *) mat->data;
MatPartitioning_Scotch *scotch = (MatPartitioning_Scotch *) part->data;
PetscTruth flg;
#ifdef PETSC_HAVE_UNISTD_H
int fd_stdout, fd_pipe[2], count,err;
#endif
PetscFunctionBegin;
/* check if the matrix is sequential, use MatGetSubMatrices if necessary */
ierr = MPI_Comm_size(((PetscObject)mat)->comm, &size);CHKERRQ(ierr);
ierr = PetscTypeCompare((PetscObject) mat, MATMPIADJ, &flg);CHKERRQ(ierr);
if (size > 1) {
int M, N;
IS isrow, iscol;
Mat *A;
if (flg) {
SETERRQ(0, "Distributed matrix format MPIAdj is not supported for sequential partitioners");
}
PetscPrintf(((PetscObject)part)->comm, "Converting distributed matrix to sequential: this could be a performance loss\n");CHKERRQ(ierr);
ierr = MatGetSize(mat, &M, &N);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF, M, 0, 1, &isrow);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF, N, 0, 1, &iscol);CHKERRQ(ierr);
ierr = MatGetSubMatrices(mat, 1, &isrow, &iscol, MAT_INITIAL_MATRIX, &A);CHKERRQ(ierr);
matSeq = *A;
ierr = PetscFree(A);CHKERRQ(ierr);
ierr = ISDestroy(isrow);CHKERRQ(ierr);
ierr = ISDestroy(iscol);CHKERRQ(ierr);
} else
matSeq = mat;
/* convert the the matrix to MPIADJ type if necessary */
if (!flg) {
ierr = MatConvert(matSeq, MATMPIADJ, MAT_INITIAL_MATRIX, &matMPI);CHKERRQ(ierr);
} else {
matMPI = matSeq;
}
adj = (Mat_MPIAdj *) matMPI->data; /* finaly adj contains adjacency graph */
ierr = MPI_Comm_rank(((PetscObject)part)->comm, &rank);CHKERRQ(ierr);
{
/* definition of Scotch library arguments */
SCOTCH_Strat stratptr; /* scotch strategy */
SCOTCH_Graph grafptr; /* scotch graph */
#if defined(DOES_NOT_COMPILE_DUE_TO_BROKEN_INTERFACE)
int vertnbr = mat->rmap->N; /* number of vertices in full graph */
int *verttab = adj->i; /* start of edge list for each vertex */
int *edgetab = adj->j; /* edge list data */
int edgenbr = adj->nz; /* number of edges */
int *velotab = NULL; /* not used by petsc interface */
int *vlbltab = NULL;
int *edlotab = NULL;
int flagval = 3; /* (cf doc scotch no weight edge & vertices) */
#endif
int baseval = 0; /* 0 for C array indexing */
char strategy[256];
ierr = PetscMalloc((mat->rmap->N) * sizeof(int), &parttab);CHKERRQ(ierr);
/* redirect output to buffer scotch -> mesg_log */
#ifdef PETSC_HAVE_UNISTD_H
fd_stdout = dup(1);
pipe(fd_pipe);
close(1);
dup2(fd_pipe[1], 1);
ierr = PetscMalloc(SIZE_LOG * sizeof(char), &(scotch->mesg_log));CHKERRQ(ierr);
#endif
/* library call */
/* Construction of the scotch graph object */
ierr = SCOTCH_graphInit(&grafptr);
#if defined(DOES_NOT_COMPILE_DUE_TO_BROKEN_INTERFACE)
ierr = SCOTCH_graphBuild((SCOTCH_Graph *) &grafptr,
(const SCOTCH_Num) vertnbr,
(const SCOTCH_Num) verttab,
(const SCOTCH_Num *)velotab,
(const SCOTCH_Num *)vlbltab,
(const SCOTCH_Num *)edgenbr,
(const SCOTCH_Num *)edgetab,
(const SCOTCH_Num) edlotab,
(const SCOTCH_Num *)baseval,
(const SCOTCH_Num *)flagval);CHKERRQ(ierr);
#else
SETERRQ(PETSC_ERR_SUP,"Scotch interface currently broken");
#endif
ierr = SCOTCH_graphCheck(&grafptr);CHKERRQ(ierr);
/* Construction of the strategy */
if (scotch->strategy[0] != 0) {
ierr = PetscStrcpy(strategy, scotch->strategy);CHKERRQ(ierr);
} else {
PetscStrcpy(strategy, "b{strat=");
if (scotch->multilevel) {
/* PetscStrcat(strategy,"m{vert=");
sprintf(strategy+strlen(strategy),"%d",scotch->nbvtxcoarsed);
PetscStrcat(strategy,",asc="); */
sprintf(strategy, "b{strat=m{vert=%d,asc=",
scotch->nbvtxcoarsed);
} else
PetscStrcpy(strategy, "b{strat=");
switch (scotch->global_method) {
case MP_SCOTCH_GREEDY:
PetscStrcat(strategy, "h");
break;
case MP_SCOTCH_GPS:
PetscStrcat(strategy, "g");
break;
case MP_SCOTCH_GR_GPS:
PetscStrcat(strategy, "g|h");
}
switch (scotch->local_method) {
case MP_SCOTCH_KERNIGHAN_LIN:
if (scotch->multilevel)
PetscStrcat(strategy, ",low=f}");
else
PetscStrcat(strategy, " f");
break;
case MP_SCOTCH_NONE:
if (scotch->multilevel)
PetscStrcat(strategy, ",asc=x}");
default:
break;
}
PetscStrcat(strategy, " x}");
}
PetscPrintf(((PetscObject)part)->comm, "strategy=[%s]\n", strategy);
ierr = SCOTCH_stratInit(&stratptr);CHKERRQ(ierr);
/*
TODO: Correct this part
Commented because this doesn't exists anymore
ierr = SCOTCH_stratMap(&stratptr, strategy);CHKERRQ(ierr);
*/
/* check for option mapping */
if (!scotch->map) {
/* ********************************************
* *
* TODO: Correct this part *
* *
* Won't work with this tmp SCOTCH_Strat... *
* *
* I just modified it to make scotch compile, *
* to be able to use PaStiX... *
* *
**********************************************/
#if defined (DOES_NOT_COMPILE_DUE_TO_BROKEN_INTERFACE)
SCOTCH_Strat tmp;
ierr = SCOTCH_graphPart((const SCOTCH_Graph *)&grafptr,
(const SCOTCH_Num) &stratptr,
(const SCOTCH_Strat *)&tmp, /* The Argument changed from scotch 3.04 it was part->n, */
(SCOTCH_Num *) parttab);CHKERRQ(ierr);
#else
SETERRQ(PETSC_ERR_SUP,"Scotch interface currently broken");
#endif
ierr = PetscPrintf(PETSC_COMM_SELF, "Partition simple without mapping\n");
} else {
SCOTCH_Graph grafarch;
SCOTCH_Num *listtab;
SCOTCH_Num listnbr = 0;
SCOTCH_Arch archptr; /* file in scotch architecture format */
SCOTCH_Strat archstrat;
int arch_total_size, *parttab_tmp,err;
int cpt;
char buf[256];
FILE *file1, *file2;
char host_buf[256];
/* generate the graph that represents the arch */
file1 = fopen(scotch->arch, "r");
if (!file1) SETERRQ1(PETSC_ERR_FILE_OPEN, "Scotch: unable to open architecture file %s", scotch->arch);
ierr = SCOTCH_graphInit(&grafarch);CHKERRQ(ierr);
ierr = SCOTCH_graphLoad(&grafarch, file1, baseval, 3);CHKERRQ(ierr);
ierr = SCOTCH_graphCheck(&grafarch);CHKERRQ(ierr);
SCOTCH_graphSize(&grafarch, &arch_total_size, &cpt);
err = fclose(file1);
if (err) SETERRQ(PETSC_ERR_SYS,"fclose() failed on file");
printf("total size = %d\n", arch_total_size);
/* generate the list of nodes currently working */
ierr = PetscGetHostName(host_buf, 256);CHKERRQ(ierr);
ierr = PetscStrlen(host_buf, &j);CHKERRQ(ierr);
file2 = fopen(scotch->host_list, "r");
if (!file2) SETERRQ1(PETSC_ERR_FILE_OPEN, "Scotch: unable to open host list file %s", scotch->host_list);
i = -1;
flg = PETSC_FALSE;
while (!feof(file2) && !flg) {
i++;
fgets(buf, 256, file2);
PetscStrncmp(buf, host_buf, j, &flg);
}
err = fclose(file2);
if (err) SETERRQ(PETSC_ERR_SYS,"fclose() failed on file");
if (!flg) SETERRQ1(PETSC_ERR_LIB, "Scotch: unable to find '%s' in host list file", host_buf);
listnbr = size;
ierr = PetscMalloc(sizeof(SCOTCH_Num) * listnbr, &listtab);CHKERRQ(ierr);
ierr = MPI_Allgather(&i, 1, MPI_INT, listtab, 1, MPI_INT, ((PetscObject)part)->comm);CHKERRQ(ierr);
printf("listnbr = %d, listtab = ", listnbr);
for (i = 0; i < listnbr; i++)
printf("%d ", listtab[i]);
printf("\n");
err = fflush(stdout);
if (err) SETERRQ(PETSC_ERR_SYS,"fflush() failed on file");
ierr = SCOTCH_stratInit(&archstrat);CHKERRQ(ierr);
/**************************************************************
* *
* TODO: Correct this part *
* *
* Commented because this doesn't exists anymore *
* *
* ierr = SCOTCH_stratBipart(&archstrat, "fx");CHKERRQ(ierr); *
**************************************************************/
ierr = SCOTCH_archInit(&archptr);CHKERRQ(ierr);
ierr = SCOTCH_archBuild(&archptr, &grafarch, listnbr, listtab,
&archstrat);CHKERRQ(ierr);
ierr = PetscMalloc((mat->rmap->N) * sizeof(int), &parttab_tmp);CHKERRQ(ierr);
/************************************************************************************
* *
* TODO: Correct this part *
* *
* Commented because this doesn't exists anymore *
* *
* ierr = SCOTCH_mapInit(&mappptr, &grafptr, &archptr, parttab_tmp);CHKERRQ(ierr); *
* *
* ierr = SCOTCH_mapCompute(&mappptr, &stratptr);CHKERRQ(ierr); *
* *
* ierr = SCOTCH_mapView(&mappptr, stdout);CHKERRQ(ierr); *
************************************************************************************/
/* now we have to set in the real parttab at the good place */
/* because the ranks order are different than position in */
/* the arch graph */
for (i = 0; i < mat->rmap->N; i++) {
parttab[i] = parttab_tmp[i];
}
ierr = PetscFree(listtab);CHKERRQ(ierr);
SCOTCH_archExit(&archptr);
/*************************************************
* TODO: Correct this part *
* *
* Commented because this doesn't exists anymore *
* SCOTCH_mapExit(&mappptr); *
*************************************************/
SCOTCH_stratExit(&archstrat);
}
/* dump to mesg_log... */
#ifdef PETSC_HAVE_UNISTD_H
err = fflush(stdout);
if (err) SETERRQ(PETSC_ERR_SYS,"fflush() failed on stdout");
count = read(fd_pipe[0], scotch->mesg_log, (SIZE_LOG - 1) * sizeof(char));
if (count < 0)
count = 0;
scotch->mesg_log[count] = 0;
close(1);
dup2(fd_stdout, 1);
close(fd_stdout);
close(fd_pipe[0]);
close(fd_pipe[1]);
#endif
SCOTCH_graphExit(&grafptr);
SCOTCH_stratExit(&stratptr);
}
if (ierr)
SETERRQ(PETSC_ERR_LIB, scotch->mesg_log);
/* Creation of the index set */
ierr = MPI_Comm_rank(((PetscObject)part)->comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(((PetscObject)part)->comm, &size);CHKERRQ(ierr);
nb_locals = mat->rmap->N / size;
locals = parttab + rank * nb_locals;
if (rank < mat->rmap->N % size) {
nb_locals++;
locals += rank;
} else
locals += mat->rmap->N % size;
ierr = ISCreateGeneral(((PetscObject)part)->comm, nb_locals, locals, partitioning);CHKERRQ(ierr);
/* destroying old objects */
ierr = PetscFree(parttab);CHKERRQ(ierr);
if (matSeq != mat) {
ierr = MatDestroy(matSeq);CHKERRQ(ierr);
}
if (matMPI != mat) {
ierr = MatDestroy(matMPI);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
