/*@C
PetscGetFullPath - Given a filename, returns the fully qualified file name.
Not Collective
Input Parameters:
+ path - pathname to qualify
. fullpath - pointer to buffer to hold full pathname
- flen - size of fullpath
Level: developer
Concepts: full path
Concepts: path^full
.seealso: PetscGetRelativePath()
@*/
PetscErrorCode PetscGetFullPath(const char path[],char fullpath[],size_t flen)
{
PetscErrorCode ierr;
size_t ln;
PetscBool flg;
PetscFunctionBegin;
if (path[0] == '/') {
ierr = PetscStrncmp("/tmp_mnt/",path,9,&flg);CHKERRQ(ierr);
if (flg) {ierr = PetscStrncpy(fullpath,path + 8,flen);CHKERRQ(ierr);}
else {ierr = PetscStrncpy(fullpath,path,flen);CHKERRQ(ierr);}
fullpath[flen-1] = 0;
PetscFunctionReturn(0);
}
ierr = PetscStrncpy(fullpath,path,flen);CHKERRQ(ierr);
fullpath[flen-1] = 0;
/* Remove the various "special" forms (~username/ and ~/) */
if (fullpath[0] == '~') {
char tmppath[PETSC_MAX_PATH_LEN],*rest;
if (fullpath[1] == '/') {
ierr = PetscGetHomeDirectory(tmppath,PETSC_MAX_PATH_LEN);CHKERRQ(ierr);
rest = fullpath + 2;
} else {
#if defined(PETSC_HAVE_PWD_H)
struct passwd *pwde;
char *p,*name;
/* Find username */
name = fullpath + 1;
p = name;
while (*p && *p != '/') p++;
*p = 0;
rest = p + 1;
pwde = getpwnam(name);
if (!pwde) PetscFunctionReturn(0);
ierr = PetscStrcpy(tmppath,pwde->pw_dir);CHKERRQ(ierr);
#else
PetscFunctionReturn(0);
#endif
}
ierr = PetscStrlen(tmppath,&ln);CHKERRQ(ierr);
if (tmppath[ln-1] != '/') {ierr = PetscStrcat(tmppath+ln-1,"/");CHKERRQ(ierr);}
ierr = PetscStrcat(tmppath,rest);CHKERRQ(ierr);
ierr = PetscStrncpy(fullpath,tmppath,flen);CHKERRQ(ierr);
fullpath[flen-1] = 0;
} else {
ierr = PetscGetWorkingDirectory(fullpath,flen);CHKERRQ(ierr);
ierr = PetscStrlen(fullpath,&ln);CHKERRQ(ierr);
ierr = PetscStrncpy(fullpath+ln,"/",flen - ln);CHKERRQ(ierr);
fullpath[flen-1] = 0;
ierr = PetscStrlen(fullpath,&ln);CHKERRQ(ierr);
if (path[0] == '.' && path[1] == '/') {
ierr = PetscStrncat(fullpath,path+2,flen - ln - 1);CHKERRQ(ierr);
} else {
ierr = PetscStrncat(fullpath,path,flen - ln - 1);CHKERRQ(ierr);
}
fullpath[flen-1] = 0;
}
/* Remove the automounter part of the path */
ierr = PetscStrncmp(fullpath,"/tmp_mnt/",9,&flg);CHKERRQ(ierr);
if (flg) {
char tmppath[PETSC_MAX_PATH_LEN];
ierr = PetscStrcpy(tmppath,fullpath + 8);CHKERRQ(ierr);
ierr = PetscStrcpy(fullpath,tmppath);CHKERRQ(ierr);
}
/* We could try to handle things like the removal of .. etc */
PetscFunctionReturn(0);
}
int main( int argc, char **argv )
{
Mat hmat,smat;
PetscInt n=0,row,col, nev;
PetscScalar number;
PetscViewer view;
PetscBool flag;
int ierr,i;
char path[PETSC_MAX_PATH_LEN]="", temporary[PETSC_MAX_PATH_LEN]="";
char infilename[PETSC_MAX_PATH_LEN]="", outfilename[PETSC_MAX_PATH_LEN]="";
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetString(PETSC_NULL,"-in",infilename,PETSC_MAX_PATH_LEN-1,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-out",outfilename,PETSC_MAX_PATH_LEN-1,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscGetWorkingDirectory(path,PETSC_MAX_PATH_LEN);
if ( strcmp(infilename, "") == 0 ||
strcmp(outfilename, "") == 0 ||
n == 0 ){
SETERRQ(PETSC_COMM_WORLD,1,"Error in parameterlist.\nExample call: ./convertToPETScBin -in matrix.hmat -out matrix.dat -n 1912");
}
// number = 2.0 + 3.0 * PETSC_i;
// PetscPrintf(PETSC_COMM_WORLD,"number: %g i%g\n", number);
// std::cout << number
PetscPrintf(PETSC_COMM_WORLD,"processing %s into %s\n", infilename, outfilename);
ierr = MatCreateSeqAIJ(PETSC_COMM_WORLD,n,n,n,PETSC_NULL,&hmat);
FILE *file;
double real, imag;
PetscScalar complex;
PetscScalar myreal;
strcat(temporary, path); strcat(temporary, "/"); strcat(temporary, infilename); strcpy(infilename, temporary);
ierr = PetscFOpen(PETSC_COMM_SELF,infilename,"r",&file);CHKERRQ(ierr);
while ( fscanf(file,"%d %d %le %le\n",&row,&col,(double*)&real, (double*)&imag) != EOF ){
row = row - 1; col = col -1; // adjustment
if ( row == col ){
complex = real /*+ imag*PETSC_i*/;
ierr = MatSetValues(hmat,1,&row,1,&col,&complex,INSERT_VALUES);CHKERRQ(ierr);
}else{
complex = real /*+ imag*PETSC_i */;
ierr = MatSetValues(hmat,1,&row,1,&col,&complex,INSERT_VALUES);CHKERRQ(ierr);
complex = real /*- imag*PETSC_i */;
ierr = MatSetValues(hmat,1,&col,1,&row,&complex,INSERT_VALUES);CHKERRQ(ierr);
}
}
fclose(file);
ierr = MatAssemblyBegin(hmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(hmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatIsHermitian(hmat,0.00000000000001,&flag); CHKERRQ(ierr);
if ( !flag ){
SETERRQ(PETSC_COMM_WORLD,1,"Error. Output matrix is not hermitian.");
}
// writing
strcpy(temporary,"");
strcat(temporary, path); strcat(temporary, "/"); strcat(temporary, outfilename); strcpy(outfilename, temporary);
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,outfilename,FILE_MODE_WRITE,&view);CHKERRQ(ierr);
ierr = MatView(hmat,view);CHKERRQ(ierr);
ierr = PetscViewersDestroy(&view);
ierr = SlepcFinalize();CHKERRQ(ierr);
return 0;
}
int main( int argc, char **argv )
{
int ierr,i,j;
char infilename[PETSC_MAX_PATH_LEN]="", temporary[PETSC_MAX_PATH_LEN]="", path[PETSC_MAX_PATH_LEN]="";
PetscViewer viewer;
PetscBool isTail=PETSC_FALSE,isRight=PETSC_FALSE;
Mat mat;
PetscInt idxn[DIM], idxm[DIM], m, n, windowX=0, windowY=0;
PetscScalar values[DIM*DIM];
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetString(PETSC_NULL,"-file",infilename,PETSC_MAX_PATH_LEN-1,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(PETSC_NULL, "-tail", &isTail, NULL);
ierr = PetscOptionsGetBool(PETSC_NULL, "-right", &isRight, NULL);
ierr = PetscGetWorkingDirectory(path,PETSC_MAX_PATH_LEN);
// concat filename
strcat(temporary, path); strcat(temporary, "/"); strcat(temporary, infilename); strcpy(infilename, temporary);
if ( strcmp(infilename, "") == 0 ){
SETERRQ(PETSC_COMM_WORLD,1,"Specifiy the filename!\nExample call: ./inspectBinary -file matrix.dat");
}
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,infilename,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&mat);CHKERRQ(ierr);
ierr = MatSetFromOptions(mat);CHKERRQ(ierr);
ierr = MatLoad(mat,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
MatGetSize(mat,&m,&n);
if ( isTail == PETSC_TRUE ){
windowY = m - DIM;
}
if ( isRight == PETSC_TRUE ){
windowX = n - DIM;
}
for ( i = 0 ; i < DIM ; ++i ){
idxm[i] = i + windowY; idxn[i] = i + windowX;
}
MatGetValues(mat,DIM,idxm,DIM,idxn,values);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Dimension: %d rows x %d columns:\n", m, n);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"row index idxm:");CHKERRQ(ierr);
for ( i = 0 ; i < DIM ; ++i ){
ierr = PetscPrintf(PETSC_COMM_WORLD,"%d, ", idxm[i]);CHKERRQ(ierr);
}
ierr = PetscPrintf(PETSC_COMM_WORLD,"\ncol index idxn:");CHKERRQ(ierr);
for ( i = 0 ; i < DIM ; ++i ){
ierr = PetscPrintf(PETSC_COMM_WORLD,"%d, ", idxn[i]);CHKERRQ(ierr);
}
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n\n\n");CHKERRQ(ierr);
for ( i = 0 ; i < DIM ; ++i ){
for ( j = 0 ; j < DIM ; ++j ){
ierr = PetscPrintf(PETSC_COMM_WORLD,"(%2.10e/ %2.10e) ", PetscRealPart(values[i*DIM + j]), PetscImaginaryPart(values[i*DIM + j]) );CHKERRQ(ierr);
}
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n");CHKERRQ(ierr);
}
ierr = SlepcFinalize();CHKERRQ(ierr);
return 0;
}
/*@C
PetscSharedWorkingDirectory - Determines if all processors in a communicator share a
working directory or have different ones.
Collective on MPI_Comm
Input Parameters:
. comm - MPI_Communicator that may share working directory
Output Parameters:
. shared - PETSC_TRUE or PETSC_FALSE
Options Database Keys:
+ -shared_working_directory
. -not_shared_working_directory
Environmental Variables:
+ PETSC_SHARED_WORKING_DIRECTORY
. PETSC_NOT_SHARED_WORKING_DIRECTORY
Level: developer
Notes:
Stores the status as a MPI attribute so it does not have
to be redetermined each time.
Assumes that all processors in a communicator either
1) have a common working directory or
2) each has a separate working directory
eventually we can write a fancier one that determines which processors
share a common working directory.
This will be very slow on runs with a large number of processors since
it requires O(p*p) file opens.
@*/
PetscErrorCode PetscSharedWorkingDirectory(MPI_Comm comm,PetscBool *shared)
{
PetscErrorCode ierr;
PetscMPIInt size,rank,*tagvalp,sum,cnt,i;
PetscBool flg,iflg;
FILE *fd;
static PetscMPIInt Petsc_WD_keyval = MPI_KEYVAL_INVALID;
int err;
PetscFunctionBegin;
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
if (size == 1) {
*shared = PETSC_TRUE;
PetscFunctionReturn(0);
}
ierr = PetscOptionsGetenv(comm,"PETSC_SHARED_WORKING_DIRECTORY",NULL,0,&flg);CHKERRQ(ierr);
if (flg) {
*shared = PETSC_TRUE;
PetscFunctionReturn(0);
}
ierr = PetscOptionsGetenv(comm,"PETSC_NOT_SHARED_WORKING_DIRECTORY",NULL,0,&flg);CHKERRQ(ierr);
if (flg) {
*shared = PETSC_FALSE;
PetscFunctionReturn(0);
}
if (Petsc_WD_keyval == MPI_KEYVAL_INVALID) {
ierr = MPI_Keyval_create(MPI_NULL_COPY_FN,Petsc_DelTmpShared,&Petsc_WD_keyval,0);CHKERRQ(ierr);
}
ierr = MPI_Attr_get(comm,Petsc_WD_keyval,(void**)&tagvalp,(int*)&iflg);CHKERRQ(ierr);
if (!iflg) {
char filename[PETSC_MAX_PATH_LEN];
/* This communicator does not yet have a shared attribute */
ierr = PetscMalloc1(1,&tagvalp);CHKERRQ(ierr);
ierr = MPI_Attr_put(comm,Petsc_WD_keyval,tagvalp);CHKERRQ(ierr);
ierr = PetscGetWorkingDirectory(filename,240);CHKERRQ(ierr);
ierr = PetscStrcat(filename,"/petsctestshared");CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
/* each processor creates a file and all the later ones check */
/* this makes sure no subset of processors is shared */
*shared = PETSC_FALSE;
for (i=0; i<size-1; i++) {
if (rank == i) {
fd = fopen(filename,"w");
if (!fd) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to open test file %s",filename);
err = fclose(fd);
if (err) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SYS,"fclose() failed on file");
}
ierr = MPI_Barrier(comm);CHKERRQ(ierr);
if (rank >= i) {
fd = fopen(filename,"r");
if (fd) cnt = 1;
else cnt = 0;
if (fd) {
err = fclose(fd);
if (err) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SYS,"fclose() failed on file");
}
} else cnt = 0;
ierr = MPIU_Allreduce(&cnt,&sum,1,MPI_INT,MPI_SUM,comm);CHKERRQ(ierr);
if (rank == i) unlink(filename);
if (sum == size) {
*shared = PETSC_TRUE;
break;
} else if (sum != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP_SYS,"Subset of processes share working directory");
}
*tagvalp = (int)*shared;
} else *shared = (PetscBool) *tagvalp;
ierr = PetscInfo1(0,"processors %s working directory\n",(*shared) ? "shared" : "do NOT share");CHKERRQ(ierr);
PetscFunctionReturn(0);
}