PetscErrorCode ISView_General_Binary(IS is,PetscViewer viewer)
{
PetscErrorCode ierr;
IS_General *isa = (IS_General*) is->data;
PetscMPIInt rank,size,mesgsize,tag = ((PetscObject)viewer)->tag, mesglen;
PetscInt n,N,len,j,tr[2];
int fdes;
MPI_Status status;
PetscInt message_count,flowcontrolcount,*values;
PetscFunctionBegin;
ierr = PetscLayoutGetLocalSize(is->map, &n);CHKERRQ(ierr);
ierr = PetscLayoutGetSize(is->map, &N);CHKERRQ(ierr);
ierr = PetscViewerBinaryGetDescriptor(viewer,&fdes);CHKERRQ(ierr);
/* determine maximum message to arrive */
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)is),&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PetscObjectComm((PetscObject)is),&size);CHKERRQ(ierr);
tr[0] = IS_FILE_CLASSID;
tr[1] = N;
ierr = PetscViewerBinaryWrite(viewer,tr,2,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr);
ierr = MPI_Reduce(&n,&len,1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)is));CHKERRQ(ierr);
ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr);
if (!rank) {
ierr = PetscBinaryWrite(fdes,isa->idx,n,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr);
ierr = PetscMalloc1(len,&values);CHKERRQ(ierr);
ierr = PetscMPIIntCast(len,&mesgsize);CHKERRQ(ierr);
/* receive and save messages */
for (j=1; j<size; j++) {
ierr = PetscViewerFlowControlStepMaster(viewer,j,&message_count,flowcontrolcount);CHKERRQ(ierr);
ierr = MPI_Recv(values,mesgsize,MPIU_INT,j,tag,PetscObjectComm((PetscObject)is),&status);CHKERRQ(ierr);
ierr = MPI_Get_count(&status,MPIU_INT,&mesglen);CHKERRQ(ierr);
ierr = PetscBinaryWrite(fdes,values,(PetscInt)mesglen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr);
}
ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr);
ierr = PetscFree(values);CHKERRQ(ierr);
} else {
ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr);
ierr = PetscMPIIntCast(n,&mesgsize);CHKERRQ(ierr);
ierr = MPI_Send(isa->idx,mesgsize,MPIU_INT,0,tag,PetscObjectComm((PetscObject)is));CHKERRQ(ierr);
ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*@C
PetscBinarySynchronizedWrite - writes to a binary file.
Collective on MPI_Comm
Input Parameters:
+ comm - the MPI communicator
. fd - the file
. n - the number of items to write
. p - the buffer
. istemp - the buffer may be changed
- type - the type of items to write (PETSC_INT, PETSC_DOUBLE or PETSC_SCALAR)
Level: developer
Notes:
Process 0 does a PetscBinaryWrite()
PetscBinarySynchronizedWrite() uses byte swapping to work on all machines.
Integers are stored on the file as 32 long, regardless of whether
they are stored in the machine as 32 or 64, this means the same
binary file may be read on any machine.
Notes:
because byte-swapping may be done on the values in data it cannot be declared const
WARNING: This is NOT like PetscSynchronizedFPrintf()! This routine ignores calls on all but process 0,
while PetscSynchronizedFPrintf() has all processes print their strings in order.
Concepts: files^synchronized writing of binary files
Concepts: binary files^reading, synchronized
.seealso: PetscBinaryWrite(), PetscBinaryOpen(), PetscBinaryClose(), PetscBinaryRead(), PetscBinarySynchronizedRead(),
PetscBinarySynchronizedSeek()
@*/
PetscErrorCode PetscBinarySynchronizedWrite(MPI_Comm comm,int fd,void *p,PetscInt n,PetscDataType type,PetscBool istemp)
{
PetscErrorCode ierr;
PetscMPIInt rank;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
if (!rank) {
ierr = PetscBinaryWrite(fd,p,n,type,istemp);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode writeProfileSurfaceScalarData(char *fileName, PetscScalar *arr, PetscInt numValsPerProfile, PetscTruth appendToFile)
{
PetscErrorCode ierr;
PetscScalar *tmpArr;
PetscInt *displs, *rcounts, cumpro;
PetscInt ipro;
size_t m1, m2;
/* off_t off, offset; */
PetscViewer fd;
PetscInt fp;
/* PetscInt iShift; */
PetscMPIInt numProcessors, myId;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&myId);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&numProcessors);CHKERRQ(ierr);
m1 = numValsPerProfile*totalNumProfiles*sizeof(PetscScalar);
m2 = numProcessors*sizeof(PetscInt);
/* Allocate memory for temporary arrays */
ierr = PetscMalloc(m1,&tmpArr);CHKERRQ(ierr);
ierr = PetscMalloc(m2,&displs);CHKERRQ(ierr);
ierr = PetscMalloc(m2,&rcounts);CHKERRQ(ierr);
cumpro=0;
for (ipro=1; ipro<=numProcessors; ipro++) {
displs[ipro-1]=numValsPerProfile*cumpro;
rcounts[ipro-1]=numValsPerProfile*gNumProfiles[ipro-1];
cumpro = cumpro + gNumProfiles[ipro-1];
/* ierr=PetscPrintf(PETSC_COMM_WORLD,"cumpro=%d, displs=%d\n",cumpro,displs[ipro-1],rcounts[ipro-1]);CHKERRQ(ierr); */
}
MPI_Gatherv(arr,numValsPerProfile*lNumProfiles,MPI_DOUBLE,tmpArr,rcounts,displs,MPI_DOUBLE,0, PETSC_COMM_WORLD);
if (myId==0) { /* this shouldn't really be necessary, but without it, all processors seem to be writing in append mode */
if (appendToFile) {
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,fileName,FILE_MODE_APPEND,&fd);CHKERRQ(ierr);
} else {
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,fileName,FILE_MODE_WRITE,&fd);CHKERRQ(ierr);
}
ierr = PetscViewerBinaryGetDescriptor(fd,&fp);CHKERRQ(ierr);
ierr = PetscBinaryWrite(fp,tmpArr,numValsPerProfile*totalNumProfiles,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr);
ierr = PetscViewerDestroy(fd);CHKERRQ(ierr);
}
ierr = PetscFree(tmpArr);CHKERRQ(ierr);
ierr = PetscFree(displs);CHKERRQ(ierr);
ierr = PetscFree(rcounts);CHKERRQ(ierr);
return 0;
}
/*@C
PetscHTTPRequest - Send a request to an HTTP server
Input Parameters:
+ type - either "POST" or "GET"
. url - URL of request host/path
. header - additional header information, may be NULL
. ctype - data type of body, for example application/json
. body - data to send to server
. sock - obtained with PetscOpenSocket()
- buffsize - size of buffer
Output Parameter:
. buff - everything returned from server
Level: advanced
.seealso: PetscHTTPSRequest(), PetscOpenSocket(), PetscHTTPSConnect(), PetscPullJSONValue()
@*/
PetscErrorCode PetscHTTPRequest(const char type[],const char url[],const char header[],const char ctype[],const char body[],int sock,char buff[],size_t buffsize)
{
char *request;
size_t request_len;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscHTTPBuildRequest(type,url,header,ctype,body,&request);CHKERRQ(ierr);
ierr = PetscStrlen(request,&request_len);CHKERRQ(ierr);
ierr = PetscBinaryWrite(sock,request,request_len,PETSC_CHAR,PETSC_FALSE);CHKERRQ(ierr);
ierr = PetscFree(request);CHKERRQ(ierr);
PetscBinaryRead(sock,buff,buffsize,PETSC_CHAR);
buff[buffsize-1] = 0;
ierr = PetscInfo1(NULL,"HTTP result follows: \n%s\n",buff);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode writeBinaryScalarData(char *fileName, PetscScalar *arr, PetscInt N, PetscTruth appendToFile)
{
PetscErrorCode ierr;
PetscViewer fd;
PetscInt fp;
PetscMPIInt myId;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&myId);CHKERRQ(ierr);
if (myId==0) { /* this shouldn't really be necessary, but without it, all processors seem to be writing in append mode */
if (appendToFile) {
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,fileName,FILE_MODE_APPEND,&fd);CHKERRQ(ierr);
} else {
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,fileName,FILE_MODE_WRITE,&fd);CHKERRQ(ierr);
}
ierr = PetscViewerBinaryGetDescriptor(fd,&fp);CHKERRQ(ierr);
ierr = PetscBinaryWrite(fp,arr,N,PETSC_SCALAR,PETSC_FALSE);CHKERRQ(ierr);
ierr = PetscViewerDestroy(fd);CHKERRQ(ierr);
}
return 0;
}
int main(int argc,char **args)
{
PetscErrorCode ierr;
PetscMPIInt size;
int fd;
PetscInt i,m = 10,sz;
PetscScalar *avec,*array;
Vec vec;
PetscViewer view_out,view_in;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_SELF,1,"This is a uniprocessor example only!");
ierr = PetscOptionsGetInt(PETSC_NULL,"-m",&m,PETSC_NULL);CHKERRQ(ierr);
/* ---------------------------------------------------------------------- */
/* PART 1: Write some data to a file in binary format */
/* ---------------------------------------------------------------------- */
/* Allocate array and set values */
ierr = PetscMalloc(m*sizeof(PetscScalar),&array);CHKERRQ(ierr);
for (i=0; i<m; i++) {
array[i] = i*10.0;
}
/* Open viewer for binary output */
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,"input.dat",FILE_MODE_WRITE,&view_out);CHKERRQ(ierr);
ierr = PetscViewerBinaryGetDescriptor(view_out,&fd);CHKERRQ(ierr);
/* Write binary output */
ierr = PetscBinaryWrite(fd,&m,1,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr);
ierr = PetscBinaryWrite(fd,array,m,PETSC_SCALAR,PETSC_FALSE);CHKERRQ(ierr);
/* Destroy the output viewer and work array */
ierr = PetscViewerDestroy(&view_out);CHKERRQ(ierr);
ierr = PetscFree(array);CHKERRQ(ierr);
/* ---------------------------------------------------------------------- */
/* PART 2: Read data from file and form a vector */
/* ---------------------------------------------------------------------- */
/* Open input binary viewer */
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,"input.dat",FILE_MODE_READ,&view_in);CHKERRQ(ierr);
ierr = PetscViewerBinaryGetDescriptor(view_in,&fd);CHKERRQ(ierr);
/* Create vector and get pointer to data space */
ierr = VecCreate(PETSC_COMM_SELF,&vec);CHKERRQ(ierr);
ierr = VecSetSizes(vec,PETSC_DECIDE,m);CHKERRQ(ierr);
ierr = VecSetFromOptions(vec);CHKERRQ(ierr);
ierr = VecGetArray(vec,&avec);CHKERRQ(ierr);
/* Read data into vector */
ierr = PetscBinaryRead(fd,&sz,1,PETSC_INT);CHKERRQ(ierr);
if (sz <=0) SETERRQ(PETSC_COMM_SELF,1,"Error: Must have array length > 0");
ierr = PetscPrintf(PETSC_COMM_SELF,"reading data in binary from input.dat, sz =%D ...\n",sz);CHKERRQ(ierr);
ierr = PetscBinaryRead(fd,avec,sz,PETSC_SCALAR);CHKERRQ(ierr);
/* View vector */
ierr = VecRestoreArray(vec,&avec);CHKERRQ(ierr);
ierr = VecView(vec,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
/* Free data structures */
ierr = VecDestroy(&vec);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&view_in);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode VecView_Seq_Binary(Vec xin,PetscViewer viewer)
{
PetscErrorCode ierr;
int fdes;
PetscInt n = xin->map->n,classid=VEC_FILE_CLASSID;
FILE *file;
const PetscScalar *xv;
#if defined(PETSC_HAVE_MPIIO)
PetscBool isMPIIO;
#endif
PetscBool skipHeader;
PetscViewerFormat format;
PetscFunctionBegin;
/* Write vector header */
ierr = PetscViewerBinaryGetSkipHeader(viewer,&skipHeader);CHKERRQ(ierr);
if (!skipHeader) {
ierr = PetscViewerBinaryWrite(viewer,&classid,1,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr);
ierr = PetscViewerBinaryWrite(viewer,&n,1,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr);
}
/* Write vector contents */
#if defined(PETSC_HAVE_MPIIO)
ierr = PetscViewerBinaryGetUseMPIIO(viewer,&isMPIIO);CHKERRQ(ierr);
if (!isMPIIO) {
#endif
ierr = PetscViewerBinaryGetDescriptor(viewer,&fdes);CHKERRQ(ierr);
ierr = VecGetArrayRead(xin,&xv);CHKERRQ(ierr);
ierr = PetscBinaryWrite(fdes,(void*)xv,n,PETSC_SCALAR,PETSC_FALSE);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(xin,&xv);CHKERRQ(ierr);
ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr);
if (format == PETSC_VIEWER_BINARY_MATLAB) {
MPI_Comm comm;
FILE *info;
const char *name;
ierr = PetscObjectGetName((PetscObject)xin,&name);CHKERRQ(ierr);
ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr);
ierr = PetscViewerBinaryGetInfoPointer(viewer,&info);CHKERRQ(ierr);
ierr = PetscFPrintf(comm,info,"#--- begin code written by PetscViewerBinary for MATLAB format ---#\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,info,"#$$ Set.%s = PetscBinaryRead(fd);\n",name);CHKERRQ(ierr);
ierr = PetscFPrintf(comm,info,"#--- end code written by PetscViewerBinary for MATLAB format ---#\n\n");CHKERRQ(ierr);
}
#if defined(PETSC_HAVE_MPIIO)
} else {
MPI_Offset off;
MPI_File mfdes;
PetscMPIInt lsize;
ierr = PetscMPIIntCast(n,&lsize);CHKERRQ(ierr);
ierr = PetscViewerBinaryGetMPIIODescriptor(viewer,&mfdes);CHKERRQ(ierr);
ierr = PetscViewerBinaryGetMPIIOOffset(viewer,&off);CHKERRQ(ierr);
ierr = MPI_File_set_view(mfdes,off,MPIU_SCALAR,MPIU_SCALAR,(char*)"native",MPI_INFO_NULL);CHKERRQ(ierr);
ierr = VecGetArrayRead(xin,&xv);CHKERRQ(ierr);
ierr = MPIU_File_write_all(mfdes,(void*)xv,lsize,MPIU_SCALAR,MPI_STATUS_IGNORE);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(xin,&xv);CHKERRQ(ierr);
ierr = PetscViewerBinaryAddMPIIOOffset(viewer,n*sizeof(PetscScalar));CHKERRQ(ierr);
}
#endif
ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr);
if (file) {
if (((PetscObject)xin)->prefix) {
ierr = PetscFPrintf(PETSC_COMM_SELF,file,"-%svecload_block_size %D\n",((PetscObject)xin)->prefix,PetscAbs(xin->map->bs));CHKERRQ(ierr);
} else {
ierr = PetscFPrintf(PETSC_COMM_SELF,file,"-vecload_block_size %D\n",PetscAbs(xin->map->bs));CHKERRQ(ierr);
}
}
PetscFunctionReturn(0);
}
void PETSC_STDCALL petscbinarywrite_(int *fd,void*p,PetscInt *n,PetscDataType *type,PetscTruth *istemp, int *__ierr ){
*__ierr = PetscBinaryWrite(*fd,p,*n,*type,*istemp);
}
static PetscErrorCode ISView_General_Binary(IS is,PetscViewer viewer)
{
PetscErrorCode ierr;
PetscBool skipHeader,useMPIIO;
IS_General *isa = (IS_General*) is->data;
PetscMPIInt rank,size,mesgsize,tag = ((PetscObject)viewer)->tag, mesglen;
PetscInt n,N,len,j,tr[2];
int fdes;
MPI_Status status;
PetscInt message_count,flowcontrolcount,*values;
PetscFunctionBegin;
/* ierr = ISGetLayout(is,&map);CHKERRQ(ierr); */
ierr = PetscLayoutGetLocalSize(is->map, &n);CHKERRQ(ierr);
ierr = PetscLayoutGetSize(is->map, &N);CHKERRQ(ierr);
tr[0] = IS_FILE_CLASSID;
tr[1] = N;
ierr = PetscViewerBinaryGetSkipHeader(viewer,&skipHeader);CHKERRQ(ierr);
if (!skipHeader) {
ierr = PetscViewerBinaryWrite(viewer,tr,2,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr);
}
ierr = PetscViewerBinaryGetUseMPIIO(viewer,&useMPIIO);CHKERRQ(ierr);
#if defined(PETSC_HAVE_MPIIO)
if (useMPIIO) {
MPI_File mfdes;
MPI_Offset off;
PetscMPIInt lsize;
PetscInt rstart;
const PetscInt *iarray;
ierr = PetscMPIIntCast(n,&lsize);CHKERRQ(ierr);
ierr = PetscViewerBinaryGetMPIIODescriptor(viewer,&mfdes);CHKERRQ(ierr);
ierr = PetscViewerBinaryGetMPIIOOffset(viewer,&off);CHKERRQ(ierr);
ierr = PetscLayoutGetRange(is->map,&rstart,NULL);CHKERRQ(ierr);
off += rstart*(MPI_Offset)sizeof(PetscInt); /* off is MPI_Offset, not PetscMPIInt */
ierr = MPI_File_set_view(mfdes,off,MPIU_INT,MPIU_INT,(char*)"native",MPI_INFO_NULL);CHKERRQ(ierr);
ierr = ISGetIndices(is,&iarray);CHKERRQ(ierr);
ierr = MPIU_File_write_all(mfdes,(void*)iarray,lsize,MPIU_INT,MPI_STATUS_IGNORE);CHKERRQ(ierr);
ierr = ISRestoreIndices(is,&iarray);CHKERRQ(ierr);
ierr = PetscViewerBinaryAddMPIIOOffset(viewer,N*(MPI_Offset)sizeof(PetscInt));CHKERRQ(ierr);
PetscFunctionReturn(0);
}
#endif
ierr = PetscViewerBinaryGetDescriptor(viewer,&fdes);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)is),&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PetscObjectComm((PetscObject)is),&size);CHKERRQ(ierr);
/* determine maximum message to arrive */
ierr = MPI_Reduce(&n,&len,1,MPIU_INT,MPI_MAX,0,PetscObjectComm((PetscObject)is));CHKERRQ(ierr);
ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr);
if (!rank) {
ierr = PetscBinaryWrite(fdes,isa->idx,n,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr);
ierr = PetscMalloc1(len,&values);CHKERRQ(ierr);
ierr = PetscMPIIntCast(len,&mesgsize);CHKERRQ(ierr);
/* receive and save messages */
for (j=1; j<size; j++) {
ierr = PetscViewerFlowControlStepMaster(viewer,j,&message_count,flowcontrolcount);CHKERRQ(ierr);
ierr = MPI_Recv(values,mesgsize,MPIU_INT,j,tag,PetscObjectComm((PetscObject)is),&status);CHKERRQ(ierr);
ierr = MPI_Get_count(&status,MPIU_INT,&mesglen);CHKERRQ(ierr);
ierr = PetscBinaryWrite(fdes,values,(PetscInt)mesglen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr);
}
ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr);
ierr = PetscFree(values);CHKERRQ(ierr);
} else {
ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr);
ierr = PetscMPIIntCast(n,&mesgsize);CHKERRQ(ierr);
ierr = MPI_Send(isa->idx,mesgsize,MPIU_INT,0,tag,PetscObjectComm((PetscObject)is));CHKERRQ(ierr);
ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}