Openpmd-api: ADIOS1: SerialIOTest needs MPI with Parallel Lib
Even with #228 there are way more calls to MPI_ functions when linking a parallel ADIOS1 lib. That leads to the need to actually start serial programs, such as SerialIOTest, with mpirun/exec.
That's sad. Is the MPI-moc library the only way to call the serial ADIOS API? If so, a lot more refactoring inside ADIOS src/core/bp_utils.c (incomplete below) and a little more inside src/read/read_bp.c would be needed:
diff --git a/src/core/bp_utils.c b/src/core/bp_utils.c
index 1ac8990a..94ef1532 100644
--- a/src/core/bp_utils.c
+++ b/src/core/bp_utils.c
@@ -70,6 +70,78 @@ inline BP_FILE * GET_BP_FILE (const ADIOS_FILE * fp)
void * bp_read_data_from_buffer(struct adios_bp_buffer_struct_v1 *b, enum ADIOS_DATATYPES type, int nelems);
int bp_parse_characteristics (struct adios_bp_buffer_struct_v1 * b, struct adios_index_var_struct_v1 ** root, uint64_t j);
+/* dummies: for building serial apps against a parallel ADIOS lib */
+#if defined(__APPLE__) || defined(__WIN32__) || defined(__CYGWIN__)
+# define lseek64 lseek
+# define open64 open
+#endif
+
+static char mpierrmsg_dummy[MPI_MAX_ERROR_STRING];
+
+static int typesize_dummy(MPI_Datatype type)
+{
+ switch( type )
+ {
+ case MPI_INT : return sizeof( int );
+ break;
+ case MPI_CHAR: return sizeof( char );
+ break;
+ case MPI_REAL : return sizeof( float );
+ break;
+ case MPI_DOUBLE : return sizeof( double );
+ break;
+ case MPI_UNSIGNED_LONG_LONG : return sizeof( unsigned long long );
+ break;
+ case MPI_UINT64_T : return sizeof( uint64_t );
+ break;
+ default : return 1 ;
+ }
+ return 1;
+}
+
+int MPI_File_open_dummy(MPI_Comm comm, char *filename, int amode, MPI_Info info, MPI_File *fh)
+{
+ *fh = open64 (filename, amode);
+ if (*fh == -1) {
+ snprintf(mpierrmsg_dummy, MPI_MAX_ERROR_STRING, "File not found: %s", filename);
+ return -1;
+ }
+ return MPI_SUCCESS;
+}
+
+int MPI_File_close_dummy(MPI_File *fh) { return close(*fh); }
+
+int MPI_File_get_size_dummy(MPI_File fh, MPI_Offset *size) {
+ uint64_t curpos = lseek64(fh, 0, SEEK_CUR); // get the current seek pos
+ uint64_t endpos = lseek64(fh, 0, SEEK_END); // go to end, returned is the size in bytes
+ lseek64(fh, curpos, SEEK_SET); // go back where we were
+ *size = (MPI_Offset) endpos;
+ //printf("MPI_File_get_size: fh=%d, size=%lld\n", fh, *size);
+ return MPI_SUCCESS;
+}
+
+int MPI_File_read_dummy(MPI_File fh, void *buf, int count, MPI_Datatype datatype, MPI_Status *status)
+{
+ // FIXME: int count can read only 2GB (*datatype size) array at max
+ uint64_t bytes_to_read = count * typesize_dummy(datatype);
+ uint64_t bytes_read;
+ bytes_read = read (fh, buf, bytes_to_read);
+ if (bytes_read != bytes_to_read) {
+ snprintf(mpierrmsg_dummy, MPI_MAX_ERROR_STRING, "could not read %" PRIu64 " bytes. read only: %" PRIu64 "\n", bytes_to_read, bytes_read);
+ return -2;
+ }
+ *status = bytes_read;
+ //printf("MPI_File_read: fh=%d, count=%d, typesize=%d, bytes read=%lld\n", fh, count, datatype, *status);
+ return MPI_SUCCESS;
+}
+
+int MPI_File_seek_dummy(MPI_File fh, MPI_Offset offset, int whence)
+{
+ uint64_t off = (uint64_t) offset;
+ lseek64 (fh, off, whence);
+ //printf("MPI_File_seek: fh=%d, offset=%lld, whence=%d\n", fh, off, whence);
+ return MPI_SUCCESS;
+}
void bp_alloc_aligned (struct adios_bp_buffer_struct_v1 * b, uint64_t size)
@@ -233,18 +305,23 @@ static int bp_read_open (const char * filename,
MPI_Comm comm,
BP_FILE * fh)
{
- int err;
- int rank;
+ int err = MPI_SUCCESS;
+ int rank = 0;
- MPI_Comm_rank (comm, &rank);
+ if (comm != MPI_COMM_NULL)
+ MPI_Comm_rank (comm, &rank);
// variable definition
MPI_Offset file_size;
// open a file by the multiple processors within the same
// communicator
- err = MPI_File_open (comm, (char *) filename, MPI_MODE_RDONLY,
- (MPI_Info) MPI_INFO_NULL, &(fh->mpi_fh));
+ if (comm == MPI_COMM_NULL)
+ err = MPI_File_open_dummy (comm, (char *) filename, MPI_MODE_RDONLY,
+ (MPI_Info) MPI_INFO_NULL, &(fh->mpi_fh));
+ else
+ err = MPI_File_open (comm, (char *) filename, MPI_MODE_RDONLY,
+ (MPI_Info) MPI_INFO_NULL, &(fh->mpi_fh));
if (err != MPI_SUCCESS) {
char e [MPI_MAX_ERROR_STRING];
int len = 0;
@@ -254,7 +331,10 @@ static int bp_read_open (const char * filename,
return adios_flag_no;
}
- MPI_File_get_size (fh->mpi_fh, &file_size);
+ if (comm == MPI_COMM_NULL)
+ MPI_File_get_size_dummy (fh->mpi_fh, &file_size);
+ else
+ MPI_File_get_size (fh->mpi_fh, &file_size);
fh->b->file_size = file_size;
fh->mfooter.file_size = file_size;
@@ -265,26 +345,43 @@ static int bp_read_open_rootonly (const char * filename,
MPI_Comm comm,
BP_FILE * fh)
{
- int err;
- int rank;
+ int err = MPI_SUCCESS;
+ int rank = 0;
- MPI_Comm_rank (comm, &rank);
+ if (comm != MPI_COMM_NULL)
+ MPI_Comm_rank (comm, &rank);
// variable definition
MPI_Offset file_size = 0;
if (rank == 0)
{
- // open a file by one processor then broadcast the size and the success
- err = MPI_File_open (MPI_COMM_SELF, (char *) filename, MPI_MODE_RDONLY,
- (MPI_Info) MPI_INFO_NULL, &(fh->mpi_fh));
- if (err == MPI_SUCCESS) {
- MPI_File_get_size (fh->mpi_fh, &file_size);
- err = 0;
+ if (comm == MPI_COMM_NULL)
+ {
+ // open a file by one processor then broadcast the size and the success
+ err = MPI_File_open_dummy (MPI_COMM_SELF, (char *) filename, MPI_MODE_RDONLY,
+ (MPI_Info) MPI_INFO_NULL, &(fh->mpi_fh));
+ if (err == MPI_SUCCESS) {
+ MPI_File_get_size_dummy (fh->mpi_fh, &file_size);
+ err = 0;
+ }
+ }
+ else
+ {
+ // open a file by one processor then broadcast the size and the success
+ err = MPI_File_open (MPI_COMM_SELF, (char *) filename, MPI_MODE_RDONLY,
+ (MPI_Info) MPI_INFO_NULL, &(fh->mpi_fh));
+ if (err == MPI_SUCCESS) {
+ MPI_File_get_size (fh->mpi_fh, &file_size);
+ err = 0;
+ }
}
}
- MPI_Bcast (&err, 1, MPI_INT, 0, comm);
- MPI_Bcast (&file_size, 1, MPI_UNSIGNED_LONG_LONG, 0, comm);
+ if (comm != MPI_COMM_NULL)
+ {
+ MPI_Bcast (&err, 1, MPI_INT, 0, comm);
+ MPI_Bcast (&file_size, 1, MPI_UNSIGNED_LONG_LONG, 0, comm);
+ }
fh->b->file_size = file_size;
fh->mfooter.file_size = file_size;
if (err)
@@ -305,9 +402,10 @@ int bp_open (const char * fname,
MPI_Comm comm,
BP_FILE * fh)
{
- int rank;
+ int rank = 0;
- MPI_Comm_rank (comm, &rank);
+ if (comm != MPI_COMM_NULL)
+ MPI_Comm_rank (comm, &rank);
adios_buffer_struct_init (fh->b);
@@ -326,7 +424,8 @@ int bp_open (const char * fname,
}
/* Broadcast to all other processors */
- MPI_Bcast (&fh->mfooter, sizeof (struct bp_minifooter), MPI_BYTE, 0, comm);
+ if (comm != MPI_COMM_NULL)
+ MPI_Bcast (&fh->mfooter, sizeof (struct bp_minifooter), MPI_BYTE, 0, comm);
if (fh->mfooter.pgs_index_offset > 0)
{
@@ -336,7 +435,12 @@ int bp_open (const char * fname,
* secure for future if a metadata+data BP file will ever have subfiles.
*/
if (rank == 0)
- MPI_File_close(&fh->mpi_fh);
+ {
+ if (comm == MPI_COMM_NULL)
+ MPI_File_close_dummy(&fh->mpi_fh);
+ else
+ MPI_File_close(&fh->mpi_fh);
+ }
if (bp_read_open (fname, comm, fh))
{
return -1;
@@ -357,7 +461,8 @@ int bp_open (const char * fname,
}
}
- MPI_Barrier (comm);
+ if (comm != MPI_COMM_NULL)
+ MPI_Barrier (comm);
// Broadcast the index which may be bigger than 2GB, so do it in chunks
uint64_t bytes_sent = 0;
int32_t to_send = 0;
@@ -373,8 +478,8 @@ int bp_open (const char * fname,
{
to_send = footer_size - bytes_sent;
}
-
- MPI_Bcast (fh->b->buff + bytes_sent, to_send, MPI_BYTE, 0, comm);
+ if (comm != MPI_COMM_NULL)
+ MPI_Bcast (fh->b->buff + bytes_sent, to_send, MPI_BYTE, 0, comm);
bytes_sent += to_send;
}
@@ -604,8 +709,13 @@ int bp_close (BP_FILE * fh)
MPI_File mpi_fh = fh->mpi_fh;
adios_errno = 0;
- if (fh->mpi_fh != MPI_FILE_NULL)
- MPI_File_close (&mpi_fh);
+ if (mpi_fh != MPI_FILE_NULL)
+ {
+ if (fh->comm == MPI_COMM_NULL)
+ MPI_File_close_dummy (&mpi_fh);
+ else
+ MPI_File_close (&mpi_fh);
+ }
close_all_BP_subfiles (fh);
@@ -820,8 +930,16 @@ int bp_read_minifooter (BP_FILE * bp_struct)
memset (b->buff, 0, MINIFOOTER_SIZE);
b->offset = 0;
}
- MPI_File_seek (bp_struct->mpi_fh, (MPI_Offset) attrs_end, MPI_SEEK_SET);
- MPI_File_read (bp_struct->mpi_fh, b->buff, MINIFOOTER_SIZE, MPI_BYTE, &status);
+ if (bp_struct->comm == MPI_FILE_NULL)
+ {
+ MPI_File_seek_dummy (bp_struct->mpi_fh, (MPI_Offset) attrs_end, MPI_SEEK_SET);
+ MPI_File_read_dummy (bp_struct->mpi_fh, b->buff, MINIFOOTER_SIZE, MPI_BYTE, &status);
+ }
+ else
+ {
+ MPI_File_seek (bp_struct->mpi_fh, (MPI_Offset) attrs_end, MPI_SEEK_SET);
+ MPI_File_read (bp_struct->mpi_fh, b->buff, MINIFOOTER_SIZE, MPI_BYTE, &status);
+ }
/*memset (&mh->pgs_index_offset, 0, MINIFOOTER_SIZE);
memcpy (&mh->pgs_index_offset, b->buff, MINIFOOTER_SIZE);*/
@@ -900,9 +1018,14 @@ int bp_read_minifooter (BP_FILE * bp_struct)
/* It will be sent to all processes */
uint64_t footer_size = mh->file_size - mh->pgs_index_offset;
bp_realloc_aligned (b, footer_size);
- MPI_File_seek (bp_struct->mpi_fh,
- (MPI_Offset) mh->pgs_index_offset,
- MPI_SEEK_SET);
+ if (bp_struct->comm == MPI_FILE_NULL)
+ MPI_File_seek_dummy (bp_struct->mpi_fh,
+ (MPI_Offset) mh->pgs_index_offset,
+ MPI_SEEK_SET);
+ else
+ MPI_File_seek (bp_struct->mpi_fh,
+ (MPI_Offset) mh->pgs_index_offset,
+ MPI_SEEK_SET);
// if we need to read > 2 GB, need to do it in parts
// since count is limited to MAX_MPIWRITE_SIZE (signed 32-bit max).
@@ -921,7 +1044,10 @@ int bp_read_minifooter (BP_FILE * bp_struct)
to_read = footer_size - bytes_read;
}
- err = MPI_File_read (bp_struct->mpi_fh, b->buff+bytes_read, to_read, MPI_BYTE, &status);
+ if (bp_struct->comm == MPI_FILE_NULL)
+ err = MPI_File_read_dummy (bp_struct->mpi_fh, b->buff+bytes_read, to_read, MPI_BYTE, &status);
+ else
+ err = MPI_File_read (bp_struct->mpi_fh, b->buff+bytes_read, to_read, MPI_BYTE, &status);
if (err != MPI_SUCCESS)
{
char e [MPI_MAX_ERROR_STRING];
diff --git a/src/read/read_bp.c b/src/read/read_bp.c
index e3c9a42f..2b4a59f5 100644
--- a/src/read/read_bp.c
+++ b/src/read/read_bp.c
@@ -1721,14 +1721,15 @@ ADIOS_FILE * adios_read_bp_open (const char * fname, MPI_Comm comm, enum ADIOS_L
ADIOS_FILE * adios_read_bp_open_file (const char * fname, MPI_Comm comm)
{
- int rank;
+ int rank = 0;
BP_PROC * p;
BP_FILE * fh;
ADIOS_FILE * fp;
log_debug ("adios_read_bp_open_file\n");
- MPI_Comm_rank (comm, &rank);
+ if (comm != MPI_COMM_NULL)
+ MPI_Comm_rank (comm, &rank);
fh = BP_FILE_alloc (fname, comm);
ax3l
😕1
All 8 comments
@C0nsultant I think there is a second solution that we can try.
If we separate the ADIOS1 serial and parallel backend translation units well, we could link ADIOS1 twice. We then create a serial and parallel adios library artifact that we then link into the final library.
With that workflow, we can use the always provided _nompi libs with the mock properly as ADIOS intended it to be used.
ax3l
on 13 Jun 2018
Oh wow, that draft of CMake magic looks messy...
ax3l
on 13 Jun 2018
@C0nsultant is it possible to get rid of MPI types and includes in include/openPMD/IO/ADIOS/ADIOS1IOHandler.hpp the same way as in include/openPMD/IO/HDF5/HDF5IOHandler.hpp?
They should not be needed there and can be set to e.g. MPI_COMM_NULL in the implementation, we have still the ParallelADIOS1IOHandler.hpp for MPI comm passing.
ax3l
on 13 Jun 2018
All the MPI crux is in there precisely because ADIOS designed their _NOMPI to use the mock provided in <adios_mpi.h>.
If your propsed split works, we should be able to pull it out of the interface into the implementation by hard-coding MPI_COMM_NULL indstead of relying on ADIOS1IOHandlerImpl::m_mpiComm. This will induce modifications in both ADIOS1IOHandlerImpl and ParallelADIOS1IOHandlerImpl.
I'll give it a try.
C0nsultant
on 13 Jun 2018
Yes, for the first part, but I think that can be hidden inside ADIOS1IOHandler.cpp for the serial mock.
ax3l
on 13 Jun 2018
👍1
That should be the way to go. It will probably lead to code duplication in ParallelADIOS1IOHandlerImpl, though. Currently both Impls rely on the fact that the interface is the same, no matter if _NOMPI. If the relevant variables are not available in the interface, we'll have to duplicate somewhere.
C0nsultant
on 13 Jun 2018
👍1
Yes, don't let us optimize on that coincident and keep it separate as in HDF5, even if a bit code is doubled then. This will allow me to separate the translation units better for linking against the static and the parallel ADIOS1 libs.
ax3l
on 13 Jun 2018
Opened a upstream issue in https://github.com/ornladios/ADIOS/issues/183
ax3l
on 14 Jun 2018
❤1
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