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Merged
merged 6 commits into from
Apr 6, 2025
Merged

Support OpenMPI #62

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b88c234
bug fix: use Python objects, instead of C
wkliao Apr 5, 2025
502c989
bug fix: explicitly use MPI.Datatype in function argument
wkliao Apr 5, 2025
4c64c65
support OpenMPI used to build mpi4py and PnetCDF
wkliao Apr 5, 2025
2013eed
add TESTMPIRUN to make ptests command line
wkliao Apr 5, 2025
6a0e74e
Github action: add CI for using OpenMPI
wkliao Apr 5, 2025
d6d0005
Github action: pnetcdf master now requires newer autotools
wkliao Apr 5, 2025
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59 changes: 29 additions & 30 deletions src/pnetcdf/_Variable.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,6 @@ cimport numpy
numpy.import_array()


ctypedef MPI.Datatype Datatype
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Is this change necessary to fix the OpenMPI issue? this should just create an alias



cdef class Variable:
Expand Down Expand Up @@ -699,7 +698,7 @@ cdef class Variable:
self._put(dataput,a,b,c)


def _put_var1(self, value, tuple index, bufcount, Datatype buftype, collective = True):
def _put_var1(self, value, tuple index, bufcount, MPI.Datatype buftype, collective = True):
cdef int ierr, ndims
cdef size_t *indexp
cdef MPI_Offset buffcount
Expand Down Expand Up @@ -735,7 +734,7 @@ cdef class Variable:
_check_err(ierr)
free(indexp)

def _put_var(self, ndarray data, bufcount, Datatype buftype, collective = True):
def _put_var(self, ndarray data, bufcount, MPI.Datatype buftype, collective = True):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down Expand Up @@ -765,7 +764,7 @@ cdef class Variable:
PyArray_DATA(data), buffcount, bufftype)
_check_err(ierr)

def _put_vara(self, start, count, ndarray data, bufcount, Datatype buftype, collective = True):
def _put_vara(self, start, count, ndarray data, bufcount, MPI.Datatype buftype, collective = True):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down Expand Up @@ -802,7 +801,7 @@ cdef class Variable:
PyArray_DATA(data), buffcount, bufftype)
_check_err(ierr)

def _put_varn(self, ndarray data, num, starts, counts=None, bufcount=None, buftype=None, collective = True):
def _put_varn(self, ndarray data, num, starts, counts=None, bufcount=None, MPI.Datatype buftype=None, collective = True):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down Expand Up @@ -862,7 +861,7 @@ cdef class Variable:
bufftype)
_check_err(ierr)

def put_varn_all(self, data, num, starts, counts=None, bufcount=None, buftype=None):
def put_varn_all(self, data, num, starts, counts=None, bufcount=None, MPI.Datatype buftype=None):
"""
put_varn_all(self, data, num, starts, counts=None, bufcount=None, buftype=None)

Expand Down Expand Up @@ -967,7 +966,7 @@ cdef class Variable:
self._put_varn(data, num, starts, counts, bufcount = bufcount,
buftype = buftype, collective = True)

def put_varn(self, data, num, starts, counts=None, bufcount=None, buftype=None):
def put_varn(self, data, num, starts, counts=None, bufcount=None, MPI.Datatype buftype=None):
"""
put_varn(self, data, num, starts, counts=None, bufcount=None, buftype=None)

Expand All @@ -979,7 +978,7 @@ cdef class Variable:
self._put_varn(data, num, starts, counts, bufcount = bufcount,
buftype = buftype, collective = False)

def iput_varn(self, data, num, starts, counts=None, bufcount=None, buftype=None):
def iput_varn(self, data, num, starts, counts=None, bufcount=None, MPI.Datatype buftype=None):
"""
iput_varn(self, data, num, starts, counts=None, bufcount=None, buftype=None)

Expand Down Expand Up @@ -1008,7 +1007,7 @@ cdef class Variable:
return self._iput_varn(data, num, starts, counts, bufcount, buftype,
buffered=False)

def bput_varn(self, data, num, starts, counts=None, bufcount=None, buftype=None):
def bput_varn(self, data, num, starts, counts=None, bufcount=None, MPI.Datatype buftype=None):
"""
bput_varn(self, data, num, starts, counts=None, bufcount=None, buftype=None)

Expand All @@ -1035,7 +1034,7 @@ cdef class Variable:
"""
return self._iput_varn(data, num, starts, counts, bufcount, buftype, buffered=True)

def _put_vars(self, start, count, stride, ndarray data, bufcount, Datatype buftype, collective = True):
def _put_vars(self, start, count, stride, ndarray data, bufcount, MPI.Datatype buftype, collective = True):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down Expand Up @@ -1078,7 +1077,7 @@ cdef class Variable:
_check_err(ierr)


def _put_varm(self, ndarray data, start, count, stride, imap, bufcount, Datatype buftype, collective = True):
def _put_varm(self, ndarray data, start, count, stride, imap, bufcount, MPI.Datatype buftype, collective = True):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down Expand Up @@ -1131,7 +1130,7 @@ cdef class Variable:



def put_var_all(self, data, start=None, count=None, stride=None, imap=None, bufcount=None, buftype=None):
def put_var_all(self, data, start=None, count=None, stride=None, imap=None, bufcount=None, MPI.Datatype buftype=None):
"""
put_var_all(self, data, start=None, count=None, stride=None, imap=None, bufcount=None, buftype=None)

Expand Down Expand Up @@ -1423,7 +1422,7 @@ cdef class Variable:
free(countp)
free(stridep)

def _get_var1(self, ndarray buff, index, bufcount, Datatype buftype, collective = True):
def _get_var1(self, ndarray buff, index, bufcount, MPI.Datatype buftype, collective = True):
cdef int ierr, ndims
cdef size_t *indexp
cdef MPI_Offset buffcount
Expand Down Expand Up @@ -1453,7 +1452,7 @@ cdef class Variable:
free(indexp)


def _get_var(self, ndarray buff, bufcount, Datatype buftype, collective = True):
def _get_var(self, ndarray buff, bufcount, MPI.Datatype buftype, collective = True):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand All @@ -1479,7 +1478,7 @@ cdef class Variable:
_check_err(ierr)


def _get_vara(self, ndarray buff, start, count, bufcount, Datatype buftype, collective = True):
def _get_vara(self, ndarray buff, start, count, bufcount, MPI.Datatype buftype, collective = True):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down Expand Up @@ -1513,7 +1512,7 @@ cdef class Variable:

_check_err(ierr)

def _get_varn(self, ndarray data, num, starts, counts, bufcount, Datatype buftype, collective = True):
def _get_varn(self, ndarray data, num, starts, counts, bufcount, MPI.Datatype buftype, collective = True):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down Expand Up @@ -1569,7 +1568,7 @@ cdef class Variable:

_check_err(ierr)

def _get_vars(self, ndarray buff, start, count, stride, bufcount, Datatype buftype, collective = True):
def _get_vars(self, ndarray buff, start, count, stride, bufcount, MPI.Datatype buftype, collective = True):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down Expand Up @@ -1606,7 +1605,7 @@ cdef class Variable:

_check_err(ierr)

def _get_varm(self, ndarray buff, start, count, stride, imap, bufcount, Datatype buftype, collective = True):
def _get_varm(self, ndarray buff, start, count, stride, imap, bufcount, MPI.Datatype buftype, collective = True):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down Expand Up @@ -2058,7 +2057,7 @@ cdef class Variable:
else:
return data

def _iput_var(self, ndarray data, bufcount, Datatype buftype, buffered = False):
def _iput_var(self, ndarray data, bufcount, MPI.Datatype buftype, buffered = False):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down Expand Up @@ -2090,7 +2089,7 @@ cdef class Variable:
_check_err(ierr)
return request

def _iput_var1(self, value, index, bufcount, Datatype buftype, buffered=False):
def _iput_var1(self, value, index, bufcount, MPI.Datatype buftype, buffered=False):
cdef int ierr, ndims
cdef size_t *indexp
cdef MPI_Offset buffcount
Expand Down Expand Up @@ -2127,7 +2126,7 @@ cdef class Variable:
_check_err(ierr)
return request

def _iput_vara(self, start, count, ndarray data, bufcount, Datatype buftype, buffered=False):
def _iput_vara(self, start, count, ndarray data, bufcount, MPI.Datatype buftype, buffered=False):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down Expand Up @@ -2166,7 +2165,7 @@ cdef class Variable:
_check_err(ierr)
return request

def _iput_vars(self, start, count, stride, ndarray data, bufcount, Datatype buftype, buffered=False):
def _iput_vars(self, start, count, stride, ndarray data, bufcount, MPI.Datatype buftype, buffered=False):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down Expand Up @@ -2206,7 +2205,7 @@ cdef class Variable:
_check_err(ierr)
return request

def _iput_varn(self, ndarray data, num, starts, counts, bufcount, Datatype buftype, buffered=False):
def _iput_varn(self, ndarray data, num, starts, counts, bufcount, MPI.Datatype buftype, buffered=False):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down Expand Up @@ -2270,7 +2269,7 @@ cdef class Variable:
_check_err(ierr)
return request

def _iput_varm(self, ndarray data, start, count, stride, imap, bufcount, Datatype buftype, buffered=False):
def _iput_varm(self, ndarray data, start, count, stride, imap, bufcount, MPI.Datatype buftype, buffered=False):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down Expand Up @@ -2405,7 +2404,7 @@ cdef class Variable:
else:
raise ValueError("Invalid input arguments for iput_var")

def _iget_var(self, ndarray data, bufcount, Datatype buftype):
def _iget_var(self, ndarray data, bufcount, MPI.Datatype buftype):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand All @@ -2425,7 +2424,7 @@ cdef class Variable:
return request


def _iget_var1(self, ndarray buff, index, bufcount, Datatype buftype):
def _iget_var1(self, ndarray buff, index, bufcount, MPI.Datatype buftype):
cdef int ierr, ndims
cdef size_t *indexp
cdef MPI_Offset buffcount
Expand All @@ -2452,7 +2451,7 @@ cdef class Variable:
return request


def _iget_vara(self, ndarray data, start, count, bufcount, Datatype buftype):
def _iget_vara(self, ndarray data, start, count, bufcount, MPI.Datatype buftype):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down Expand Up @@ -2481,7 +2480,7 @@ cdef class Variable:
_check_err(ierr)
return request

def _iget_vars(self, ndarray buff, start, count, stride, bufcount, Datatype buftype):
def _iget_vars(self, ndarray buff, start, count, stride, bufcount, MPI.Datatype buftype):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down Expand Up @@ -2513,7 +2512,7 @@ cdef class Variable:
_check_err(ierr)
return request

def iget_varn(self, ndarray data, num, starts, counts=None, bufcount=None, Datatype buftype=None):
def iget_varn(self, ndarray data, num, starts, counts=None, bufcount=None, MPI.Datatype buftype=None):
"""
iget_varn(self, data, num, starts, counts=None, bufcount=None, buftype=None)

Expand Down Expand Up @@ -2585,7 +2584,7 @@ cdef class Variable:
_check_err(ierr)
return request

def _iget_varm(self, ndarray buff, start, count, stride, imap, bufcount, Datatype buftype):
def _iget_varm(self, ndarray buff, start, count, stride, imap, bufcount, MPI.Datatype buftype):
cdef int ierr, ndims
cdef MPI_Offset buffcount
cdef MPI_Datatype bufftype
Expand Down
22 changes: 11 additions & 11 deletions src/pnetcdf/_utils.pyx
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This should fix the OpenMPI compatibility issue. mpi4py.MPI are Python-level objects that safely wrap the underlying MPI_Datatype, regardless of whether it is an integer (as in MPICH) or a pointer (as in OpenMPI).

Original file line number Diff line number Diff line change
Expand Up @@ -44,17 +44,17 @@ _nptonctype = {'S1' : NC_CHAR_C,
'f4' : NC_FLOAT_C,
'f8' : NC_DOUBLE_C}

_nptompitype = {'S1' : MPI_CHAR,
'i1' : MPI_BYTE,
'u1' : MPI_UNSIGNED_CHAR,
'i2' : MPI_SHORT,
'u2' : MPI_UNSIGNED_SHORT,
'i4' : MPI_INT,
'u4' : MPI_UNSIGNED,
'i8' : MPI_LONG_LONG,
'u8' : MPI_UNSIGNED_LONG_LONG,
'f4' : MPI_FLOAT,
'f8' : MPI_DOUBLE}
_nptompitype = {'S1' : MPI.CHAR,
'i1' : MPI.BYTE,
'u1' : MPI.UNSIGNED_CHAR,
'i2' : MPI.SHORT,
'u2' : MPI.UNSIGNED_SHORT,
'i4' : MPI.INT,
'u4' : MPI.UNSIGNED,
'i8' : MPI.LONG_LONG,
'u8' : MPI.UNSIGNED_LONG_LONG,
'f4' : MPI.FLOAT,
'f8' : MPI.DOUBLE}


"""_nptompitype = {'S1' : MPI_CHAR,
Expand Down