Skip to content

Commit

Permalink
Merge pull request #1846 from glotzerlab/fix-illegal-instruction
Browse files Browse the repository at this point in the history 
Fix illegal instruction on osx-64 when returning 0 length arrays
  • Loading branch information
@joaander
joaander authored Jul 18, 2024
2 parents 1d850c8 + df6b84d commit 8e39db3
Show file tree
Hide file tree
Showing 4 changed files with 123 additions and 40 deletions.
21 changes: 18 additions & 3 deletions hoomd/BondedGroupData.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1418,7 +1418,12 @@ pybind11::object BondedGroupData<group_size, Group, name, has_type_mapping>::Sna
assert(has_type_mapping);
auto self_cpp
= self.cast<BondedGroupData<group_size, Group, name, has_type_mapping>::Snapshot*>();
return pybind11::array(self_cpp->type_id.size(), &self_cpp->type_id[0], self);

if (self_cpp->type_id.size() == 0)
{
return pybind11::array(pybind11::dtype::of<unsigned int>(), 0, nullptr);
}
return pybind11::array(self_cpp->type_id.size(), self_cpp->type_id.data(), self);
}

/*! \returns a numpy array that wraps the value data element.
Expand All @@ -1432,7 +1437,12 @@ pybind11::object BondedGroupData<group_size, Group, name, has_type_mapping>::Sna
assert(!has_type_mapping);
auto self_cpp
= self.cast<BondedGroupData<group_size, Group, name, has_type_mapping>::Snapshot*>();
return pybind11::array(self_cpp->val.size(), &self_cpp->val[0], self);

if (self_cpp->val.size() == 0)
{
return pybind11::array(pybind11::dtype::of<Scalar>(), 0, nullptr);
}
return pybind11::array(self_cpp->val.size(), self_cpp->val.data(), self);
}

/*! \returns a numpy array that wraps the groups data element.
Expand All @@ -1449,7 +1459,12 @@ BondedGroupData<group_size, Group, name, has_type_mapping>::Snapshot::getBondedT
std::vector<size_t> dims(2);
dims[0] = self_cpp->groups.size();
dims[1] = group_size;
return pybind11::array(dims, (unsigned int*)&self_cpp->groups[0], self);

if (dims[0] == 0)
{
return pybind11::array(pybind11::dtype::of<unsigned int>(), dims, nullptr);
}
return pybind11::array(dims, (unsigned int*)self_cpp->groups.data(), self);
}

/*! \returns A python list of type names
Expand Down
48 changes: 26 additions & 22 deletions hoomd/GSDReader.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -222,25 +222,25 @@ void GSDReader::readParticles()

// the snapshot already has default values, if a chunk is not found, the value
// is already at the default, and the failed read is not a problem
readChunk(&m_snapshot->particle_data.type[0], m_frame, "particles/typeid", N * 4, N);
readChunk(&m_snapshot->particle_data.mass[0], m_frame, "particles/mass", N * 4, N);
readChunk(&m_snapshot->particle_data.charge[0], m_frame, "particles/charge", N * 4, N);
readChunk(&m_snapshot->particle_data.diameter[0], m_frame, "particles/diameter", N * 4, N);
readChunk(&m_snapshot->particle_data.body[0], m_frame, "particles/body", N * 4, N);
readChunk(&m_snapshot->particle_data.inertia[0],
readChunk(m_snapshot->particle_data.type.data(), m_frame, "particles/typeid", N * 4, N);
readChunk(m_snapshot->particle_data.mass.data(), m_frame, "particles/mass", N * 4, N);
readChunk(m_snapshot->particle_data.charge.data(), m_frame, "particles/charge", N * 4, N);
readChunk(m_snapshot->particle_data.diameter.data(), m_frame, "particles/diameter", N * 4, N);
readChunk(m_snapshot->particle_data.body.data(), m_frame, "particles/body", N * 4, N);
readChunk(m_snapshot->particle_data.inertia.data(),
m_frame,
"particles/moment_inertia",
N * 12,
N);
readChunk(&m_snapshot->particle_data.pos[0], m_frame, "particles/position", N * 12, N);
readChunk(&m_snapshot->particle_data.orientation[0],
readChunk(m_snapshot->particle_data.pos.data(), m_frame, "particles/position", N * 12, N);
readChunk(m_snapshot->particle_data.orientation.data(),
m_frame,
"particles/orientation",
N * 16,
N);
readChunk(&m_snapshot->particle_data.vel[0], m_frame, "particles/velocity", N * 12, N);
readChunk(&m_snapshot->particle_data.angmom[0], m_frame, "particles/angmom", N * 16, N);
readChunk(&m_snapshot->particle_data.image[0], m_frame, "particles/image", N * 12, N);
readChunk(m_snapshot->particle_data.vel.data(), m_frame, "particles/velocity", N * 12, N);
readChunk(m_snapshot->particle_data.angmom.data(), m_frame, "particles/angmom", N * 16, N);
readChunk(m_snapshot->particle_data.image.data(), m_frame, "particles/image", N * 12, N);
}

/*! Read the same data chunks for topology
Expand All @@ -253,8 +253,8 @@ void GSDReader::readTopology()
if (N > 0)
{
m_snapshot->bond_data.resize(N);
readChunk(&m_snapshot->bond_data.type_id[0], m_frame, "bonds/typeid", N * 4, N);
readChunk(&m_snapshot->bond_data.groups[0], m_frame, "bonds/group", N * 8, N);
readChunk(m_snapshot->bond_data.type_id.data(), m_frame, "bonds/typeid", N * 4, N);
readChunk(m_snapshot->bond_data.groups.data(), m_frame, "bonds/group", N * 8, N);
}

N = 0;
Expand All @@ -263,8 +263,8 @@ void GSDReader::readTopology()
if (N > 0)
{
m_snapshot->angle_data.resize(N);
readChunk(&m_snapshot->angle_data.type_id[0], m_frame, "angles/typeid", N * 4, N);
readChunk(&m_snapshot->angle_data.groups[0], m_frame, "angles/group", N * 12, N);
readChunk(m_snapshot->angle_data.type_id.data(), m_frame, "angles/typeid", N * 4, N);
readChunk(m_snapshot->angle_data.groups.data(), m_frame, "angles/group", N * 12, N);
}

N = 0;
Expand All @@ -273,8 +273,8 @@ void GSDReader::readTopology()
if (N > 0)
{
m_snapshot->dihedral_data.resize(N);
readChunk(&m_snapshot->dihedral_data.type_id[0], m_frame, "dihedrals/typeid", N * 4, N);
readChunk(&m_snapshot->dihedral_data.groups[0], m_frame, "dihedrals/group", N * 16, N);
readChunk(m_snapshot->dihedral_data.type_id.data(), m_frame, "dihedrals/typeid", N * 4, N);
readChunk(m_snapshot->dihedral_data.groups.data(), m_frame, "dihedrals/group", N * 16, N);
}

N = 0;
Expand All @@ -283,8 +283,8 @@ void GSDReader::readTopology()
if (N > 0)
{
m_snapshot->improper_data.resize(N);
readChunk(&m_snapshot->improper_data.type_id[0], m_frame, "impropers/typeid", N * 4, N);
readChunk(&m_snapshot->improper_data.groups[0], m_frame, "impropers/group", N * 16, N);
readChunk(m_snapshot->improper_data.type_id.data(), m_frame, "impropers/typeid", N * 4, N);
readChunk(m_snapshot->improper_data.groups.data(), m_frame, "impropers/group", N * 16, N);
}

N = 0;
Expand All @@ -297,7 +297,11 @@ void GSDReader::readTopology()
for (unsigned int i = 0; i < N; i++)
m_snapshot->constraint_data.val[i] = Scalar(data[i]);

readChunk(&m_snapshot->constraint_data.groups[0], m_frame, "constraints/group", N * 8, N);
readChunk(m_snapshot->constraint_data.groups.data(),
m_frame,
"constraints/group",
N * 8,
N);
}

if (m_handle.header.schema_version >= gsd_make_version(1, 1))
Expand All @@ -308,8 +312,8 @@ void GSDReader::readTopology()
if (N > 0)
{
m_snapshot->pair_data.resize(N);
readChunk(&m_snapshot->pair_data.type_id[0], m_frame, "pairs/typeid", N * 4, N);
readChunk(&m_snapshot->pair_data.groups[0], m_frame, "pairs/group", N * 8, N);
readChunk(m_snapshot->pair_data.type_id.data(), m_frame, "pairs/typeid", N * 4, N);
readChunk(m_snapshot->pair_data.groups.data(), m_frame, "pairs/group", N * 8, N);
}
}
}
Expand Down
76 changes: 64 additions & 12 deletions hoomd/ParticleData.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3832,7 +3832,11 @@ template<class Real> pybind11::object SnapshotParticleData<Real>::getPosNP(pybin
std::vector<size_t> dims(2);
dims[0] = self_cpp->pos.size();
dims[1] = 3;
return pybind11::array(dims, (Real*)&self_cpp->pos[0], self);
if (dims[0] == 0)
{
return pybind11::array(pybind11::dtype::of<Real>(), dims, nullptr);
}
return pybind11::array(dims, (Real*)self_cpp->pos.data(), self);
}

/*! \returns a numpy array that wraps the pos data element.
Expand All @@ -3848,7 +3852,11 @@ template<class Real> pybind11::object SnapshotParticleData<Real>::getVelNP(pybin
std::vector<size_t> dims(2);
dims[0] = self_cpp->pos.size();
dims[1] = 3;
return pybind11::array(dims, (Real*)&self_cpp->vel[0], self);
if (dims[0] == 0)
{
return pybind11::array(pybind11::dtype::of<Real>(), dims, nullptr);
}
return pybind11::array(dims, (Real*)self_cpp->vel.data(), self);
}

/*! \returns a numpy array that wraps the pos data element.
Expand All @@ -3864,7 +3872,11 @@ template<class Real> pybind11::object SnapshotParticleData<Real>::getAccelNP(pyb
std::vector<size_t> dims(2);
dims[0] = self_cpp->pos.size();
dims[1] = 3;
return pybind11::array(dims, (Real*)&self_cpp->accel[0], self);
if (dims[0] == 0)
{
return pybind11::array(pybind11::dtype::of<Real>(), dims, nullptr);
}
return pybind11::array(dims, (Real*)self_cpp->accel.data(), self);
}

/*! \returns a numpy array that wraps the type data element.
Expand All @@ -3877,7 +3889,11 @@ template<class Real> pybind11::object SnapshotParticleData<Real>::getTypeNP(pybi
// mark as dirty when accessing internal data
self_cpp->is_accel_set = false;

return pybind11::array(self_cpp->type.size(), &self_cpp->type[0], self);
if (self_cpp->type.size() == 0)
{
return pybind11::array(pybind11::dtype::of<unsigned int>(), 0, nullptr);
}
return pybind11::array(self_cpp->type.size(), self_cpp->type.data(), self);
}

/*! \returns a numpy array that wraps the mass data element.
Expand All @@ -3890,7 +3906,11 @@ template<class Real> pybind11::object SnapshotParticleData<Real>::getMassNP(pybi
// mark as dirty when accessing internal data
self_cpp->is_accel_set = false;

return pybind11::array(self_cpp->mass.size(), &self_cpp->mass[0], self);
if (self_cpp->mass.size() == 0)
{
return pybind11::array(pybind11::dtype::of<Real>(), 0, nullptr);
}
return pybind11::array(self_cpp->mass.size(), self_cpp->mass.data(), self);
}

/*! \returns a numpy array that wraps the charge data element.
Expand All @@ -3903,7 +3923,11 @@ template<class Real> pybind11::object SnapshotParticleData<Real>::getChargeNP(py
// mark as dirty when accessing internal data
self_cpp->is_accel_set = false;

return pybind11::array(self_cpp->charge.size(), &self_cpp->charge[0], self);
if (self_cpp->charge.size() == 0)
{
return pybind11::array(pybind11::dtype::of<Real>(), 0, nullptr);
}
return pybind11::array(self_cpp->charge.size(), self_cpp->charge.data(), self);
}

/*! \returns a numpy array that wraps the diameter data element.
Expand All @@ -3917,7 +3941,11 @@ pybind11::object SnapshotParticleData<Real>::getDiameterNP(pybind11::object self
// mark as dirty when accessing internal data
self_cpp->is_accel_set = false;

return pybind11::array(self_cpp->diameter.size(), &self_cpp->diameter[0], self);
if (self_cpp->diameter.size() == 0)
{
return pybind11::array(pybind11::dtype::of<Real>(), 0, nullptr);
}
return pybind11::array(self_cpp->diameter.size(), self_cpp->diameter.data(), self);
}

/*! \returns a numpy array that wraps the image data element.
Expand All @@ -3933,7 +3961,12 @@ template<class Real> pybind11::object SnapshotParticleData<Real>::getImageNP(pyb
std::vector<size_t> dims(2);
dims[0] = self_cpp->pos.size();
dims[1] = 3;
return pybind11::array(dims, (int*)&self_cpp->image[0], self);

if (dims[0] == 0)
{
return pybind11::array(pybind11::dtype::of<int>(), dims, nullptr);
}
return pybind11::array(dims, (int*)self_cpp->image.data(), self);
}

/*! \returns a numpy array that wraps the body data element.
Expand All @@ -3946,7 +3979,11 @@ template<class Real> pybind11::object SnapshotParticleData<Real>::getBodyNP(pybi
// mark as dirty when accessing internal data
self_cpp->is_accel_set = false;

return pybind11::array(self_cpp->body.size(), (int*)&self_cpp->body[0], self);
if (self_cpp->body.size() == 0)
{
return pybind11::array(pybind11::dtype::of<Real>(), 0, nullptr);
}
return pybind11::array(self_cpp->body.size(), (int*)self_cpp->body.data(), self);
}

/*! \returns a numpy array that wraps the orientation data element.
Expand All @@ -3963,7 +4000,12 @@ pybind11::object SnapshotParticleData<Real>::getOrientationNP(pybind11::object s
std::vector<size_t> dims(2);
dims[0] = self_cpp->pos.size();
dims[1] = 4;
return pybind11::array(dims, (Real*)&self_cpp->orientation[0], self);

if (dims[0] == 0)
{
return pybind11::array(pybind11::dtype::of<Real>(), dims, nullptr);
}
return pybind11::array(dims, (Real*)self_cpp->orientation.data(), self);
}

/*! \returns a numpy array that wraps the moment of inertia data element.
Expand All @@ -3980,7 +4022,12 @@ pybind11::object SnapshotParticleData<Real>::getMomentInertiaNP(pybind11::object
std::vector<size_t> dims(2);
dims[0] = self_cpp->inertia.size();
dims[1] = 3;
return pybind11::array(dims, (Real*)&self_cpp->inertia[0], self);

if (dims[0] == 0)
{
return pybind11::array(pybind11::dtype::of<Real>(), dims, nullptr);
}
return pybind11::array(dims, (Real*)self_cpp->inertia.data(), self);
}

/*! \returns a numpy array that wraps the angular momentum data element.
Expand All @@ -3996,7 +4043,12 @@ template<class Real> pybind11::object SnapshotParticleData<Real>::getAngmomNP(py
std::vector<size_t> dims(2);
dims[0] = self_cpp->angmom.size();
dims[1] = 4;
return pybind11::array(dims, (Real*)&self_cpp->angmom[0], self);

if (dims[0] == 0)
{
return pybind11::array(pybind11::dtype::of<Real>(), dims, nullptr);
}
return pybind11::array(dims, (Real*)self_cpp->angmom.data(), self);
}

/*! \returns A python list of type names
Expand Down
18 changes: 15 additions & 3 deletions hoomd/mpcd/ParticleDataSnapshot.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -176,7 +176,11 @@ void export_ParticleDataSnapshot(pybind11::module& m)
std::vector<ssize_t> dims(2);
dims[0] = self_cpp->position.size();
dims[1] = 3;
return pybind11::array(dims, (Scalar*)&self_cpp->position[0], self);
if (dims[0] == 0)
{
return pybind11::array(pybind11::dtype::of<Scalar>(), dims, nullptr);
}
return pybind11::array(dims, (Scalar*)self_cpp->position.data(), self);
})
.def_property_readonly(
"velocity",
Expand All @@ -187,14 +191,22 @@ void export_ParticleDataSnapshot(pybind11::module& m)
std::vector<ssize_t> dims(2);
dims[0] = self_cpp->velocity.size();
dims[1] = 3;
return pybind11::array(dims, (Scalar*)&self_cpp->velocity[0], self);
if (dims[0] == 0)
{
return pybind11::array(pybind11::dtype::of<Scalar>(), dims, nullptr);
}
return pybind11::array(dims, (Scalar*)self_cpp->velocity.data(), self);
})
.def_property_readonly(
"typeid",
[](pybind11::object self)
{
auto self_cpp = self.cast<ParticleDataSnapshot*>();
return pybind11::array(self_cpp->type.size(), &self_cpp->type[0], self);
if (self_cpp->type.size() == 0)
{
return pybind11::array(pybind11::dtype::of<unsigned int>(), 0, nullptr);
}
return pybind11::array(self_cpp->type.size(), self_cpp->type.data(), self);
})
.def_readwrite("mass", &mpcd::ParticleDataSnapshot::mass)
.def_property(
Expand Down

0 comments on commit 8e39db3

Please sign in to comment.