def calcEField(mol, wfn, file='eField'):
points, X, Y, Z = generatePoints(mol)
culled = molCull(mol, X, Y, Z)
culledPoints_X = X[culled].flat
culledPoints_Y = Y[culled].flat
culledPoints_Z = Z[culled].flat
culledPoints = np.column_stack((culledPoints_X, culledPoints_Y, culledPoints_Z))
numThreads = psi4.get_num_threads()
lenThread = round(culledPoints.shape[0]/numThreads)
count = 0
pointsThreadList = []
for i in range(numThreads):
pointsThreadList += [culledPoints[count:count+lenThread]]
count += lenThread
if count < culledPoints.shape[0]:
pointsThreadList += [culledPoints[count:culledPoints.shape[0]-count]]
wfn.to_file('wfn')
results = Parallel(n_jobs=numThreads)(delayed(palFieldCompute)(i) for i in pointsThreadList)
for count, i in enumerate(results):
if count == 0:
field = i[0]
points = i[1]
else:
field = np.concatenate((field, i[0]))
points = np.concatenate((points, i[1]))
np.save(f'{file}-vecs', field)
np.save(f'{file}-points', points)
def test_threaded_blas(args):
threads = int(args.nthread)
times = {}
size = [200, 500, 2000, 4000]
threads = [1, threads]
for th in threads:
psi4.set_num_threads(th)
for sz in size:
nruns = max(1, int(1.e10 / (sz**3)))
a = psi4.core.Matrix(sz, sz)
b = psi4.core.Matrix(sz, sz)
c = psi4.core.Matrix(sz, sz)
tp4 = time.time()
for n in range(nruns):
c.gemm(False, False, 1.0, a, b, 0.0)
retp4 = (time.time() - tp4) / nruns
tnp = time.time()
for n in range(nruns):
np.dot(a, b, out=np.asarray(c))
retnp = (time.time() - tnp) / nruns
print(
"Time for threads %2d, size %5d: Psi4: %12.6f NumPy: %12.6f" %
(th, sz, retp4, retnp))
if sz == 4000:
times["p4-n{}".format(th)] = retp4
times["np-n{}".format(th)] = retnp
assert psi4.get_num_threads() == th
rat1 = times["np-n" + str(threads[-1])] / times["p4-n" + str(threads[-1])]
rat2 = times["p4-n" + str(threads[0])] / times["p4-n" + str(threads[-1])]
print(" NumPy@n%d : Psi4@n%d ratio (want ~1): %.2f" %
(threads[-1], threads[-1], rat1))
print(" Psi4@n%d : Psi4@n%d ratio (want ~%d): %.2f" %
(threads[0], threads[-1], threads[-1], rat2))
if args.passfail:
assert math.isclose(
rat1, 1.0,
rel_tol=0.2), 'PsiAPI:NumPy speedup {} !~= 1.0'.format(rat1)
assert math.isclose(rat2, threads[-1],
rel_tol=0.4), 'PsiAPI speedup {} !~= {}'.format(
rat2, threads[-1])
def disabled_test_threaded_blas():
threads = multiprocessing.cpu_count()
threads = int(threads / 2)
times = {}
size = [200, 500, 2000, 5000]
threads = [1, threads]
for th in threads:
psi4.set_num_threads(th)
for sz in size:
nruns = max(1, int(1.e10 / (sz**3)))
a = psi4.core.Matrix(sz, sz)
b = psi4.core.Matrix(sz, sz)
c = psi4.core.Matrix(sz, sz)
tp4 = time.time()
for n in range(nruns):
c.gemm(False, False, 1.0, a, b, 0.0)
retp4 = (time.time() - tp4) / nruns
tnp = time.time()
for n in range(nruns):
np.dot(a, b, out=np.asarray(c))
retnp = (time.time() - tnp) / nruns
print(
"Time for threads %2d, size %5d: Psi4: %12.6f NumPy: %12.6f" %
(th, sz, retp4, retnp))
if sz == 5000:
times["p4-n{}".format(th)] = retp4
times["np-n{}".format(th)] = retnp
assert psi4.get_num_threads() == th
rat1 = times["np-n" + str(threads[-1])] / times["p4-n" + str(threads[-1])]
rat2 = times["p4-n" + str(threads[0])] / times["p4-n" + str(threads[-1])]
print(" NumPy@n%d : Psi4@n%d ratio (want ~1): %.2f" %
(threads[-1], threads[-1], rat1))
print(" Psi4@n%d : Psi4@n%d ratio (want ~%d): %.2f" %
(threads[0], threads[-1], threads[-1], rat2))
assert pytest.approx(rat1, 0.2) == 1.0
assert pytest.approx(rat2, 0.8) == threads[-1]
def test_threaded_blas(args):
threads = int(args.nthread)
times = {}
size = [200, 500, 2000, 4000]
threads = [1, threads]
for th in threads:
psi4.set_num_threads(th)
for sz in size:
nruns = max(1, int(1.e10 / (sz ** 3)))
a = psi4.core.Matrix(sz, sz)
b = psi4.core.Matrix(sz, sz)
c = psi4.core.Matrix(sz, sz)
tp4 = time.time()
for n in range(nruns):
c.gemm(False, False, 1.0, a, b, 0.0)
retp4 = (time.time() - tp4) / nruns
tnp = time.time()
for n in range(nruns):
np.dot(a, b, out=np.asarray(c))
retnp = (time.time() - tnp) / nruns
print("Time for threads %2d, size %5d: Psi4: %12.6f NumPy: %12.6f" % (th, sz, retp4, retnp))
if sz == 4000:
times["p4-n{}".format(th)] = retp4
times["np-n{}".format(th)] = retnp
assert psi4.get_num_threads() == th
rat1 = times["np-n" + str(threads[-1])] / times["p4-n" + str(threads[-1])]
rat2 = times["p4-n" + str(threads[0])] / times["p4-n" + str(threads[-1])]
print(" NumPy@n%d : Psi4@n%d ratio (want ~1): %.2f" % (threads[-1], threads[-1], rat1))
print(" Psi4@n%d : Psi4@n%d ratio (want ~%d): %.2f" % (threads[0], threads[-1], threads[-1], rat2))
if args.passfail:
assert math.isclose(rat1, 1.0, rel_tol=0.2), 'PsiAPI:NumPy speedup {} !~= 1.0'.format(rat1)
assert math.isclose(rat2, threads[-1], rel_tol=0.4), 'PsiAPI speedup {} !~= {}'.format(rat2, threads[-1])
def disabled_test_threaded_blas():
threads = multiprocessing.cpu_count()
threads = int(threads / 2)
times = {}
size = [200, 500, 2000, 5000]
threads = [1, threads]
for th in threads:
psi4.set_num_threads(th)
for sz in size:
nruns = max(1, int(1.e10 / (sz ** 3)))
a = psi4.core.Matrix(sz, sz)
b = psi4.core.Matrix(sz, sz)
c = psi4.core.Matrix(sz, sz)
tp4 = time.time()
for n in range(nruns):
c.gemm(False, False, 1.0, a, b, 0.0)
retp4 = (time.time() - tp4) / nruns
tnp = time.time()
for n in range(nruns):
np.dot(a, b, out=np.asarray(c))
retnp = (time.time() - tnp) / nruns
print("Time for threads %2d, size %5d: Psi4: %12.6f NumPy: %12.6f" % (th, sz, retp4, retnp))
if sz == 5000:
times["p4-n{}".format(th)] = retp4
times["np-n{}".format(th)] = retnp
assert psi4.get_num_threads() == th
rat1 = times["np-n" + str(threads[-1])] / times["p4-n" + str(threads[-1])]
rat2 = times["p4-n" + str(threads[0])] / times["p4-n" + str(threads[-1])]
print(" NumPy@n%d : Psi4@n%d ratio (want ~1): %.2f" % (threads[-1], threads[-1], rat1))
print(" Psi4@n%d : Psi4@n%d ratio (want ~%d): %.2f" % (threads[0], threads[-1], threads[-1], rat2))
assert pytest.approx(rat1, 0.2) == 1.0
assert pytest.approx(rat2, 0.8) == threads[-1]
