def check_dot(gatype):
if 0 == me:
print '> Checking dot ...',
np.random.seed(12345) # everyone has same seed
g_a = create_global_array(gatype)
g_b = create_global_array(gatype)
a = create_local_a(gatype)
b = np.random.random_sample((n,n))
if MIRROR:
if 0 == iproc:
ga.put(g_b, b)
ga.put(g_a, a)
else:
if 0 == me:
ga.put(g_b, b)
ga.put(g_a, a)
ga.sync()
sum1 = np.sum(a*b)
sum2 = ga.dot(g_a, g_b)
if mismatch(sum1, sum2):
ga.error('dot wrong %s != %s' % (sum1, sum2))
if 0 == me:
print 'OK'
ga.destroy(g_a)
ga.destroy(g_b)
def check_scatter(gatype):
nptype = ga.dtype(gatype)
if 0 == me:
print '> Checking scatter (might be slow)...',
g_a = create_global_array(gatype)
a = create_local_a(gatype)
if 0 == me:
ga.put(g_a, a)
ga.sync()
ijv = np.zeros((m,2), dtype=np.int64)
v = np.zeros(m, dtype=nptype)
random.seed(ga.nodeid()*51 + 1) # different seed for each proc
for j in range(10):
check = None
if MIRROR:
check = random.randint(0,lprocs-1) == iproc
else:
check = random.randint(0,nproc-1) == me
if check:
for loop in range(m):
ijv[loop,:] = (random.randint(0,n-1),random.randint(0,n-1))
v[loop] = ijv[loop,0]+ijv[loop,1]
ga.scatter(g_a, v, ijv)
for loop in range(m):
value = ga.get(g_a, ijv[loop], ijv[loop]+1).flatten()
if not v[loop] == value:
ga.error('scatter failed')
if 0 == me:
print 'OK'
ga.destroy(g_a)
def check_gather(gatype):
if 0 == me:
print '> Checking gather (might be slow)...',
g_a = create_global_array(gatype)
a = create_local_a(gatype)
if 0 == me:
ga.put(g_a, a)
ga.sync()
ijv = np.zeros((m,2), dtype=np.int64)
random.seed(ga.nodeid()*51 + 1) # different seed for each proc
for j in range(10):
itmp = None
if MIRROR:
itmp = random.randint(0,lprocs-1)
else:
itmp = random.randint(0,nproc-1)
if itmp == me:
for loop in range(m):
ijv[loop,:] = (random.randint(0,n-1),random.randint(0,n-1))
#if ijv[loop,0] > ijv[loop,1]:
# ijv[loop,:] = ijv[loop,::-1] # reverse
result = ga.gather(g_a, ijv)
for loop in range(m):
value = ga.get(g_a, ijv[loop], ijv[loop]+1).flatten()
if not result[loop] == value:
ga.error('gather failed')
if 0 == me:
print 'OK'
ga.destroy(g_a)
def check_get(gatype):
"""check nloop random gets from each node"""
if 0 == me:
print '> Checking random get (%d calls)...' % nloop
g_a = create_global_array(gatype)
a = create_local_a(gatype)
if 0 == me:
ga.put(g_a, a)
ga.sync()
nwords = 0
random.seed(ga.nodeid()*51+1) # different seed for each proc
for loop in range(nloop):
ilo,ihi = random.randint(0, nloop-1),random.randint(0, nloop-1)
if ihi < ilo: ilo,ihi = ihi,ilo
jlo,jhi = random.randint(0, nloop-1),random.randint(0, nloop-1)
if jhi < jlo: jlo,jhi = jhi,jlo
nwords += (ihi-ilo+1)*(jhi-jlo+1)
ihi += 1
jhi += 1
result = ga.get(g_a, (ilo,jlo), (ihi,jhi))
if not np.all(result == a[ilo:ihi,jlo:jhi]):
ga.error('random get failed')
if 0 == me and loop % max(1,nloop/20) == 0:
print ' call %d node %d checking get((%d,%d),(%d,%d)) total %f' % (
loop, me, ilo, ihi, jlo, jhi, nwords)
if 0 == me:
print 'OK'
ga.destroy(g_a)
def check_put_disjoint(gatype):
"""each node fills in disjoint sections of the array"""
if 0 == me:
print '> Checking disjoint put ...',
g_a = create_global_array(gatype)
a = create_local_a(gatype)
inc = (n-1)/20 + 1
ij = 0
for i in range(0,n,inc):
for j in range(0,n,inc):
check = False
if MIRROR:
check = ij % lprocs == iproc
else:
check = ij % nproc == me
if check:
lo = [i,j]
hi = [min(i+inc,n), min(j+inc,n)]
piece = a[ga.zip(lo,hi)]
ga.put(g_a, piece, lo, hi)
# the following check is not part of the original test.F
result = ga.get(g_a, lo, hi)
if not np.all(result == piece):
ga.error("put followed by get failed", 1)
ga.sync()
ij += 1
ga.sync()
# all nodes check all of a
b = ga.get(g_a)
if not np.all(a == b):
ga.error('put failed, exiting')
if 0 == me:
print 'OK'
ga.destroy(g_a)
def check_print_patch(gatype):
g_a = create_global_array(gatype)
a = create_local_a(gatype)
if n > 7:
if 0 == me:
print '> Checking ga.print_patch --- should match'
print a[2:5,2:7]
ga.print_patch(g_a, (2,2), (5,7))
ga.destroy(g_a)
def check_zero(gatype):
if 0 == me:
print '> Checking zero ...',
g_a = create_global_array(gatype)
ga.zero(g_a)
a = ga.get(g_a)
if not np.all(a == 0):
ga.error('ga.zero failed')
if 0 == me:
print 'OK'
ga.destroy(g_a)
def verify_using_ga(g_a, g_b, g_c):
g_v = ga.duplicate(g_c)
ga.gemm(False,False,N,N,N,1,g_a,g_b,0,g_v)
c = ga.access(g_c)
v = ga.access(g_v)
if c is not None:
val = int(np.abs(np.sum(c-v))>0.0001)
else:
val = 0
val = ga.gop_add(val)
ga.destroy(g_v)
return val == 0
def verify_using_ga(g_a, g_b, g_c):
g_v = ga.duplicate(g_c)
ga.gemm(False, False, N, N, N, 1, g_a, g_b, 0, g_v)
c = ga.access(g_c)
v = ga.access(g_v)
if c is not None:
val = int(np.abs(np.sum(c - v)) > 0.0001)
else:
val = 0
val = ga.gop_add(val)
ga.destroy(g_v)
return val == 0
def check_copy(gatype):
if 0 == me:
print '> Checking copy ...',
g_a = create_global_array(gatype)
g_b = create_global_array(gatype)
a = create_local_a(gatype)
if 0 == me:
ga.put(g_a, a)
ga.copy(g_a, g_b)
if not np.all(a == ga.get(g_b)):
ga.error('copy failed')
if 0 == me:
print 'OK'
ga.destroy(g_a)
ga.destroy(g_b)
def check_scale(gatype):
if 0 == me:
print '> Checking scale ...',
g_a = create_global_array(gatype)
a = create_local_a(gatype)
if 0 == me:
ga.put(g_a, a)
ga.sync()
ga.scale(g_a, 0.123)
a *= 0.123
if np.any(np.vectorize(mismatch)(a,ga.get(g_a))):
ga.error('add failed')
if 0 == me:
print 'OK'
ga.destroy(g_a)
def TRANSPOSE1D():
# Configure array dimensions. Force an unequal data distribution.
dims = [nprocs*TOTALELEMS + nprocs/2]
chunk = [TOTALELEMS] # minimum data on each process
# create a global array g_a and duplicate it to get g_b
g_a = ga.create(ga.C_INT, dims, "array A", chunk)
if not g_a: ga.error("create failed: A")
if not me: print "Created Array A"
g_b = ga.duplicate(g_a, "array B")
if not g_b: ga.error("duplicate failed")
if not me: print "Created Array B"
# initialize data in g_a
if not me:
print "Initializing matrix A"
ga.put(g_a, np.arange(dims[0], dtype=np.int32))
# Synchronize all processors to guarantee that everyone has data
# before proceeding to the next step.
ga.sync()
# Start initial phase of inversion by inverting the data held locally on
# each processor. Start by finding out which data each processor owns.
lo,hi = ga.distribution(g_a)
# Get locally held data and copy it into local buffer a
a = ga.get(g_a, lo, hi)
# Invert data locally
b = a[::-1]
# Invert data globally by copying locally inverted blocks into
# their inverted positions in the GA
ga.put(g_b, b, dims[0]-hi[0], dims[0]-lo[0])
# Synchronize all processors to make sure inversion is complete
ga.sync()
# Check to see if inversion is correct
if not me: verify(g_a, g_b)
# Deallocate arrays
ga.destroy(g_a)
ga.destroy(g_b)
def TRANSPOSE1D():
# Configure array dimensions. Force an unequal data distribution.
dims = [nprocs * TOTALELEMS + nprocs / 2]
chunk = [TOTALELEMS] # minimum data on each process
# create a global array g_a and duplicate it to get g_b
g_a = ga.create(ga.C_INT, dims, "array A", chunk)
if not g_a: ga.error("create failed: A")
if not me: print "Created Array A"
g_b = ga.duplicate(g_a, "array B")
if not g_b: ga.error("duplicate failed")
if not me: print "Created Array B"
# initialize data in g_a
if not me:
print "Initializing matrix A"
ga.put(g_a, np.arange(dims[0], dtype=np.int32))
# Synchronize all processors to guarantee that everyone has data
# before proceeding to the next step.
ga.sync()
# Start initial phase of inversion by inverting the data held locally on
# each processor. Start by finding out which data each processor owns.
lo, hi = ga.distribution(g_a)
# Get locally held data and copy it into local buffer a
a = ga.get(g_a, lo, hi)
# Invert data locally
b = a[::-1]
# Invert data globally by copying locally inverted blocks into
# their inverted positions in the GA
ga.put(g_b, b, dims[0] - hi[0], dims[0] - lo[0])
# Synchronize all processors to make sure inversion is complete
ga.sync()
# Check to see if inversion is correct
if not me: verify(g_a, g_b)
# Deallocate arrays
ga.destroy(g_a)
ga.destroy(g_b)
def verify(g_a, g_b, g_c):
g_chk = ga.duplicate(g_a, "array check")
if not g_chk: ga.error("duplicate failed")
ga.sync()
ga.gemm(False, False, TOTALELEMS, TOTALELEMS, TOTALELEMS, 1.0, g_a, g_b,
0.0, g_chk);
ga.sync()
ga.add(g_c, g_chk, g_chk, 1.0, -1.0)
rchk = ga.dot(g_chk, g_chk)
if not me:
print "Normed difference in matrices: %12.4f" % rchk
if not (-TOLERANCE < rchk < TOLERANCE):
ga.error("Matrix multiply verify failed")
else:
print "Matrix Multiply OK"
ga.destroy(g_chk)
def check_add(gatype):
if 0 == me:
print '> Checking add ...',
g_a = create_global_array(gatype)
g_b = create_global_array(gatype)
a = create_local_a(gatype)
b = create_local_b(gatype)
alpha = None
beta = None
if 0 == me:
ga.put(g_a, a)
ga.sync();
np.random.seed(12345) # everyone has same seed
if gatype in [ga.C_SCPL,ga.C_DCPL]:
b_real = np.random.random_sample((n,n))
b_imag = np.random.random_sample((n,n))
b[:] = np.vectorize(complex)(b_real,b_imag)
alpha = complex(0.1,-0.1)
beta = complex(0.9,-0.9)
else:
b[:] = np.random.random_sample((n,n))
alpha = 0.1
beta = 0.9
a = alpha*a + beta*b
if MIRROR:
if 0 == iproc:
ga.put(g_b, b)
else:
if 0 == me:
ga.put(g_b, b)
ga.sync()
ga.add(g_a, g_b, g_b, alpha, beta)
b = ga.get(g_b, buffer=b)
if np.any(np.vectorize(mismatch)(b,a)):
ga.error('add failed')
if 0 == me:
print 'OK'
ga.destroy(g_a)
ga.destroy(g_b)
def check_accumulate_overlap(gatype):
if 0 == me:
print '> Checking overlapping accumulate ...',
g_a = create_global_array(gatype)
ga.zero(g_a)
ga.acc(g_a, [1], (n/2,n/2), (n/2+1,n/2+1), 1)
ga.sync()
if MIRROR:
if 0 == iproc:
x = abs(ga.get(g_a, (n/2,n/2), (n/2+1,n/2+1))[0,0] - lprocs)
if not 0 == x:
ga.error('overlapping accumulate failed -- expected %s got %s'%(
x, lprocs))
else:
if 0 == me:
x = abs(ga.get(g_a, (n/2,n/2), (n/2+1,n/2+1))[0,0] - nproc)
if not 0 == x:
ga.error('overlapping accumulate failed -- expected %s got %s'%(
x, nproc))
if 0 == me:
print 'OK'
ga.destroy(g_a)
def check_accumulate_disjoint(gatype):
"""Each node accumulates into disjoint sections of the array."""
if 0 == me:
print '> Checking disjoint accumulate ...',
g_a = create_global_array(gatype)
a = create_local_a(gatype)
b = np.fromfunction(lambda i,j: i+j+2, (n,n), dtype=ga.dtype(gatype))
if 0 == me:
ga.put(g_a, a)
ga.sync()
inc = (n-1)/20 + 1
ij = 0
for i in range(0,n,inc):
for j in range(0,n,inc):
x = 10.0
lo = [i,j]
hi = [min(i+inc,n), min(j+inc,n)]
piece = b[ga.zip(lo,hi)]
check = False
if MIRROR:
check = ij % lprocs == iproc
else:
check = ij % nproc == me
if check:
ga.acc(g_a, piece, lo, hi, x)
ga.sync()
ij += 1
# each process applies all updates to its local copy
a[ga.zip(lo,hi)] += x * piece
ga.sync()
# all nodes check all of a
if not np.all(ga.get(g_a) == a):
ga.error('acc failed')
if 0 == me:
print 'OK'
ga.destroy(g_a)
def matrix_multiply():
# Configure array dimensions. Force an unequal data distribution.
dims = [TOTALELEMS]*NDIM
chunk = [TOTALELEMS/nprocs-1]*NDIM
# Create a global array g_a and duplicate it to get g_b and g_c.
g_a = ga.create(ga.C_DBL, dims, "array A", chunk)
if not g_a: ga.error("create failed: A")
if not me: print "Created Array A"
g_b = ga.duplicate(g_a, "array B")
g_c = ga.duplicate(g_a, "array C")
if not g_b or not g_c: ga.eror("duplicate failed")
if not me: print "Created Arrays B and C"
# Initialize data in matrices a and b.
if not me: print "Initializing matrix A and B"
a = np.random.rand(*dims)*29
b = np.random.rand(*dims)*37
# Copy data to global arrays g_a and g_b.
if not me:
ga.put(g_a, a)
ga.put(g_b, b)
# Synchronize all processors to make sure everyone has data.
ga.sync()
# Determine which block of data is locally owned. Note that
# the same block is locally owned for all GAs.
lo,hi = ga.distribution(g_c)
# Get the blocks from g_a and g_b needed to compute this block in
# g_c and copy them into the local buffers a and b.
a = ga.get(g_a, (lo[0],0), (hi[0],dims[0]))
b = ga.get(g_b, (0,lo[1]), (dims[1],hi[1]))
# Do local matrix multiplication and store the result in local
# buffer c. Start by evaluating the transpose of b.
btrns = b.transpose()
# Multiply a and b to get c.
c = np.dot(a,b)
# Copy c back to g_c.
ga.put(g_c, c, lo, hi)
verify(g_a, g_b, g_c)
# Deallocate arrays.
ga.destroy(g_a)
ga.destroy(g_b)
ga.destroy(g_c)
# put some fake data into input arrays A and B
if me == 0:
ga.put(g_a, np.random.random(N*N))
ga.put(g_b, np.random.random(N*N))
ga.sync()
if me == 0:
print "srumma...",
srumma(g_a, g_b, g_c, CHUNK_SIZE, MULTIPLIER, g_counter)
if me == 0:
print "done"
if me == 0:
print "verifying using ga.gemm...",
ok = verify_using_ga(g_a, g_b, g_c)
if me == 0:
if ok:
print "OKAY"
else:
print "FAILED"
if me == 0:
print "verifying using np.dot...",
ok = verify_using_np(g_a, g_b, g_c)
if me == 0:
if ok:
print "OKAY"
else:
print "FAILED"
ga.destroy(g_a)
ga.destroy(g_b)
ga.destroy(g_c)
ga.destroy(g_counter)
nprocs = ga.nnodes()
myrank = ga.nodeid()
g_pi = ga.create(ga.C_DBL, [1])
one_time = False
if len(sys.argv) == 2:
n = int(sys.argv[1])
one_time = True
while True:
if not one_time:
if myrank == 0:
n = get_n()
n = ga.brdcst(n)
else:
n = ga.brdcst(0)
if n == 0:
break
ga.zero(g_pi)
mypi = comp_pi(n, myrank, nprocs)
ga.acc(g_pi, mypi)
ga.sync()
if myrank == 0:
pi = ga.get(g_pi)[0]
prn_pi(pi, PI)
if one_time:
break
ga.destroy(g_pi)
g_c = ga.create(ga.C_DBL, [N,N])
# put some fake data into input arrays A and B
if me == 0:
ga.put(g_a, np.random.random(N*N))
ga.put(g_b, np.random.random(N*N))
ga.sync()
if me == 0:
print "srumma...",
srumma(g_a, g_b, g_c, CHUNK_SIZE, MULTIPLIER)
if me == 0:
print "done"
if me == 0:
print "verifying using ga.gemm...",
ok = verify_using_ga(g_a, g_b, g_c)
if me == 0:
if ok:
print "OKAY"
else:
print "FAILED"
if me == 0:
print "verifying using np.dot...",
ok = verify_using_np(g_a, g_b, g_c)
if me == 0:
if ok:
print "OKAY"
else:
print "FAILED"
ga.destroy(g_a)
ga.destroy(g_b)
ga.destroy(g_c)
nprocs = ga.nnodes()
myrank = ga.nodeid()
g_pi = ga.create(ga.C_DBL, [1])
one_time = False
if len(sys.argv) == 2:
n = int(sys.argv[1])
one_time = True
while True:
if not one_time:
if myrank == 0:
n = get_n()
n = ga.brdcst(n)
else:
n = ga.brdcst(0)
if n == 0:
break
ga.zero(g_pi)
mypi = comp_pi(n, myrank, nprocs)
ga.acc(g_pi, mypi)
ga.sync()
if myrank == 0:
pi = ga.get(g_pi)[0]
prn_pi(pi, PI)
if one_time:
break
ga.destroy(g_pi)
data = None
comm.Gather(np.array(out[1:], dtype=float), data, root=0)
start7 = time.time()
if rank == 0 and int(j) == 1:
res = os.path.abspath(
os.path.normpath(os.path.join(os.getcwd(),
'RMSD_{}.csv'.format(size))))
np.save(res, buf)
os.remove('files/newtraj_{}_{}.xtc'.format(rank, j))
os.remove('files/.newtraj_{}_{}.xtc_offsets.npz'.format(rank, j))
ga.destroy(g_a)
# Cost Calculation
init_time = start2 - start1
comm_time1 = start3 - start2
comm_time2 = start5 - start4
comm_time3 = start7 - start6
comp_time = start4 - start3
access_time = start6 - start5
tot_time = comp_time + comm_time2 + access_time
tot_time = comm.gather(tot_time, root=0)
init_time = comm.gather(init_time, root=0)
comm_time1 = comm.gather(comm_time1, root=0)
comm_time2 = comm.gather(comm_time2, root=0)
comm_time3 = comm.gather(comm_time3, root=0)
g_c = ga.create(ga.C_DBL, [N, N])
# put some fake data into input arrays A and B
if me == 0:
ga.put(g_a, np.random.random(N * N))
ga.put(g_b, np.random.random(N * N))
ga.sync()
if me == 0:
print "srumma...",
srumma(g_a, g_b, g_c, CHUNK_SIZE, MULTIPLIER)
if me == 0:
print "done"
if me == 0:
print "verifying using ga.gemm...",
ok = verify_using_ga(g_a, g_b, g_c)
if me == 0:
if ok:
print "OKAY"
else:
print "FAILED"
if me == 0:
print "verifying using np.dot...",
ok = verify_using_np(g_a, g_b, g_c)
if me == 0:
if ok:
print "OKAY"
else:
print "FAILED"
ga.destroy(g_a)
ga.destroy(g_b)
ga.destroy(g_c)
# put some fake data into input arrays A and B
if me == 0:
ga.put(g_a, np.random.random(N * N))
ga.put(g_b, np.random.random(N * N))
ga.sync()
if me == 0:
print "srumma...",
srumma(g_a, g_b, g_c, CHUNK_SIZE, MULTIPLIER, g_counter)
if me == 0:
print "done"
if me == 0:
print "verifying using ga.gemm...",
ok = verify_using_ga(g_a, g_b, g_c)
if me == 0:
if ok:
print "OKAY"
else:
print "FAILED"
if me == 0:
print "verifying using np.dot...",
ok = verify_using_np(g_a, g_b, g_c)
if me == 0:
if ok:
print "OKAY"
else:
print "FAILED"
ga.destroy(g_a)
ga.destroy(g_b)
ga.destroy(g_c)
ga.destroy(g_counter)
