def test_xyzhash_cl2():
xh = xyzHash("../dat/psi.xyzHash")
with open("xyzHash.cl") as o: KERN = o.read()
ctx,queue = clutil.my_get_gpu_context()
nxyz,xsize,ysize,zsize,grid_size = xh.num_point,xh.xsize,xh.ysize,xh.zsize,xh.grid_size
prg = pyopencl.Program(ctx,KERN%vars())
prg.build("-I/Users/sheffler/project/protoprot/ligh2t/lib "+clutil.MATHOPTS)
knl = prg.test_xyzhash
NL,NG = 64,12
out = pyopencl.array.empty(queue, (1,), dtype=numpy.int32); out.fill(0)
clpts = xh.get_coord_clarray(queue)
clgrid = xh.get_grid_clarray(queue)
kargs = (clpts.data,clgrid.data,out.data)
t = time.time()
knl(queue, (NL,NG), (NL,1) , *kargs ).wait()
print (time.time()-t)
print 64*NL*NG
print 53949
print out
def test():
ctx, queue = clutil.my_get_gpu_context()
LS, GS = 64, int(sys.argv[2])
NITER, NGPUITER = int(sys.argv[4]), int(sys.argv[3])
lh, lp = 27, 27
NC = "n"
temperature = 15.0
nstat = 7
# allocate
ranlux = pyopencl.array.empty(queue, (112 * GS,), dtype=numpy.int8)
ranlux.fill(17)
out = pyopencl.array.empty(queue, (3 * 3 * (100) * GS,), dtype=numpy.float32)
out.fill(0)
xout = pyopencl.array.empty(queue, (12 * 3 * GS,), dtype=numpy.float32)
xout.fill(0)
rout = pyopencl.array.empty(queue, (GS,), dtype=numpy.float32)
rout.fill(0)
vout = pyopencl.array.empty(queue, (GS, 6), dtype=numpy.float32)
vout.fill(0)
status = pyopencl.array.empty(queue, (GS, 2), dtype=numpy.int32)
status.fill(0)
seed = pyopencl.array.empty(queue, (1,), dtype=numpy.uint32)
seed.fill(0)
stat = pyopencl.array.empty(queue, (GS, nstat), dtype=numpy.int32)
stat.fill(0)
fstat = pyopencl.array.empty(queue, (GS, nstat), dtype=numpy.float32)
fstat.fill(0)
hist = pyopencl.array.empty(queue, (300,), dtype=numpy.uint32)
hist.fill(0)
hist6 = pyopencl.array.empty(queue, (9, 20, 23, 11, 24, 12), dtype=numpy.uint32)
hist6.fill(0)
# for temperature in (5,10,9999999999):
NC = "c"
for lp in (10, 20, 30, 40, 50):
# for temperature in [2**x for x in range(6)]+[9e9]:
for lh in (10, 20, 30, 40, 50):
NOUT = NITER * NGPUITER * GS
# if len(glob.glob("../test/hist6_bind_%i_%i_%s_%i_%i_*.dat"%(lh,lp,NC,temperature,NOUT))) > 3: continue
# for temperature in (15,):
# print temperature
# inputs
components = ("psi hyd pet ld%s len" % NC).split()
hyd_stub = get_stub(components, "hyd")
pet_stub = get_stub(components, "pet")
PSI_ET = "vec(52.126627, 53.095875, 23.992003)"
PET_ET = "vec( 5.468269, 20.041713, 11.962524)"
HYD_ET = "vec(11.842096, 39.050866, 19.269006)"
hashes = [xyzHash("../dat/%s.xyzHash" % n) for n in components]
coords = [h.get_coord_clarray(queue) for h in hashes]
grids = [h.get_grid_clarray(queue) for h in hashes]
nxpsi, nypsi, nzpsi = hashes[0].xsize, hashes[0].ysize, hashes[0].zsize
nxhyd, nyhyd, nzhyd = hashes[1].xsize, hashes[1].ysize, hashes[1].zsize
nxpet, nypet, nzpet = hashes[2].xsize, hashes[2].ysize, hashes[2].zsize
grid_size = 5.0
data = [d for d in reduce(operator.add, zip(coords, grids)) if d]
npsi, nhyd, npet = (data[i].size / 3 for i in (0, 2, 4))
nlkh, nlkp = lh * 3, lp * 3
ntot = nlkh + nlkp # npsi+nhyd+npet+nlkh+nlkp
out.fill(0)
xout.fill(0)
rout.fill(0)
vout.fill(0)
status.fill(0)
seed.fill(0)
stat.fill(0)
fstat.fill(0)
hist.fill(0)
hist6.fill(0)
kargs = [x.data for x in data + [ranlux, seed, out, xout, rout, vout, status, stat, fstat, hist, hist6]]
my_test_kernel = pyopencl.Program(ctx, KERN % vars()).build(OPTS).my_test_kernel
# os.system("rm -f ../test/*.pdb")
seed.fill(random.getrandbits(31))
t = time.time()
for ITER in range(1, NITER + 1):
my_test_kernel(queue, (LS, GS), (LS, 1), *kargs).wait()
# print lh,lp,NC,ITER,"COMPUTE RATE:",ITER*NGPUITER*GS/(time.time()-t)/1000.0
# for i in range(GS):
# #if stat.get()[i,1] == 0: continue
# if not ITER in vars(): ITER = 0
# ary = out.get()
# fn = "../test/test_%i_%i_%i.pdb"%(i,lh,lp)
# dump_pdb(ary[i*len(ary)/GS:(i+1)*len(ary)/GS],"../test/.tmp")
# os.system("echo MODEL %i >> %s"%(ITER,fn))
# os.system("cat ../test/.tmp >> "+fn)
# xform_pdb(nparray_to_XFORMs(xout.get())[3*i+0],"../pdb/hyda1_hash_bb.pdb","../test/.tmp")
# os.system("cat ../test/.tmp >> "+fn)
# xform_pdb(nparray_to_XFORMs(xout.get())[3*i+1],"../pdb/PetF_hash_bb.pdb" ,"../test/.tmp")
# os.system("cat ../test/.tmp >> "+fn)
# # xform_pdb(nparray_to_XFORMs(xout.get())[3*i+2],"../pdb/petf_hash_bb.pdb" ,"../test/hyda_%i.pdb"%i)
# dump_pdb(vout.get()[i,],"../test/.tmp","X")
# os.system("cat ../test/.tmp >> "+fn)
# os.system("echo ENDMDL >> %s"%(fn))
tag = str(random.random())
Ntrial = numpy.sum(stat.get()[:, 0])
Nhist = numpy.sum(stat.get()[:, 2])
h = hist.get() # numpy.apply_along_axis(numpy.sum, 0, hist.get())
print "DONE", lp, NC, lh, temperature, "mcmc steps/sec:", int(NOUT / (time.time() - t))
def test():
ctx, queue = clutil.my_get_gpu_context()
LS, GS = 64, int(sys.argv[2])
NITER, NGPUITER = int(sys.argv[4]), int(sys.argv[3])
lh, lp = 27, 27
NC = "n"
temperature = 15.0
nstat = 7
# allocate
ranlux = pyopencl.array.empty(queue, (112 * GS, ), dtype=numpy.int8)
ranlux.fill(17)
out = pyopencl.array.empty(queue, (3 * 3 * (100) * GS, ),
dtype=numpy.float32)
out.fill(0)
xout = pyopencl.array.empty(queue, (12 * 3 * GS, ), dtype=numpy.float32)
xout.fill(0)
rout = pyopencl.array.empty(queue, (GS, ), dtype=numpy.float32)
rout.fill(0)
vout = pyopencl.array.empty(queue, (GS, 6), dtype=numpy.float32)
vout.fill(0)
status = pyopencl.array.empty(queue, (GS, 2), dtype=numpy.int32)
status.fill(0)
seed = pyopencl.array.empty(queue, (1, ), dtype=numpy.uint32)
seed.fill(0)
stat = pyopencl.array.empty(queue, (GS, nstat), dtype=numpy.int32)
stat.fill(0)
fstat = pyopencl.array.empty(queue, (GS, nstat), dtype=numpy.float32)
fstat.fill(0)
hist = pyopencl.array.empty(queue, (300, ), dtype=numpy.uint32)
hist.fill(0)
hist6 = pyopencl.array.empty(queue, (9, 20, 23, 11, 24, 12),
dtype=numpy.uint32)
hist6.fill(0)
#for temperature in (5,10,9999999999):
NC = 'c'
for lp in (
10,
20,
30,
40,
50,
):
#for temperature in [2**x for x in range(6)]+[9e9]:
for lh in (10, 20, 30, 40, 50):
NOUT = NITER * NGPUITER * GS
#if len(glob.glob("../test/hist6_bind_%i_%i_%s_%i_%i_*.dat"%(lh,lp,NC,temperature,NOUT))) > 3: continue
#for temperature in (15,):
#print temperature
# inputs
components = ("psi hyd pet ld%s len" % NC).split()
hyd_stub = get_stub(components, "hyd")
pet_stub = get_stub(components, "pet")
PSI_ET = "vec(52.126627, 53.095875, 23.992003)"
PET_ET = "vec( 5.468269, 20.041713, 11.962524)"
HYD_ET = "vec(11.842096, 39.050866, 19.269006)"
hashes = [xyzHash("../dat/%s.xyzHash" % n) for n in components]
coords = [h.get_coord_clarray(queue) for h in hashes]
grids = [h.get_grid_clarray(queue) for h in hashes]
nxpsi, nypsi, nzpsi = hashes[0].xsize, hashes[0].ysize, hashes[
0].zsize
nxhyd, nyhyd, nzhyd = hashes[1].xsize, hashes[1].ysize, hashes[
1].zsize
nxpet, nypet, nzpet = hashes[2].xsize, hashes[2].ysize, hashes[
2].zsize
grid_size = 5.0
data = [d for d in reduce(operator.add, zip(coords, grids)) if d]
npsi, nhyd, npet = (data[i].size / 3 for i in (0, 2, 4))
nlkh, nlkp = lh * 3, lp * 3
ntot = nlkh + nlkp #npsi+nhyd+npet+nlkh+nlkp
out.fill(0)
xout.fill(0)
rout.fill(0)
vout.fill(0)
status.fill(0)
seed.fill(0)
stat.fill(0)
fstat.fill(0)
hist.fill(0)
hist6.fill(0)
kargs = [
x.data for x in data + [
ranlux, seed, out, xout, rout, vout, status, stat, fstat,
hist, hist6
]
]
my_test_kernel = pyopencl.Program(
ctx, KERN % vars()).build(OPTS).my_test_kernel
#os.system("rm -f ../test/*.pdb")
seed.fill(random.getrandbits(31))
t = time.time()
for ITER in range(1, NITER + 1):
my_test_kernel(queue, (LS, GS), (LS, 1), *kargs).wait()
#print lh,lp,NC,ITER,"COMPUTE RATE:",ITER*NGPUITER*GS/(time.time()-t)/1000.0
# for i in range(GS):
# #if stat.get()[i,1] == 0: continue
# if not ITER in vars(): ITER = 0
# ary = out.get()
# fn = "../test/test_%i_%i_%i.pdb"%(i,lh,lp)
# dump_pdb(ary[i*len(ary)/GS:(i+1)*len(ary)/GS],"../test/.tmp")
# os.system("echo MODEL %i >> %s"%(ITER,fn))
# os.system("cat ../test/.tmp >> "+fn)
# xform_pdb(nparray_to_XFORMs(xout.get())[3*i+0],"../pdb/hyda1_hash_bb.pdb","../test/.tmp")
# os.system("cat ../test/.tmp >> "+fn)
# xform_pdb(nparray_to_XFORMs(xout.get())[3*i+1],"../pdb/PetF_hash_bb.pdb" ,"../test/.tmp")
# os.system("cat ../test/.tmp >> "+fn)
# # xform_pdb(nparray_to_XFORMs(xout.get())[3*i+2],"../pdb/petf_hash_bb.pdb" ,"../test/hyda_%i.pdb"%i)
# dump_pdb(vout.get()[i,],"../test/.tmp","X")
# os.system("cat ../test/.tmp >> "+fn)
# os.system("echo ENDMDL >> %s"%(fn))
tag = str(random.random())
Ntrial = numpy.sum(stat.get()[:, 0])
Nhist = numpy.sum(stat.get()[:, 2])
h = hist.get() #numpy.apply_along_axis(numpy.sum, 0, hist.get())
print "DONE", lp, NC, lh, temperature, "mcmc steps/sec:", int(
NOUT / (time.time() - t))
