def test():
Nlocal = 64
Nglobal = 1024
ctx,queue = my_get_gpu_context()
# inputs
components = "psi hyd pet ldn lec".split()
coords = [xyzHash("../dat/%s.xyzHash"%n).get_coord_clarray(queue) for n in components]
if components[3][-1]=="c": hyd_stub = "stubrev(vec"+str(hyd_N_N)+",vec"+str(hyd_N_CA)+",vec"+str(hyd_N_C)+")"
elif components[3][-1]=="n": hyd_stub = "stubrev(vec"+str(hyd_C_C)+",vec"+str(hyd_C_CA)+",vec"+str(hyd_C_N)+")"
else: assert "CAN'T DETERMINE ORIENTATIN OF HYDA1 LINKER!!!"==None
if components[4][-1]=="c": pet_stub = "stubrev(vec"+str(pet_N_N)+",vec"+str(pet_N_CA)+",vec"+str(pet_N_C)+")"
elif components[4][-1]=="n": pet_stub = "stubrev(vec"+str(pet_C_C)+",vec"+str(pet_C_CA)+",vec"+str(pet_C_N)+")"
else: assert "CAN'T DETERMINE ORIENTATIN OF HYDA1 LINKER!!!"==None
npsi,nhyd,npet = (coords[i].size/3 for i in (0,1,2))
nlkh,nlkp = 23*3,32*3
ntot = npsi+nhyd+npet+nlkh+nlkp
ranlux = pyopencl.array.empty(queue, (112*Nglobal,), dtype=numpy.int8); ranlux.fill(17)
python_seed = random.getrandbits(31)
# outputs
out = pyopencl.array.empty(queue, (3*ntot*Nglobal,), dtype=numpy.float32)
print out.size*4/1024/1024
xout = pyopencl.array.empty(queue, (12*10,) , dtype=numpy.float32)
rout = pyopencl.array.empty(queue, (Nglobal,) , dtype=numpy.float32)
# run
kargs = [x.data for x in coords+[ranlux,out,xout,rout] ]
if os.path.exists("../test/test1.pdb"): os.rename("../test/test1.pdb","../test/test1.pdb.last")
print "build"
my_test_kernel = pyopencl.Program(ctx,KERN%vars()).build(OPTS).my_test_kernel
# print "run 1"
# my_test_kernel(queue,( 1 ,Nglobal),( 1 ,1), *kargs ); dump_pdb(out.get()[0:],"../test/test1.pdb")
print "run 2"
my_test_kernel(queue,(Nlocal,Nglobal),(Nlocal,1), *kargs ); dump_pdb(out.get()[0:],"../test/test2.pdb")
def test():
NL, NG = 64, 1024
ctx, queue = my_get_gpu_context()
# inputs
components = "psi hyd pet len ldc".split()
coords = [
xyzHash("../dat/%s.xyzHash" % n).get_coord_clarray(queue)
for n in components
]
if components[3][-1] == "c":
hyd_stub = "stubrev(vec" + str(hyd_N_N) + ",vec" + str(
hyd_N_CA) + ",vec" + str(hyd_N_C) + ")"
elif components[3][-1] == "n":
hyd_stub = "stubrev(vec" + str(hyd_C_C) + ",vec" + str(
hyd_C_CA) + ",vec" + str(hyd_C_N) + ")"
else:
assert "CAN'T DETERMINE ORIENTATIN OF HYDA1 LINKER!!!" == None
if components[4][-1] == "c":
pet_stub = "stubrev(vec" + str(pet_N_N) + ",vec" + str(
pet_N_CA) + ",vec" + str(pet_N_C) + ")"
elif components[4][-1] == "n":
pet_stub = "stubrev(vec" + str(pet_C_C) + ",vec" + str(
pet_C_CA) + ",vec" + str(pet_C_N) + ")"
else:
assert "CAN'T DETERMINE ORIENTATIN OF HYDA1 LINKER!!!" == None
npsi, nhyd, npet = (coords[i].size / 3 for i in (0, 1, 2))
lh = 50
lp = 50
nlkh, nlkp = lh * 3, lp * 3
#ntot = npsi+nhyd+npet+nlkh+nlkp
ntot = nlkh + nlkp
ranlux = pyopencl.array.empty(queue, (112 * NG, ), dtype=numpy.int8)
#print python_seed
# outputs
out = pyopencl.array.empty(queue, (3 * ntot * NG, ), dtype=numpy.float32)
xout = pyopencl.array.empty(queue, (12 * 3 * NG, ), dtype=numpy.float32)
rout = pyopencl.array.empty(queue, (NG, ), dtype=numpy.float32)
seed = pyopencl.array.empty(queue, (1, ), dtype=numpy.uint32)
kargs = [x.data for x in coords + [ranlux, seed, out, xout, rout]]
my_test_kernel = pyopencl.Program(ctx,
KERN % vars()).build(OPTS).my_test_kernel
for ITER in range(100):
seed.fill(random.getrandbits(31))
ranlux.fill(17)
my_test_kernel(queue, (NL, NG), (NL, 1),
*kargs).wait() #; print seed.get(),rout
lastout = out.get()
lastxout = xout.get()
ranlux.fill(17)
my_test_kernel(queue, (NL, NG), (NL, 1),
*kargs).wait() #; print seed.get(),rout
assert numpy.all(lastxout == xout.get())
assert numpy.all(lastout == out.get())
assert numpy.sum(
numpy.abs(out.get()[:-3] - out.get()[3:]) > 1.6) < 3 * 2 * NG
print "1 vs 64 threads same! seed:", seed.get()[0]
def test():
Nlocal = 64
Nglobal = 1024
ctx, queue = my_get_gpu_context()
# inputs
components = "psi hyd pet ldn lec".split()
coords = [
xyzHash("../dat/%s.xyzHash" % n).get_coord_clarray(queue)
for n in components
]
if components[3][-1] == "c":
hyd_stub = "stubrev(vec" + str(hyd_N_N) + ",vec" + str(
hyd_N_CA) + ",vec" + str(hyd_N_C) + ")"
elif components[3][-1] == "n":
hyd_stub = "stubrev(vec" + str(hyd_C_C) + ",vec" + str(
hyd_C_CA) + ",vec" + str(hyd_C_N) + ")"
else:
assert "CAN'T DETERMINE ORIENTATIN OF HYDA1 LINKER!!!" == None
if components[4][-1] == "c":
pet_stub = "stubrev(vec" + str(pet_N_N) + ",vec" + str(
pet_N_CA) + ",vec" + str(pet_N_C) + ")"
elif components[4][-1] == "n":
pet_stub = "stubrev(vec" + str(pet_C_C) + ",vec" + str(
pet_C_CA) + ",vec" + str(pet_C_N) + ")"
else:
assert "CAN'T DETERMINE ORIENTATIN OF HYDA1 LINKER!!!" == None
npsi, nhyd, npet = (coords[i].size / 3 for i in (0, 1, 2))
nlkh, nlkp = 23 * 3, 32 * 3
ntot = npsi + nhyd + npet + nlkh + nlkp
ranlux = pyopencl.array.empty(queue, (112 * Nglobal, ), dtype=numpy.int8)
ranlux.fill(17)
python_seed = random.getrandbits(31)
# outputs
out = pyopencl.array.empty(queue, (3 * ntot * Nglobal, ),
dtype=numpy.float32)
print out.size * 4 / 1024 / 1024
xout = pyopencl.array.empty(queue, (12 * 10, ), dtype=numpy.float32)
rout = pyopencl.array.empty(queue, (Nglobal, ), dtype=numpy.float32)
# run
kargs = [x.data for x in coords + [ranlux, out, xout, rout]]
if os.path.exists("../test/test1.pdb"):
os.rename("../test/test1.pdb", "../test/test1.pdb.last")
print "build"
my_test_kernel = pyopencl.Program(ctx,
KERN % vars()).build(OPTS).my_test_kernel
# print "run 1"
# my_test_kernel(queue,( 1 ,Nglobal),( 1 ,1), *kargs ); dump_pdb(out.get()[0:],"../test/test1.pdb")
print "run 2"
my_test_kernel(queue, (Nlocal, Nglobal), (Nlocal, 1), *kargs)
dump_pdb(out.get()[0:], "../test/test2.pdb")
def test():
NL,NG = 64,1024
ctx,queue = my_get_gpu_context()
# inputs
components = "psi hyd pet len ldc".split()
coords = [xyzHash("../dat/%s.xyzHash"%n).get_coord_clarray(queue) for n in components]
if components[3][-1]=="c": hyd_stub = "stubrev(vec"+str(hyd_N_N)+",vec"+str(hyd_N_CA)+",vec"+str(hyd_N_C)+")"
elif components[3][-1]=="n": hyd_stub = "stubrev(vec"+str(hyd_C_C)+",vec"+str(hyd_C_CA)+",vec"+str(hyd_C_N)+")"
else: assert "CAN'T DETERMINE ORIENTATIN OF HYDA1 LINKER!!!"==None
if components[4][-1]=="c": pet_stub = "stubrev(vec"+str(pet_N_N)+",vec"+str(pet_N_CA)+",vec"+str(pet_N_C)+")"
elif components[4][-1]=="n": pet_stub = "stubrev(vec"+str(pet_C_C)+",vec"+str(pet_C_CA)+",vec"+str(pet_C_N)+")"
else: assert "CAN'T DETERMINE ORIENTATIN OF HYDA1 LINKER!!!"==None
npsi,nhyd,npet = (coords[i].size/3 for i in (0,1,2))
lh = 50
lp = 50
nlkh,nlkp = lh*3,lp*3
#ntot = npsi+nhyd+npet+nlkh+nlkp
ntot = nlkh+nlkp
ranlux = pyopencl.array.empty(queue, (112*NG,), dtype=numpy.int8)
#print python_seed
# outputs
out = pyopencl.array.empty(queue, (3*ntot*NG,), dtype=numpy.float32)
xout = pyopencl.array.empty(queue, (12*3*NG,) , dtype=numpy.float32)
rout = pyopencl.array.empty(queue, (NG,) , dtype=numpy.float32)
seed = pyopencl.array.empty(queue, (1,) , dtype=numpy.uint32)
kargs = [x.data for x in coords+[ranlux,seed,out,xout,rout] ]
my_test_kernel = pyopencl.Program(ctx,KERN%vars()).build(OPTS).my_test_kernel
for ITER in range(100):
seed.fill(random.getrandbits(31))
ranlux.fill(17)
my_test_kernel(queue,(NL,NG),(NL,1), *kargs ).wait()#; print seed.get(),rout
lastout = out.get()
lastxout = xout.get()
ranlux.fill(17)
my_test_kernel(queue,(NL,NG),(NL,1), *kargs ).wait()#; print seed.get(),rout
assert numpy.all(lastxout == xout.get())
assert numpy.all(lastout == out.get())
assert numpy.sum(numpy.abs(out.get()[:-3]-out.get()[3:])>1.6) < 3*2*NG
print "1 vs 64 threads same! seed:",seed.get()[0]
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))
