def process_results(out, xout, rout, Nglobal):
print "NUM 0 coords:", sum(out.get() == 0.0)
if int(
os.popen(
"diff ../test/test1.pdb ../test/test2.pdb | wc -l").read()):
print "OUTPUTS DO NOT MATCH!!!!!!!!!!"
else:
print "OUTPUTS MATCH!"
if int(
os.popen("diff ../test/test1.pdb ../test/test1.pdb.last | wc -l").
read()):
print "OUTPUT DOES NOT MATCH PREVIOUS!!!!!!!!!!"
else:
print "PREVIOUS OUTPUT MATCHS!"
xform_pdb(
nparray_to_XFORMs(xout.get())[0], "../pdb/hyda1_hash.pdb",
"../test/hyda1_xform.pdb")
xform_pdb(
nparray_to_XFORMs(xout.get())[1], "../pdb/petf_hash.pdb",
"../test/petf_xform.pdb")
print rout
ary = out.get()
for i in range(Nglobal):
dump_pdb(ary[i * len(ary) / Nglobal:(i + 1) * len(ary) / Nglobal],
"../test/GI_%i.pdb" % i)
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 process_results(out,xout,rout,NG):
print "NUM 0 coords:",sum(out.get()==0.0)
if int(os.popen("diff ../test/test1.pdb ../test/test2.pdb | wc -l").read()):
print "OUTPUTS DO NOT MATCH!!!!!!!!!!"
else: print "OUTPUTS MATCH!"
if int(os.popen("diff ../test/test1.pdb ../test/test1.pdb.last | wc -l").read()):
print "OUTPUT DOES NOT MATCH PREVIOUS!!!!!!!!!!"
else: print "PREVIOUS OUTPUT MATCHS!"
ary = out.get()
for i in range(NG):
dump_pdb(ary[i*len(ary)/NG:(i+1)*len(ary)/NG],"../test/GI_%i.pdb"%i)
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 process_results(out,xout,rout,Nglobal):
print "NUM 0 coords:",sum(out.get()==0.0)
if int(os.popen("diff ../test/test1.pdb ../test/test2.pdb | wc -l").read()):
print "OUTPUTS DO NOT MATCH!!!!!!!!!!"
else: print "OUTPUTS MATCH!"
if int(os.popen("diff ../test/test1.pdb ../test/test1.pdb.last | wc -l").read()):
print "OUTPUT DOES NOT MATCH PREVIOUS!!!!!!!!!!"
else: print "PREVIOUS OUTPUT MATCHS!"
xform_pdb(nparray_to_XFORMs(xout.get())[0],"../pdb/hyda1_hash.pdb","../test/hyda1_xform.pdb")
xform_pdb(nparray_to_XFORMs(xout.get())[1],"../pdb/petf_hash.pdb" ,"../test/petf_xform.pdb")
print rout
ary = out.get()
for i in range(Nglobal):
dump_pdb(ary[i*len(ary)/Nglobal:(i+1)*len(ary)/Nglobal],"../test/GI_%i.pdb"%i)
def process_results(out, xout, rout, NG):
print "NUM 0 coords:", sum(out.get() == 0.0)
if int(
os.popen(
"diff ../test/test1.pdb ../test/test2.pdb | wc -l").read()):
print "OUTPUTS DO NOT MATCH!!!!!!!!!!"
else:
print "OUTPUTS MATCH!"
if int(
os.popen("diff ../test/test1.pdb ../test/test1.pdb.last | wc -l").
read()):
print "OUTPUT DOES NOT MATCH PREVIOUS!!!!!!!!!!"
else:
print "PREVIOUS OUTPUT MATCHS!"
ary = out.get()
for i in range(NG):
dump_pdb(ary[i * len(ary) / NG:(i + 1) * len(ary) / NG],
"../test/GI_%i.pdb" % i)
