The code below should be put into a script and run using mpiexec. It's primary function is to pass a MPI Comm object to pygsti.algorithms.germselection.build_up_breadth.
from __future__ import print_function
import time
import pygsti
import pygsti.construction as pc
from pygsti.construction import std2Q_XYICNOT
from pygsti.algorithms import germselection as germsel
from mpi4py import MPI
comm = MPI.COMM_WORLD
def do_greedy_germsel(target_model, forced_germs, candidate_counts,
seedStart, outFilename, comm):
#candidate_counts is a dict of keys = germ lengths, values = # of germs at that length
tStart = time.time()
candidate_germs = []
for i,(germLength, count) in enumerate(candidate_counts.items()):
if count == "all upto":
candidate_germs.extend( pc.list_all_circuits_without_powers_and_cycles(
target_model.operations.keys(), maxLength=germLength) )
else:
candidate_germs.extend( pc.list_random_circuits_onelen(
target_model.operations.keys(), germLength, count, seed=seedStart+i))
available_germs = pygsti.tools.remove_duplicates( forced_germs + candidate_germs )
print("%d available germs" % len(available_germs))
germs = germsel.build_up_breadth(target_model, available_germs,
randomizationStrength=1e-3, numCopies=3, seed=1234,
opPenalty=10.0, scoreFunc='all', tol=1e-6, threshold=1e5,
pretest=False, force=forced_germs, verbosity=5, comm=comm, memLimit=0.5*(1024**3))
if comm is None or comm.Get_rank() == 0:
print("Germs (%d) = \n" % len(germs), "\n".join(map(str,germs)))
print("Total time = %mdl" % (time.time()-tStart))
pickle.dump(germs,open(outFilename,"wb"))
return germs
#2Q case
target_model = std2Q_XYICNOT.target_model()
forced_germs = pygsti.construction.circuit_list([(gl,) for gl in target_model.operations.keys()]) #singletons
candidate_counts = { 3:"all upto", 4:30, 5:20, 6:20, 7:20, 8:20} # germLength:num_candidates
seedStart = 4
do_greedy_germsel(target_model, forced_germs, candidate_counts,
seedStart, "germs_EXAMPLE.pkl", comm)
201 available germs
Starting germ set optimization. Lower score is better.
Memory estimate of 13.6 GB (0.5 GB limit) for all-Jac mode.
Memory estimate of 0.2 GB (0.5 GB limit) for single-Jac mode.
Initial germ set computation Iter 1 of 6 Gii:
Initial germ set computation Iter 2 of 6 Gix:
Initial germ set computation Iter 3 of 6 Giy:
Initial germ set computation Iter 4 of 6 Gxi:
Initial germ set computation Iter 5 of 6 Gyi:
Initial germ set computation Iter 6 of 6 Gcnot:
Outer iteration: 1 of 1282 amplified, 6 germs
Inner iter over candidate germs Iter 001 of 195 GiiGix:
Score: major=-114.0 minor=275.7550232560748, N: 194
Inner iter over candidate germs Iter 002 of 195 GiiGiy:
Score: major=-114.0 minor=275.75224428270565, N: 194
Inner iter over candidate germs Iter 003 of 195 GiiGxi:
Score: major=-114.0 minor=303.12985712455384, N: 194
Inner iter over candidate germs Iter 004 of 195 GiiGyi:
Score: major=-114.0 minor=359.3300959231123, N: 194
Inner iter over candidate germs Iter 005 of 195 GiiGcnot:
Score: major=-114.0 minor=276.26872683842225, N: 194
Inner iter over candidate germs Iter 006 of 195 GixGiy:
Score: major=-114.0 minor=257.4426897879849, N: 194
Inner iter over candidate germs Iter 007 of 195 GixGxi:
Score: major=-114.0 minor=341.5696468598034, N: 194
Inner iter over candidate germs Iter 008 of 195 GixGyi:
Score: major=-114.0 minor=282.338674492408, N: 194
Inner iter over candidate germs Iter 009 of 195 GixGcnot:
Score: major=-114.0 minor=577.5866443200878, N: 194
Inner iter over candidate germs Iter 010 of 195 GiyGxi:
Score: major=-114.0 minor=294.80873540347477, N: 194
Inner iter over candidate germs Iter 011 of 195 GiyGyi:
Score: major=-114.0 minor=274.01388120453754, N: 194
Inner iter over candidate germs Iter 012 of 195 GiyGcnot:
Score: major=-114.0 minor=292.4187770509611, N: 194
Inner iter over candidate germs Iter 013 of 195 GxiGyi:
Score: major=-114.0 minor=257.14469808616536, N: 194
Inner iter over candidate germs Iter 014 of 195 GxiGcnot:
Score: major=-114.0 minor=295.19014734007106, N: 194
Inner iter over candidate germs Iter 015 of 195 GyiGcnot:
Score: major=-114.0 minor=262.24440122325194, N: 194
Inner iter over candidate germs Iter 016 of 195 GiiGiiGix:
Score: major=-104.0 minor=245.73088449107456, N: 194
Inner iter over candidate germs Iter 017 of 195 GiiGiiGiy:
Score: major=-104.0 minor=236.10434931549185, N: 194
Inner iter over candidate germs Iter 018 of 195 GiiGiiGxi:
Score: major=-104.0 minor=257.4811389850852, N: 194
Inner iter over candidate germs Iter 019 of 195 GiiGiiGyi:
Score: major=-104.0 minor=295.32017448143534, N: 194
Inner iter over candidate germs Iter 020 of 195 GiiGiiGcnot:
Score: major=-104.0 minor=274.607408708754, N: 194
Inner iter over candidate germs Iter 021 of 195 GiiGixGix:
Score: major=-104.0 minor=453.2493918611686, N: 194
Inner iter over candidate germs Iter 022 of 195 GiiGixGiy:
Score: major=-104.0 minor=275.1564063981899, N: 194
Inner iter over candidate germs Iter 023 of 195 GiiGixGxi:
Score: major=-104.0 minor=304.47418773769414, N: 194
Inner iter over candidate germs Iter 024 of 195 GiiGixGyi:
Score: major=-104.0 minor=278.44120228187916, N: 194
Inner iter over candidate germs Iter 025 of 195 GiiGixGcnot:
Score: major=-104.0 minor=352.1721810679982, N: 194
Inner iter over candidate germs Iter 026 of 195 GiiGiyGix:
Score: major=-104.0 minor=266.57020870563014, N: 194
Inner iter over candidate germs Iter 027 of 195 GiiGiyGiy:
Score: major=-104.0 minor=448.32104717482, N: 194
Inner iter over candidate germs Iter 028 of 195 GiiGiyGxi:
Score: major=-104.0 minor=297.3316824804599, N: 194
Inner iter over candidate germs Iter 029 of 195 GiiGiyGyi:
Score: major=-104.0 minor=283.54615357575017, N: 194
Inner iter over candidate germs Iter 030 of 195 GiiGiyGcnot:
Score: major=-104.0 minor=297.12854592193526, N: 194
Inner iter over candidate germs Iter 031 of 195 GiiGxiGix:
Score: major=-104.0 minor=307.71199183761695, N: 194
Inner iter over candidate germs Iter 032 of 195 GiiGxiGiy:
Score: major=-104.0 minor=307.7674841723881, N: 194
Inner iter over candidate germs Iter 033 of 195 GiiGxiGxi:
Score: major=-104.0 minor=410.0988255344368, N: 194
Inner iter over candidate germs Iter 034 of 195 GiiGxiGyi:
Score: major=-104.0 minor=284.3153092741726, N: 194
Inner iter over candidate germs Iter 035 of 195 GiiGxiGcnot:
Score: major=-104.0 minor=303.8102280854164, N: 194
Inner iter over candidate germs Iter 036 of 195 GiiGyiGix:
Score: major=-104.0 minor=283.5892520489328, N: 194
Inner iter over candidate germs Iter 037 of 195 GiiGyiGiy:
Score: major=-104.0 minor=283.3226206509195, N: 194
Inner iter over candidate germs Iter 038 of 195 GiiGyiGxi:
Score: major=-104.0 minor=273.5504913809546, N: 194
Inner iter over candidate germs Iter 039 of 195 GiiGyiGyi:
Score: major=-104.0 minor=563.1049081486988, N: 194
Inner iter over candidate germs Iter 040 of 195 GiiGyiGcnot:
Score: major=-104.0 minor=277.18869907206283, N: 194
Inner iter over candidate germs Iter 041 of 195 GiiGcnotGix:
Score: major=-104.0 minor=352.3317810063291, N: 194
Inner iter over candidate germs Iter 042 of 195 GiiGcnotGiy:
Score: major=-104.0 minor=298.1019089981339, N: 194
Inner iter over candidate germs Iter 043 of 195 GiiGcnotGxi:
Score: major=-104.0 minor=309.6778947901517, N: 194
Inner iter over candidate germs Iter 044 of 195 GiiGcnotGyi:
Score: major=-104.0 minor=279.3478112644729, N: 194
Inner iter over candidate germs Iter 045 of 195 GiiGcnotGcnot:
Score: major=-104.0 minor=375.6548612782157, N: 194
Inner iter over candidate germs Iter 046 of 195 GixGixGiy:
Score: major=-104.0 minor=327.9840714902066, N: 194
Inner iter over candidate germs Iter 047 of 195 GixGixGxi:
Score: major=-104.0 minor=755.1272055918537, N: 194
Inner iter over candidate germs Iter 048 of 195 GixGixGyi:
Score: major=-104.0 minor=362.97934478595647, N: 194
Inner iter over candidate germs Iter 049 of 195 GixGixGcnot:
Score: major=-104.0 minor=532.4198103374531, N: 194
Inner iter over candidate germs Iter 050 of 195 GixGiyGiy:
Score: major=-104.0 minor=293.57122809494956, N: 194
Inner iter over candidate germs Iter 051 of 195 GixGiyGxi:
Score: major=-104.0 minor=313.06071440109775, N: 194
Inner iter over candidate germs Iter 052 of 195 GixGiyGyi:
Score: major=-104.0 minor=291.50473798603565, N: 194
Inner iter over candidate germs Iter 053 of 195 GixGiyGcnot:
Score: major=-104.0 minor=284.2173572664501, N: 194
Inner iter over candidate germs Iter 054 of 195 GixGxiGiy:
--------------------------------------------------------------------------- KeyboardInterrupt Traceback (most recent call last) <ipython-input-1-4ee4fa17b7fa> in <module>() 44 seedStart = 4 45 do_greedy_germsel(target_model, forced_germs, candidate_counts, ---> 46 seedStart, "germs_EXAMPLE.pkl", comm) <ipython-input-1-4ee4fa17b7fa> in do_greedy_germsel(target_model, forced_germs, candidate_counts, seedStart, outFilename, comm) 30 randomizationStrength=1e-3, numCopies=3, seed=1234, 31 opPenalty=10.0, scoreFunc='all', tol=1e-6, threshold=1e5, ---> 32 pretest=False, force=forced_germs, verbosity=5, comm=comm, memLimit=0.5*(1024**3)) 33 34 if comm is None or comm.Get_rank() == 0: ~/research/pyGSTi/packages/pygsti/algorithms/germselection.py in build_up_breadth(modelList, germsList, randomize, randomizationStrength, numCopies, seed, opPenalty, scoreFunc, tol, threshold, check, force, pretest, memLimit, comm, profiler, verbosity) 1309 worstScore = max( worstScore, compute_composite_germ_score( 1310 partialDerivDaggerDeriv=testDDD[None,:,:], initN=initN, -> 1311 **nonAC_kwargs)) 1312 testDDDs.append(testDDD) #save in case this is a keeper 1313 ~/research/pyGSTi/packages/pygsti/algorithms/germselection.py in compute_composite_germ_score(scoreFn, thresholdAC, initN, partialDerivDaggerDeriv, model, partialGermsList, eps, numGaugeParams, opPenalty, germLengths, l1Penalty) 429 430 combinedDDD = _np.sum(partialDerivDaggerDeriv, axis=0) --> 431 sortedEigenvals = _np.sort(_np.real(_nla.eigvalsh(combinedDDD))) 432 observableEigenvals = sortedEigenvals[numGaugeParams:] 433 N_AC = 0 /usr/local/lib/python3.7/site-packages/numpy/linalg/linalg.py in eigvalsh(a, UPLO) 1126 t, result_t = _commonType(a) 1127 signature = 'D->d' if isComplexType(t) else 'd->d' -> 1128 w = gufunc(a, signature=signature, extobj=extobj) 1129 return w.astype(_realType(result_t), copy=False) 1130 KeyboardInterrupt:
Above is keyboard-interrupted on purpose, as this output was produced with a single processor and it would have taken a very long time.