From b58855bb5440b45796ee580232adbc8aad862568 Mon Sep 17 00:00:00 2001
From: Peter Schubert <Peter.Schubert@hhu.de>
Date: Sun, 24 Jul 2022 13:14:30 +0200
Subject: [PATCH] Multiprocessing implemented for FVA (validated on macOS)
---
modelpruner/core/model_pruner.py | 192 ++++++++++++++++++++---------
modelpruner/models/fba_model.py | 73 +++++++----
modelpruner/problems/lp_problem.py | 21 ++--
3 files changed, 195 insertions(+), 91 deletions(-)
diff --git a/modelpruner/core/model_pruner.py b/modelpruner/core/model_pruner.py
index fabf464..d83be00 100644
--- a/modelpruner/core/model_pruner.py
+++ b/modelpruner/core/model_pruner.py
@@ -5,7 +5,6 @@ import os
import re
import time
import math
-import copy
import numpy as np
import multiprocessing as mp
import json
@@ -14,30 +13,72 @@ from modelpruner.models.fba_model import FbaModel
from modelpruner.core.protected_parts import ProtectedParts
global _fba_model
-global _pf
+global _pfs
-def init_worker(fba_model, pf):
+def _init_worker(fba_model, pfs):
+ """Multiprocessing initializer for workers.
+
+ Configure global parameters for the worker process
+
+ :param fba_model: Fba model to apply FVA
+ :type fba_model: Class FbaModel
+ :param pfs: Protected Functions
+ :type pfs: dict, key: function id, value: class ProtectedFunction
+ """
global _fba_model
- global _pf
+ global _pfs
_fba_model = fba_model.copy()
- _pf = pf
+ _pfs = pfs
+
+def _worker(rids):
+ """Mulitprocessing worker to run FVA for selected reactions over all conditions.
-def worker(rid):
+ Checked that best performance achieved when worker performs FVA for
+ all protected functions and a larger range for reactions.
+
+ :param rids: reactions for FVA
+ :type rids: list-like of str
+ """
global _fba_model
- global _pf
+ global _pfs
+
+ flux_min_pfs = np.zeros((len(_pfs), len(rids)))
+ flux_max_pfs = np.zeros((len(_pfs), len(rids)))
- return _fba_model.fva_pf_flux_ranges(_pf, [rid])
+ for idx, pf in enumerate(_pfs.values()):
+ res = _fba_model.fva_pf_flux_ranges(pf, rids)
+ if res['success'] is True:
+ flux_min_pfs[idx] = res['min']
+ flux_max_pfs[idx] = res['max']
+ else:
+ print(f'FBA for condition {pf.obj_id} is not feasible')
+ flux_min_pfs[idx] = np.nan
+ flux_max_pfs[idx] = np.nan
+ break
+ # delete linear problem
+ # del _fba_model.delete_fba_lp()
+ res = {'success': True, 'rids': rids, 'min_pfs': flux_min_pfs, 'max_pfs': flux_max_pfs}
+ return res
class ModelPruner:
def __init__(self, sbml_fname, protected_parts, resume=False):
-
+ """Init
+
+ :param sbml_fname: pathname of original model (ending with '.xml')
+ :type sbml_fname: str
+ :param protected_parts: pathname of protected parts file or dict
+ :type protected_parts: str or dict with protected parts information
+ :param resume: Indicator if to resume pruning from stored snapshot
+ :type resume: bool, optional (default: False)
+ """
self.tolerance = 1e-7 # later accessible by set_params() ?
- self.cpus = int(os.cpu_count() * 0.8)
+ self.cpus = int(os.cpu_count() - 0)
+ self.min_mp_total_flux = 1000
self._snapshot_sbml = re.sub(r'.xml$', '_snapshot.xml', sbml_fname)
self._snapshot_json = re.sub(r'.xml$', '_snapshot.json', sbml_fname)
@@ -52,7 +93,7 @@ class ModelPruner:
with open(self._snapshot_json, 'r') as f:
snapshot_data = json.load(f)
self.protected_rids = set(snapshot_data['protected_rids'])
- print(f'snapshot restored at {len(self.fba_model.rids):4d} remaining reactions '
+ print(f'Snapshot restored at {len(self.fba_model.rids):4d} remaining reactions '
f'from: {self._snapshot_json}')
else:
self.protected_rids = self.nrp.protected_rids
@@ -62,19 +103,24 @@ class ModelPruner:
self.fba_model.update_model_flux_bounds(self.nrp.overwrite_bounds)
self.fba_model.update_model_reversible(self.get_pp_reversible_reactions())
- print('determine optimal values for protected functions')
+ print('Determine optimal values for protected functions')
self.set_function_optimum()
print('Check consistency of protected parts')
self.check_protected_parts()
def get_total_protected_rids(self):
+ """Determine protected reactions, incl. those leading to protected metabolites.
+
+ :return: total protected reaction ids
+ :rtype: set of str
+
+ """
# identify reactions that need protection due to protected metabolites
# over and above the protected rids provided in protected parts
sid_mask = np.array([True if sid in self.protected_sids else False
for sid in self.fba_model.sids])
- psf_mask = np.any(self.fba_model.s_mat[sid_mask] != 0, axis=0)
+ psf_mask = self.fba_model.s_mat_coo.tocsr()[sid_mask].getnnz(axis=0)
protected_sid_rids = set(self.fba_model.rids[psf_mask])
-
protected_rids = self.nrp.protected_rids.union(protected_sid_rids)
return protected_rids
@@ -109,7 +155,10 @@ class ModelPruner:
pf.set_target_ub(pf.target_frac * pf.optimal)
def check_protected_parts(self):
+ """Report on consisteny issues wrt to protected parts.
+ E.g. report on reactions and metabolties that do not exist in the model
+ """
extra_p_rids = self.protected_rids.difference(set(self.fba_model.rids))
extra_p_sids = self.protected_sids.difference(set(self.fba_model.sids))
pf_rids = set()
@@ -117,27 +166,27 @@ class ModelPruner:
pf_rids |= {rid for rid in pf.objective}
pf_rids |= {rid for rid in pf.overwrite_bounds}
if pf.fba_success is False:
- print(f'protected function {pf.obj_id} has unsuccessful FBA '
+ print(f'Protected function {pf.obj_id} has unsuccessful FBA '
f' with optimal value {pf.optimal}')
extra_pf_rids = pf_rids.difference(set(self.fba_model.rids))
pf_unprotected_rids = pf_rids.difference(set(self.protected_rids))
if len(extra_p_rids) > 0:
- print('protected reactions that do not exist in model:', extra_p_rids)
+ print('Protected reactions that do not exist in model:', extra_p_rids)
if len(extra_p_sids) > 0:
- print('protected metabolites that do not exist in model:', extra_p_sids)
+ print('Protected metabolites that do not exist in model:', extra_p_sids)
if len(extra_pf_rids) > 0:
- print('reactions in protected functions that do not exist in model:', extra_pf_rids)
+ print('Reactions in protected functions that do not exist in model:', extra_pf_rids)
if len(pf_unprotected_rids) > 0:
- print('reactions in protected functions that are not protected:', pf_unprotected_rids)
+ print('Reactions in protected functions that are not protected:', pf_unprotected_rids)
blocked_rids = self.reaction_types_fva(self.fba_model.rids)['blocked_rids']
blocked_p_rids = self.nrp.protected_sids.intersection(blocked_rids)
blocked_pf_rids = pf_rids.intersection(blocked_rids)
if len(blocked_p_rids) > 0:
- print('protected reactions that are blocked (no flux):', blocked_p_rids)
+ print('Protected reactions that are blocked (no flux):', blocked_p_rids)
if len(blocked_pf_rids) > 0:
- print('reactions in protected functions that are blocked (no flux):', blocked_pf_rids)
+ print('Reactions in protected functions that are blocked (no flux):', blocked_pf_rids)
def identify_parallel_reactions(self):
"""Identify parallel reactions having same stoichiometry (considering reverse).
@@ -183,17 +232,24 @@ class ModelPruner:
flux_max_pfs = np.zeros((n_pf, len(free_rids)))
res = {}
- processes = min(self.cpus, len(free_rids))
- for idx, pf in enumerate(self.nrp.protected_functions.values()):
- if processes > 100:
- frid2idx = {rid: idx for idx, rid in enumerate(free_rids)}
- # place to split fva for free_rids over several
- with mp.Pool(processes, initializer=init_worker, initargs=(self.fba_model, pf)) as pool:
- for res in pool.imap_unordered(worker, free_rids):
- rid = res['rids'][0]
- flux_min_pfs[idx, frid2idx[rid]] = res['min'][0]
- flux_max_pfs[idx, frid2idx[rid]] = res['max'][0]
- else:
+ # setting up multiprocessing takes quite some resources
+ # there is a tradeoff wrt running on one processor
+ processes = min(self.cpus, int(len(free_rids)*n_pf/self.min_mp_total_flux))
+ # processes = min(self.cpus, len(free_rids))
+
+ if processes > 1:
+ print(f'Multiprocessing with {processes} processes')
+ frid2idx = {rid: idx for idx, rid in enumerate(free_rids)}
+ # delete lp problem prior to pool creation (so FbaProblem can be pickled)
+ self.fba_model.delete_fba_lp()
+ with mp.Pool(processes, initializer=_init_worker,
+ initargs=(self.fba_model, self.nrp.protected_functions)) as pool:
+ for res in pool.imap_unordered(_worker, np.array_split(free_rids, processes)):
+ idxs = [frid2idx[rid] for rid in res['rids']]
+ flux_min_pfs[:, idxs] = res['min_pfs']
+ flux_max_pfs[:, idxs] = res['max_pfs']
+ else:
+ for idx, pf in enumerate(self.nrp.protected_functions.values()):
# print(f'\nCheck FVA for pf {pf.obj_id} with {len(free_rids)} free variables')
res = self.fba_model.fva_pf_flux_ranges(pf, free_rids)
if res['success'] is True:
@@ -205,9 +261,9 @@ class ModelPruner:
flux_min_pfs[idx] = np.nan
flux_max_pfs[idx] = np.nan
break
- sys.stdout.write('\rFVA[{}{}] {:3.0f}%'.format(
- '=' * int(idx+1), ' ' * int(n_pf - idx-1), (idx+1)/n_pf*100))
- sys.stdout.flush()
+ sys.stdout.write('\rFVA[{}{}] {:3.0f}%'.format(
+ '=' * int(idx+1), ' ' * int(n_pf - idx-1), (idx+1)/n_pf*100))
+ sys.stdout.flush()
if res['success'] is False:
reaction_types = {'blocked_rids': set(), 'essential_rids': set(free_rids),
@@ -262,16 +318,27 @@ class ModelPruner:
return reaction_types
- def init_worker(self):
- global _fba_model
- _fba_model = copy.deepcopy(self.fba_model)
+ def prune(self, snapshot_freq=0):
+ """Prune the metabolic network
+
+ Once the Metabolic network has been loaded it can be pruned.
+ With snapshot_freq one can deterimine if (snapshot_freq > 0) and
+ how often intermediate results shall be store, from which one can resume in future
- @staticmethod
- def fva_single_rids(rid):
- return _fba_model.fva_single_rid(rid)
+ Step during Pruning
+ 1. identification and removal of parallel reactions
+ 2. check feasibility of the network wrt to all protected functions
+ 3. in a loop till all free reactions have been consumed
+ 3.1 identify types of remaining free reactions using FVA across all protected functions
+ 3.2 blocked reactions (zero flux across all functions) get removed
+ 3.3 essential reactions (strict positive/negative flux across conditions) get protected
+ 3.4 a single candidate reaction (supporting zero flux) gets identify and removed
- def prune(self, snapshot_freq=None):
- print(f'initial S-matrix: {self.fba_model.s_mat.shape}; '
+ :param snapshot_freq: frequency to store intermediate results (every x reactions)
+ :type snapshot_freq: int, optional (default: 0, no snapshots)
+ """
+
+ print(f'Initial S-matrix: {self.fba_model.s_mat_coo.shape}; '
f' protected reactions: {len(self.protected_rids)}:', self.protected_rids)
drop_rids = self.identify_parallel_reactions().difference(self.protected_rids)
if len(drop_rids) > 0:
@@ -279,13 +346,13 @@ class ModelPruner:
print(f'{len(drop_rids)} parallel reaction(s) dropped:', drop_rids)
feasible = np.array([self.fba_model.check_pf_feasibility(pf) for pf in self.nrp.protected_functions.values()])
- print('protected functions feasibility:', np.all(feasible))
+ print('Protected functions feasibility:', np.all(feasible))
next_snapshot = 0
- if type(snapshot_freq) is int:
+ if snapshot_freq > 0:
next_snapshot = max(0, len(self.fba_model.rids) - snapshot_freq)
- while len(self.protected_rids) < self.fba_model.s_mat.shape[1]:
+ while len(self.protected_rids) < self.fba_model.s_mat_coo.shape[1]:
free_rids = list(set(self.fba_model.rids).difference(self.protected_rids))
reaction_types = self.reaction_types_fva(free_rids)
print()
@@ -299,11 +366,11 @@ class ModelPruner:
# try to remove one reaction while still satisfying all protected functions
for rid in candidate_rids:
- # print('check feasibility of', rid)
+ # print('Check feasibility of', rid)
feasible = True
for pf in self.nrp.protected_functions.values():
feasible = self.fba_model.check_pf_feasibility(pf, zero_flux_rid=rid)
- # print(f'feasibility of {rid} is {feasible}')
+ # print(f'Feasibility of {rid} is {feasible}')
if feasible is False:
essential_rids.add(rid)
break
@@ -317,7 +384,7 @@ class ModelPruner:
print(f"{len(essential_rids)} reaction(s) added to protected reactions:", essential_rids)
if feasible is False:
- print('no more reactions to remove')
+ print('No more reactions to remove')
# store intermediate results (snapshots)
if len(self.fba_model.rids) < next_snapshot:
@@ -328,7 +395,7 @@ class ModelPruner:
next_snapshot = max(0, len(self.fba_model.rids) - snapshot_freq)
print('snapshot data saved.')
- print(f'S-matrix: {self.fba_model.s_mat.shape}; '
+ print(f'S-matrix: {self.fba_model.s_mat_coo.shape}; '
f'protected reactions: {len(self.protected_rids)}')
# check if blocked reactions exist in the finally pruned model
@@ -336,10 +403,12 @@ class ModelPruner:
# if len(blocked_rids) > 0:
# print(f'{len(blocked_rids)} blocked reaction(s) in pruned model', blocked_rids)
- # remove any snapshot files
- # for fname in [self._snapshot_sbml, self._snapshot_json]:
- # if os.path.exists(fname):
- # os.remove(fname)
+ def remove_snapshot_files(self):
+ """Remove any snapshot files still existing"""
+ for pname in [self._snapshot_sbml, self._snapshot_json]:
+ if os.path.exists(pname):
+ os.remove(pname)
+ print(f'{pname} removed')
def get_reduction_status(self):
""" Return status in model reduction process
@@ -355,6 +424,7 @@ class ModelPruner:
return status
def print_status(self):
+ """Print status of pruning process"""
status = self.get_reduction_status()
print("reactions removed/remaining/protected: "
@@ -362,11 +432,21 @@ class ModelPruner:
f"/{len(self.protected_rids):4d}; dof: {status['dof']:3d}")
def export_pruned_model(self, pruned_sbml):
+ """Export the pruned network (or snapshot) to SBML.
+
+ Component information of initial network will be carried over,
+ e.g. annotation data, groups, gene products
+
+ :param pruned_sbml: pathname of pruned network, ending with '.xml'
+ :type pruned_sbml: str
+ """
success = self.fba_model.export_pruned_model(pruned_sbml)
if success is True:
- print('pruned model exported to', pruned_sbml)
+ print('Pruned model exported to', pruned_sbml)
+ # self.remove_snapshot_files()
else:
- print('pruned model could not be exported')
+ print('Pruned model could not be exported')
def __del__(self):
+ """Delete corresponding LpProblem"""
del self.fba_model
diff --git a/modelpruner/models/fba_model.py b/modelpruner/models/fba_model.py
index 90d43b0..5712705 100644
--- a/modelpruner/models/fba_model.py
+++ b/modelpruner/models/fba_model.py
@@ -5,6 +5,7 @@ import time
import re
import math
import numpy as np
+from scipy import sparse
import sbmlxdf
from modelpruner.problems.lp_problem import LpProblem
@@ -41,12 +42,13 @@ class FbaModel:
print(f'reaction {idx} set to reversible')
self.rids_rev = self.rids[self.reversible]
self.rid2idx_rev = {rid: idx + len(self.rids) for idx, rid in enumerate(self.rids_rev)}
- self.s_mat = sbml_model.get_s_matrix().to_numpy()
+ # using a sparse matrix speeds up significantly pickling (factor > 350 for S-matrix)
+ # pickling required to support multiprocessing
+ # also data exchange from sbmlxdf.Model and towards LpProblem improves
+ self.s_mat_coo = sparse.coo_matrix(sbml_model.get_s_matrix(sparse=True))
- # TODO: create LP Problem only once (but what is impact on deepcopy()
- # function to assign new LP problem
-
- # lp problem will only be created once required. This gives chances to update e.g. flux bounds
+ # lp problem will only be created once required.
+ # this gives chances to update e.g. flux bounds and to support pickling (multiprocessing)
self.lp = None
def update_reversible_rids(self):
@@ -87,11 +89,13 @@ class FbaModel:
:return: lists of reaction ids that are parallel
:rtype: list with lists of str
"""
- fwd_rev_s_mat = np.hstack((self.s_mat, -self.s_mat[:, self.reversible]))
+
+ fwd_rev_s_mat_coo = sparse.hstack([self.s_mat_coo,
+ -self.s_mat_coo.tocsc()[:, self.reversible]])
fwd_rev_rids = np.hstack((self.rids, self.rids_rev))
# identify groups of parallel reactions
- sorted_idx = np.lexsort(fwd_rev_s_mat)
+ sorted_idx = np.lexsort(fwd_rev_s_mat_coo.todense())[0]
groups = []
consumed_idxs = set()
for pos in range(len(sorted_idx)):
@@ -100,7 +104,7 @@ class FbaModel:
group = [idx]
for adjacent_pos in range(pos + 1, len(sorted_idx)):
candiate_idx = sorted_idx[adjacent_pos]
- if np.all(fwd_rev_s_mat[:, idx] == fwd_rev_s_mat[:, candiate_idx]):
+ if (fwd_rev_s_mat_coo.getcol(idx) != fwd_rev_s_mat_coo.getcol(candiate_idx)).getnnz() == 0:
consumed_idxs.add(candiate_idx)
group.append(candiate_idx)
else:
@@ -131,14 +135,24 @@ class FbaModel:
:returns: status information in a dictionary
:rtype: dict
"""
- status = {'dof': self.s_mat.shape[1] - np.linalg.matrix_rank(self.s_mat),
+ status = {'dof': self.s_mat_coo.shape[1] - np.linalg.matrix_rank(self.s_mat_coo.todense()),
'n_rids': len(self.rids),
'n_sids': len(self.sids)}
status.update(self.full_model_shape)
return status
def export_pruned_model(self, pruned_sbml):
+ """Export the pruned network (or snapshot) to SBML.
+
+ Component information of initial network will be carried over,
+ e.g. annotation data, groups, gene products
+ History information, if available, will be updated.
+ Model will also be validated with respect to SBML compliance.
+
+ :param pruned_sbml: pathname of pruned network, ending with '.xml'
+ :type pruned_sbml: str
+ """
sbml_model = sbmlxdf.Model(self.sbml_fname)
model_dict = sbml_model.to_df()
pruned_mdict = model_dict.copy()
@@ -147,9 +161,12 @@ class FbaModel:
# update model attributes (ids, names and modification date)
pruned_mdict['modelAttrs']['id'] += '_pruned'
- pruned_mdict['modelAttrs']['name'] += '_pruned'
- pruned_mdict['modelAttrs']['metaid'] += '_pruned'
- pruned_mdict['modelAttrs']['modifiedHistory'] += '; localtime'
+ if 'name' in pruned_mdict['modelAttrs']:
+ pruned_mdict['modelAttrs']['name'] += '_pruned'
+ if 'metaid' in pruned_mdict['modelAttrs']:
+ pruned_mdict['modelAttrs']['metaid'] += '_pruned'
+ if 'modifiedHistory' in pruned_mdict['modelAttrs']:
+ pruned_mdict['modelAttrs']['modifiedHistory'] += '; localtime'
# clean groups table
keep_idxs = []
@@ -203,13 +220,23 @@ class FbaModel:
:return: LpProblem configured for FBA
:rtype: LpProblem
"""
- fwd_rev_s_mat = np.hstack((self.s_mat[:], -self.s_mat[:, self.reversible]))
+ fwd_rev_s_mat_coo = sparse.hstack([self.s_mat_coo,
+ -self.s_mat_coo.tocsc()[:, self.reversible]])
fwd_rev_col_bnds = np.hstack((np.fmax(self.flux_bounds[:], 0),
np.fmax(np.flip(-self.flux_bounds[:, self.reversible], axis=0), 0)))
- row_bnds = np.zeros((fwd_rev_s_mat.shape[0], 2))
- lp = LpProblem(fwd_rev_s_mat, row_bnds, fwd_rev_col_bnds)
+ row_bnds = np.zeros((fwd_rev_s_mat_coo.shape[0], 2))
+ lp = LpProblem(fwd_rev_s_mat_coo, row_bnds, fwd_rev_col_bnds)
return lp
+ def delete_fba_lp(self):
+ """Delete the corresponding linear problem.
+
+ E.g. required for multiprocessing so FbaModel can be pickled
+ """
+ if self.lp is not None:
+ del self.lp
+ self.lp = None
+
def set_lp_objective(self, objective, direction='maximize'):
"""Set objective coefficients and direction in linear problem
@@ -241,7 +268,7 @@ class FbaModel:
"""
if self.lp is None:
self.lp = self.create_core_fba_lp()
- print('Core LP Problem created')
+ # print('Core LP Problem created')
for rid, bound_upd in flux_bounds.items():
if rid in self.rids:
temp_bounds = self.flux_bounds[:, self.rid2idx[rid]].copy()
@@ -291,6 +318,9 @@ class FbaModel:
:param drop_rids: reaction ids to be removed from the model
:type drop_rids: set of str
"""
+ if self.lp is None:
+ self.lp = self.create_core_fba_lp()
+ # print('Core LP Problem created')
assert self.lp is not None
# remove variables (columns) from linear problem
@@ -304,16 +334,16 @@ class FbaModel:
self.reversible = self.reversible[keep_rids_mask]
self.update_reversible_rids()
self.flux_bounds = self.flux_bounds[:, keep_rids_mask]
- self.s_mat = self.s_mat[:, keep_rids_mask]
+ self.s_mat_coo = self.s_mat_coo.tocsc()[:, keep_rids_mask].tocoo()
# drop blocked metabolites due to deleted reactions
- keep_sids_mask = np.any(self.s_mat != 0, axis=1)
+ keep_sids_mask = (self.s_mat_coo.getnnz(axis=1) > 0)
row_idxs0 = [idx for idx, val in enumerate(keep_sids_mask) if val == np.bool_(False)]
if len(row_idxs0) > 0:
self.lp.remove_rows(row_idxs0)
self.sids = self.sids[keep_sids_mask]
self.sid2idx = {sid: idx for idx, sid in enumerate(self.sids)}
- self.s_mat = self.s_mat[keep_sids_mask, :]
+ self.s_mat_coo = self.s_mat_coo.tocsr()[keep_sids_mask, :].tocoo()
def fba_pf_optimize(self, pf, zero_flux_rid=None):
"""FBA optimization of current problem
@@ -329,7 +359,7 @@ class FbaModel:
"""
if self.lp is None:
self.lp = self.create_core_fba_lp()
- print('Core LP Problem created')
+ # print('Core LP Problem created')
assert self.lp is not None
if zero_flux_rid is not None:
@@ -430,9 +460,6 @@ class FbaModel:
result.__dict__['lp'] = None
return result
- def __reduce__(self):
- return self.__class__, (self.sbml_fname, )
-
def __del__(self):
print('deletion of fba_model')
del self.lp
diff --git a/modelpruner/problems/lp_problem.py b/modelpruner/problems/lp_problem.py
index 0d094a5..8324ce1 100644
--- a/modelpruner/problems/lp_problem.py
+++ b/modelpruner/problems/lp_problem.py
@@ -6,8 +6,6 @@ Peter Schubert, HHU Duesseldorf, June 2022
"""
import numpy as np
-import scipy
-import scipy.sparse
import swiglpk as glpk
@@ -61,13 +59,13 @@ scaling_options = {'GM': glpk.GLP_SF_GM,
class LpProblem:
- def __init__(self, constr_coefs, row_bnds, col_bnds):
+ def __init__(self, constr_coefs_coo, row_bnds, col_bnds):
"""create core linear problem (constraints, variable and row bounds)
Problem needs to be properly deleted usin del(LpProblem)
Note: glpk related indices start at 1 (not zero)
- :param constr_coefs: matrix with constraint coefficients
- :type constr_coefs: 2D nparray with shape(nrows, ncols)
+ :param constr_coefs_coo: matrix with constraint coefficients
+ :type constr_coefs_coo: scipy.sparce.coo_matrix with shape(nrows, ncols)
:param row_bnds: lower and upper bounds of auxhiliary (row) variables
:type row_bnds: 2D ndarray of shape(nrows, 2) (1st col: lower bounds, 2nd col: upper bounds)
:param col_bnds: lower and upper bounds of structural (col) variables
@@ -78,7 +76,7 @@ class LpProblem:
glp_presolve = glpk.GLP_OFF # or glpk.GLP_OFF (default) or GLP_ON
self.res = {}
- self.nrows, self.ncols = constr_coefs.shape
+ self.nrows, self.ncols = constr_coefs_coo.shape
assert col_bnds.shape == (2, self.ncols)
assert row_bnds.shape == (self.nrows, 2)
@@ -95,15 +93,14 @@ class LpProblem:
for i, lb_ub in enumerate(row_bnds):
var_type, lb, ub = self._get_variable_type(lb_ub)
glpk.glp_set_row_bnds(self.lp, 1 + i, var_type, lb, ub)
- constr_coefs_sparse = scipy.sparse.coo_matrix(constr_coefs)
- n_coefs = len(constr_coefs_sparse.row)
+ n_coefs = len(constr_coefs_coo.row)
ia = glpk.intArray(1 + n_coefs)
ja = glpk.intArray(1 + n_coefs)
ar = glpk.doubleArray(1 + n_coefs)
for i in range(n_coefs):
- ia[1 + i] = int(1 + constr_coefs_sparse.row[i])
- ja[1 + i] = int(1 + constr_coefs_sparse.col[i])
- ar[1 + i] = constr_coefs_sparse.data[i]
+ ia[1 + i] = int(1 + constr_coefs_coo.row[i])
+ ja[1 + i] = int(1 + constr_coefs_coo.col[i])
+ ar[1 + i] = constr_coefs_coo.data[i]
glpk.glp_load_matrix(self.lp, n_coefs, ia, ja, ar)
# configure options
@@ -307,7 +304,7 @@ class LpProblem:
def __del__(self):
"""Explicitly delete the LpProblem. (can we do without?)
"""
- print('deletion of LpProblem')
+ # print('deletion of LpProblem')
assert self.lp is not None
if getattr(self, 'lp'):
glpk.glp_delete_prob(self.lp)
--
GitLab