Source code for pysb.simulator.cupsoda

from pysb.simulator.base import Simulator, SimulatorException, SimulationResult
import pysb
import pysb.bng
import numpy as np
from scipy.constants import N_A
import os
import re
import subprocess
import tempfile
import time
import logging
from pysb.logging import EXTENDED_DEBUG
import shutil
from pysb.pathfinder import get_path
import sympy
import collections
from import Iterable
    import pandas as pd
except ImportError:
    pd = None
    import pycuda.driver as cuda
except ImportError:
    cuda = None

[docs]class CupSodaSimulator(Simulator): """An interface for running cupSODA, a CUDA implementation of LSODA. cupSODA is a graphics processing unit (GPU)-based implementation of the LSODA simulation algorithm (see references). It requires an NVIDIA GPU card with support for the CUDA framework version 7 or above. Further details of cupSODA and software can be found on github: The simplest way to install cupSODA is to use a pre-compiled version, which can be downloaded from here: Parameters ---------- model : pysb.Model Model to integrate. tspan : vector-like, optional Time values at which the integrations are sampled. The first and last values define the time range. initials : list-like, optional Initial species concentrations for all simulations. Dimensions are N_SIMS x number of species. param_values : list-like, optional Parameters for all simulations. Dimensions are N_SIMS x number of parameters. verbose : bool or int, optional Verbosity level, see :class:`pysb.simulator.base.Simulator` for further details. **kwargs: dict, optional Extra keyword arguments, including: * ``gpu``: Index of GPU to run on (default: 0) * ``vol``: System volume; required if model encoded in extrinsic (number) units (default: None) * ``obs_species_only``: Only output species contained in observables (default: True) * ``cleanup``: Delete all temporary files after the simulation is finished. Includes both BioNetGen and cupSODA files. Useful for debugging (default: True) * ``prefix``: Prefix for the temporary directory containing cupSODA input and output files (default: model name) * ``base_dir``: Directory in which temporary directory with cupSODA input and output files are placed (default: system directory determined by `tempfile.mkdtemp`) * ``integrator``: Name of the integrator to use; see `default_integrator_options` (default: 'cupsoda') * ``integrator_options``: A dictionary of keyword arguments to supply to the integrator; see `default_integrator_options`. Attributes ---------- model : pysb.Model Model passed to the constructor. tspan : numpy.ndarray Time values passed to the constructor. initials : numpy.ndarray Initial species concentrations for all simulations. Dimensions are number of simulations x number of species. param_values : numpy.ndarray Parameters for all simulations. Dimensions are number of simulations x number of parameters. verbose: bool or int Verbosity setting. See the base class :class:`pysb.simulator.base.Simulator` for further details. gpu : int or list Index of GPU being run on, or a list of integers to use multiple GPUs. Simulations will be split equally among the of GPUs. outdir : str Directory where cupSODA output files are placed. Input files are also placed here. opts: dict Dictionary of options for the integrator, which can include the following: * vol (float or None): System volume * n_blocks (int or None): Number of GPU blocks used by the simulator * atol (float): Absolute integrator tolerance * rtol (float): Relative integrator tolerance * chunksize (int or None): The maximum number of simulations to run per GPU at one time. Set this option if your GPU is running out of memory. * memory_usage ('global', 'shared', or 'sharedconstant'): The type of GPU memory to use * max_steps (int): The maximum number of internal integrator iterations (equivalent to LSODA's mxstep) integrator : str Name of the integrator in use (only "cupsoda" is supported). Notes ----- 1. If `vol` is defined, species amounts and rate constants are assumed to be in number units and are automatically converted to concentration units before generating the cupSODA input files. The species concentrations returned by cupSODA are converted back to number units during loading. 2. If `obs_species_only` is True, only the species contained within observables are output by cupSODA. All other concentrations are set to 'nan'. References ---------- 1. Harris, L.A., Nobile, M.S., Pino, J.C., Lubbock, A.L.R., Besozzi, D., Mauri, G., Cazzaniga, P., and Lopez, C.F. 2017. GPU-powered model analysis with PySB/cupSODA. Bioinformatics 33, pp.3492-3494. 2. Nobile M.S., Cazzaniga P., Besozzi D., Mauri G., 2014. GPU-accelerated simulations of mass-action kinetics models with cupSODA, Journal of Supercomputing, 69(1), pp.17-24. 3. Petzold, L., 1983. Automatic selection of methods for solving stiff and nonstiff systems of ordinary differential equations. SIAM journal on scientific and statistical computing, 4(1), pp.136-148. """ _supports = {'multi_initials': True, 'multi_param_values': True} _memory_options = {'global': '0', 'shared': '1', 'sharedconstant': '2'} default_integrator_options = { # some sane default options for a few well-known integrators 'cupsoda': { 'max_steps': 20000, # max # of internal iterations (LSODA's MXSTEP) 'atol': 1e-8, # absolute tolerance 'rtol': 1e-8, # relative tolerance 'chunksize': None, # Max number of simulations per GPU per run 'n_blocks': None, # number of GPU blocks 'memory_usage': 'sharedconstant'}} # see _memory_options dict _integrator_options_allowed = {'max_steps', 'atol', 'rtol', 'n_blocks', 'memory_usage', 'vol', 'chunksize'} def __init__(self, model, tspan=None, initials=None, param_values=None, verbose=False, **kwargs): super(CupSodaSimulator, self).__init__(model, tspan=tspan, initials=initials, param_values=param_values, verbose=verbose, **kwargs) self.gpu = kwargs.pop('gpu', (0, )) if not isinstance(self.gpu, Iterable): self.gpu = [self.gpu] self._obs_species_only = kwargs.pop('obs_species_only', True) self._cleanup = kwargs.pop('cleanup', True) self._prefix = kwargs.pop('prefix', # Sanitize the directory - cupsoda doesn't handle spaces etc. well self._prefix = re.sub('[^0-9a-zA-Z]', '_', self._prefix) self._base_dir = kwargs.pop('base_dir', None) self.integrator = kwargs.pop('integrator', 'cupsoda') integrator_options = kwargs.pop('integrator_options', {}) if kwargs: raise ValueError('Unknown keyword argument(s): {}'.format( ', '.join(kwargs.keys()) )) unknown_integrator_options = set(integrator_options.keys()).difference( self._integrator_options_allowed ) if unknown_integrator_options: raise ValueError( 'Unknown integrator_options: {}. Allowed options: {}'.format( ', '.join(unknown_integrator_options), ', '.join(self._integrator_options_allowed) ) ) # generate the equations for the model pysb.bng.generate_equations(self._model, self._cleanup, self.verbose) # build integrator options list from our defaults and any kwargs # passed to this function options = {} if self.default_integrator_options.get(self.integrator): options.update(self.default_integrator_options[ self.integrator]) # default options else: raise SimulatorException( "Integrator type '" + self.integrator + "' not recognized.") options.update(integrator_options) # overwrite # defaults self.opts = options self._out_species = None # private variables (to reduce the number of function calls) self._len_rxns = len(self._model.reactions) self._len_species = len(self._model.species) self._len_params = len(self._model.parameters) self._model_parameters_rules = self._model.parameters_rules() # Set cupsoda verbosity level logger_level = self._logger.logger.getEffectiveLevel() if logger_level <= EXTENDED_DEBUG: self._cupsoda_verbose = 2 elif logger_level <= logging.DEBUG: self._cupsoda_verbose = 1 else: self._cupsoda_verbose = 0 # regex for extracting cupSODA reported running time self._running_time_regex = re.compile(r'Running time:\s+(\d+\.\d+)') def _run_chunk(self, gpus, outdir, chunk_idx, cmtx, sims, trajectories, tout): _indirs = {} _outdirs = {} p = {} # Path to cupSODA executable bin_path = get_path('cupsoda') # Start simulations for gpu in gpus: _indirs[gpu] = os.path.join(outdir, "INPUT_GPU{}_{}".format( gpu, chunk_idx)) os.mkdir(_indirs[gpu]) _outdirs[gpu] = os.path.join(outdir, "OUTPUT_GPU{}_{}".format( gpu, chunk_idx)) # Create cupSODA input files self._create_input_files(_indirs[gpu], sims[gpu], cmtx) # Build command # ./cupSODA input_model_folder blocks output_folder simulation_ # file_prefix gpu_number fitness_calculation memory_use dump command = [bin_path, _indirs[gpu], str(self.n_blocks), _outdirs[gpu], self._prefix, str(gpu), '0', self._memory_usage, str(self._cupsoda_verbose)]"Running cupSODA: " + ' '.join(command)) # Run simulation and return trajectories p[gpu] = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE) # Read results for gpu in gpus: (p_out, p_err) = p[gpu].communicate() p_out = p_out.decode('utf-8') p_err = p_err.decode('utf-8') logger_level = self._logger.logger.getEffectiveLevel() if logger_level <= logging.INFO: run_time_match = if run_time_match:'cupSODA GPU {} chunk {} reported ' 'time: {} seconds'.format( gpu, chunk_idx, self._logger.debug('cupSODA GPU {} chunk {} stdout:\n{}'.format( gpu, chunk_idx, p_out)) if p_err: self._logger.error('cupSODA GPU {} chunk {} ' 'stderr:\n{}'.format( gpu, chunk_idx, p_err)) if p[gpu].returncode: raise SimulatorException( "cupSODA GPU {} chunk {} exception:\n{}\n{}".format( gpu, chunk_idx, p_out.rstrip("at line"), p_err.rstrip() ) ) tout_run, trajectories_run = self._load_trajectories( _outdirs[gpu], sims[gpu]) if trajectories is None: tout = tout_run trajectories = trajectories_run else: tout = np.concatenate((tout, tout_run)) trajectories = np.concatenate( (trajectories, trajectories_run)) return tout, trajectories
[docs] def run(self, tspan=None, initials=None, param_values=None): """Perform a set of integrations. Returns a :class:`.SimulationResult` object. Parameters ---------- tspan : list-like, optional Time values at which the integrations are sampled. The first and last values define the time range. initials : list-like, optional Initial species concentrations for all simulations. Dimensions are number of simulation x number of species. param_values : list-like, optional Parameters for all simulations. Dimensions are number of simulations x number of parameters. Returns ------- A :class:`SimulationResult` object Notes ----- 1. An exception is thrown if `tspan` is not defined in either `__init__`or `run`. 2. If neither `initials` nor `param_values` are defined in either `__init__` or `run` a single simulation is run with the initial concentrations and parameter values defined in the model. """ super(CupSodaSimulator, self).run(tspan=tspan, initials=initials, param_values=param_values, _run_kwargs=[]) # Create directories for cupSODA input and output files _outdirs = {} _indirs = {} start_time = time.time() cmtx = self._get_cmatrix() outdir = tempfile.mkdtemp(prefix=self._prefix + '_', dir=self._base_dir) self._logger.debug("Output directory is %s" % outdir) # Set up chunking (enforce max # sims per GPU per run) n_sims = len(self.param_values) chunksize_gpu = self.opts.get('chunksize', None) if chunksize_gpu is None: chunksize_gpu = n_sims chunksize_total = chunksize_gpu * len(self.gpu) tout = None trajectories = None chunks = np.array_split(range(n_sims), np.ceil(n_sims / chunksize_total)) try: for chunk_idx, chunk in enumerate(chunks): self._logger.debug('cupSODA chunk {} of {}'.format( (chunk_idx + 1), len(chunks))) # Split chunk equally between GPUs sims = dict(zip(self.gpu, np.array_split(chunk, len(self.gpu)))) tout, trajectories = self._run_chunk( self.gpu, outdir, chunk_idx, cmtx, sims, trajectories, tout) finally: if self._cleanup: shutil.rmtree(outdir) end_time = time.time()"cupSODA + I/O time: {} seconds".format( end_time - start_time)) return SimulationResult(self, tout, trajectories)
@property def _memory_usage(self): try: return self._memory_options[self.opts['memory_usage']] except KeyError: raise Exception('memory_usage must be one of %s', self._memory_options.keys()) @property def vol(self): vol = self.opts.get('vol', None) return vol @vol.setter def vol(self, volume): self.opts['vol'] = volume @property def n_blocks(self): n_blocks = self.opts.get('n_blocks') if n_blocks is None: default_threads_per_block = 32 bytes_per_float = 4 memory_per_thread = (self._len_species + 1) * bytes_per_float if cuda is None: threads_per_block = default_threads_per_block else: cuda.init() device = cuda.Device(self.gpu[0]) attrs = device.get_attributes() shared_memory_per_block = attrs[ cuda.device_attribute.MAX_SHARED_MEMORY_PER_BLOCK] upper_limit_threads_per_block = attrs[ cuda.device_attribute.MAX_THREADS_PER_BLOCK] max_threads_per_block = min( shared_memory_per_block / memory_per_thread, upper_limit_threads_per_block) threads_per_block = min(max_threads_per_block, default_threads_per_block) n_blocks = int( np.ceil(1. * len(self.param_values) / threads_per_block)) self._logger.debug('n_blocks set to {} (used pycuda: {})'.format( n_blocks, cuda is not None )) self.n_blocks = n_blocks return n_blocks @n_blocks.setter def n_blocks(self, n_blocks): if not isinstance(n_blocks, int): raise ValueError("n_blocks must be an integer") if n_blocks <= 0: raise ValueError("n_blocks must be greater than 0") self.opts['n_blocks'] = n_blocks def _create_input_files(self, directory, sims, cmtx): # atol_vector with open(os.path.join(directory, "atol_vector"), 'w') as atol_vector: for i in range(self._len_species): atol_vector.write(str(self.opts.get('atol'))) if i < self._len_species - 1: atol_vector.write("\n") # c_matrix with open(os.path.join(directory, "c_matrix"), 'w') as c_matrix: for i in sims: line = "" for j in range(self._len_rxns): if j > 0: line += "\t" line += str(cmtx[i][j]) c_matrix.write(line) if i != sims[-1]: c_matrix.write("\n") # cs_vector with open(os.path.join(directory, "cs_vector"), 'w') as cs_vector: self._out_species = range(self._len_species) # species to output if self._obs_species_only: self._out_species = [False for sp in self._model.species] for obs in self._model.observables: for i in obs.species: self._out_species[i] = True self._out_species = [i for i in range(self._len_species) if self._out_species[i] is True] for i in range(len(self._out_species)): if i > 0: cs_vector.write("\n") cs_vector.write(str(self._out_species[i])) # left_side with open(os.path.join(directory, "left_side"), 'w') as left_side: for i in range(self._len_rxns): line = "" for j in range(self._len_species): if j > 0: line += "\t" stoich = 0 for k in self._model.reactions[i]['reactants']: if j == k: stoich += 1 line += str(stoich) if i < self._len_rxns - 1: left_side.write(line + "\n") else: left_side.write(line) # max_steps with open(os.path.join(directory, "max_steps"), 'w') as mxsteps: mxsteps.write(str(self.opts['max_steps'])) # model_kind with open(os.path.join(directory, "modelkind"), 'w') as model_kind: # always set modelkind to 'deterministic' model_kind.write("deterministic") # MX_0 with open(os.path.join(directory, "MX_0"), 'w') as MX_0: mx0 = self.initials # if a volume has been defined, rescale populations # by N_A*vol to get concentration # (NOTE: act on a copy of self.initials, not # the original, which we don't want to modify) if self.vol: mx0 = mx0.copy() mx0 /= (N_A * self.vol) for i in sims: line = "" for j in range(self._len_species): if j > 0: line += "\t" line += str(mx0[i][j]) MX_0.write(line) if i != sims[-1]: MX_0.write("\n") # right_side with open(os.path.join(directory, "right_side"), 'w') as right_side: for i in range(self._len_rxns): line = "" for j in range(self._len_species): if j > 0: line += "\t" stochiometry = 0 for k in self._model.reactions[i]['products']: if j == k: stochiometry += 1 line += str(stochiometry) if i < self._len_rxns - 1: right_side.write(line + "\n") else: right_side.write(line) # rtol with open(os.path.join(directory, "rtol"), 'w') as rtol: rtol.write(str(self.opts.get('rtol'))) # t_vector with open(os.path.join(directory, "t_vector"), 'w') as t_vector: for t in self.tspan: t_vector.write(str(float(t)) + "\n") # time_max with open(os.path.join(directory, "time_max"), 'w') as time_max: time_max.write(str(float(self.tspan[-1]))) def _get_cmatrix(self): if self.model.tags: raise ValueError('cupSODA does not currently support local ' 'functions') self._logger.debug("Constructing the c_matrix:") c_matrix = np.zeros((len(self.param_values), self._len_rxns)) par_names = [ for p in self._model_parameters_rules] rate_mask = np.array([p in self._model_parameters_rules for p in self._model.parameters]) rate_args = [] par_vals = self.param_values[:, rate_mask] rate_order = [] for rxn in self._model.reactions: rate_args.append([arg for arg in rxn['rate'].atoms(sympy.Symbol) if not'__s')]) reactants = len(rxn['reactants']) rate_order.append(reactants) output = 0.01 * len(par_vals) output = int(output) if output > 1 else 1 for i in range(len(par_vals)): if i % output == 0: self._logger.debug(str(int(round(100. * i / len(par_vals)))) + "%") for j in range(self._len_rxns): rate = 1.0 for r in rate_args[j]: if isinstance(r, pysb.Parameter): rate *= par_vals[i][par_names.index(] elif isinstance(r, pysb.Expression): raise ValueError('cupSODA does not currently support ' 'models with Expressions') else: rate *= r # volume correction if self.vol: rate *= (N_A * self.vol) ** (rate_order[j] - 1) c_matrix[i][j] = rate self._logger.debug("100%") return c_matrix def _load_trajectories(self, directory, sims): """Read simulation results from output files. Returns `tout` and `trajectories` arrays. """ files = [filename for filename in os.listdir(directory) if re.match(self._prefix, filename)] if len(files) == 0: raise SimulatorException( "Cannot find any output files to load data from.") if len(files) != len(sims): raise SimulatorException( "Number of output files (%d) does not match number " "of requested simulations (%d)." % ( len(files), len(sims))) n_sims = len(files) trajectories = [None] * n_sims tout = [None] * n_sims traj_n = np.ones((len(self.tspan), self._len_species)) * float('nan') tout_n = np.ones(len(self.tspan)) * float('nan') # load the data indir_prefix = os.path.join(directory, self._prefix) for idx, n in enumerate(sims): trajectories[idx] = traj_n.copy() tout[idx] = tout_n.copy() filename = indir_prefix + "_" + str(idx) if not os.path.isfile(filename): raise Exception("Cannot find input file " + filename) # determine optimal loading method if idx == 0: (data, use_pandas) = self._test_pandas(filename) # load data else: if use_pandas: data = self._load_with_pandas(filename) else: data = self._load_with_openfile(filename) # store data tout[idx] = data[:, 0] trajectories[idx][:, self._out_species] = data[:, 1:] # volume correction if self.vol: trajectories[idx][:, self._out_species] *= (N_A * self.vol) return np.array(tout), np.array(trajectories) def _test_pandas(self, filename): """ calculates the fastest method to load in data Parameters ---------- filename : str filename to laod in Returns ------- np.array, bool """ # using open(filename,...) start = time.time() data = self._load_with_openfile(filename) end = time.time() load_time_openfile = end - start # using pandas if pd: start = time.time() self._load_with_pandas(filename) end = time.time() load_time_pandas = end - start if load_time_pandas < load_time_openfile: return data, True return data, False @staticmethod def _load_with_pandas(filename): data = pd.read_csv(filename, sep='\t', skiprows=None, header=None).to_numpy() return data @staticmethod def _load_with_openfile(filename): with open(filename, 'r') as f: data = [line.rstrip('\n').split() for line in f] data = np.array(data, dtype=np.float, copy=False) return data
def run_cupsoda(model, tspan, initials=None, param_values=None, integrator='cupsoda', cleanup=True, verbose=False, **kwargs): """Wrapper method for running cupSODA simulations. Parameters ---------- See ``CupSodaSimulator`` constructor. Returns ------- SimulationResult.all : list of record arrays List of trajectory sets. The first dimension contains species, observables and expressions (in that order) """ sim = CupSodaSimulator(model, tspan=tspan, integrator=integrator, cleanup=cleanup, verbose=verbose, **kwargs) simres =, param_values=param_values) return simres.all