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MesserLab / SLiM

SLiM is a genetically explicit forward simulation software package for population genetics and evolutionary biology. It is highly flexible, with a built-in scripting language, and has a cross-platform graphical modeling environment called SLiMgui.
https://messerlab.org/slim/
GNU General Public License v3.0
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inscrutible crash: memory error, probably #458

Closed petrelharp closed 1 month ago

petrelharp commented 1 month ago

Running this python script:

import stdpopsim
import tskit
import numpy as np

species = stdpopsim.get_species("HomSap")
model = species.get_demographic_model("OutOfAfrica_3G09")
contig = species.get_contig("chr17", mutation_rate=model.mutation_rate, genetic_map="HapMapII_GRCh38",
                            left=0, right=40000000.0)
dfe = species.get_dfe("Gamma_K17")
exons = species.get_annotations("ensembl_havana_104_exons")
exon_intervals = exons.get_chromosome_annotations("chr17")
contig.add_dfe(intervals=exon_intervals, DFE=dfe)
engine = stdpopsim.get_engine("slim")
samples = {"YRI": 100, "CHB": 100, "CEU": 100}

ts = engine.simulate(model, contig, samples, slim_scaling_factor=50, seed=123)

results in a "slim crashed" sort of error; asking it to please output the SLiM script (here: script.txt) and running that in SLiM results in

1: Starting burn-in...
1461: {dbg(self.source); p0.setSubpopulationSize(246);}
1525: {dbg(self.source); p = sim.addSubpopSplit(1,42,0); p.name = 'CEU';}
1525: {dbg(self.source); p0.setMigrationRates(1, 0.0125);}
1525: {dbg(self.source); p1.setMigrationRates(0, 0.0125);}
1620: {dbg(self.source); p = sim.addSubpopSplit(2,10,1); p.name = 'CHB';}
1620: {dbg(self.source); p1.setSubpopulationSize(20);}
1620: {dbg(self.source); p0.setMigrationRates(1, 0.0015);}
1620: {dbg(self.source); p0.setMigrationRates(2, 0.00095);}
1620: {dbg(self.source); p1.setMigrationRates(0, 0.0015);}
1620: {dbg(self.source); p1.setMigrationRates(2, 0.0048);}
1620: {dbg(self.source); p2.setMigrationRates(0, 0.00095);}
1620: {dbg(self.source); p2.setMigrationRates(1, 0.0048);}
1621: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1621: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1622: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1622: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1623: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1623: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1624: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1624: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1625: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1625: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1626: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1626: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1627: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1627: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1628: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1628: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1629: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1629: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1630: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1630: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1631: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1631: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1632: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1632: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1633: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1633: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1634: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1634: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1635: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1635: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1636: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1636: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1637: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(20*exp(0.2*gx))); p1.setSubpopulationSize(size);}
1637: {dbg(self.source); gx=community.tick-1620; size=asInteger(round(10*exp(0.275*gx))); p2.setSubpopulationSize(size);}
1637: {dbg(self.source); inds=p0.sampleIndividuals(100); sim.treeSeqRememberIndividuals(inds);}
1637: {dbg(self.source); inds=p1.sampleIndividuals(100); sim.treeSeqRememberIndividuals(inds);}
1637: {dbg(self.source); inds=p2.sampleIndividuals(100); sim.treeSeqRememberIndividuals(inds);}
double free or corruption (!prev)
Aborted

Running the script in SLiMgui crashes my OS (well, just the window manager, actually). There seems to be a memory error somewhere. This is with

$ slim -v
SLiM version 4.2.2, built May 28 2024 11:17:11
Git commit SHA-1: 7dc12178b00ee83de3461616981e1e087fe88624