Closed gtsambos closed 3 years ago
Hmm, actually, this doesn't seem to be just a mutation-related issue. I'm seeing it on tree sequences without mutations now too. It appears to happen more frequently in tree sequences with more samples.
Bug detected in lib/tskit/tables.c at line 7438. If you are using tskit directly please open an issue on GitHub, ideally with a reproducible example. (https://github.com/tskit-dev/tskit/issues) If you are using software that uses tskit, please report an issue to that software's issue tracker, at least initially.
Abort trap: 6
^I'm occasionally getting this bug too. Might be a different problem though.
Here's a reproducible example:
>>> import tskit, msprime
>>> tskit.__version__
'0.3.8.dev1'
>>> msprime.__version__
'1.0.1'
>>> ts = msprime.sim_ancestry(samples=100, sequence_length=1e7,
... discrete_genome=True, recombination_rate=1e-8, population_size=500,
... model='dtwf', random_seed=2022)
>>> ts.find_ibd(min_length=100000)
Python(91745,0x11b6f55c0) malloc: Incorrect checksum for freed object 0x7fdc0e1ace00: probably modified after being freed.
Corrupt value: 0x4110677c00000000
Python(91745,0x11b6f55c0) malloc: *** set a breakpoint in malloc_error_break to debug
Abort trap: 6
I'll look at this and try to recreate.
Thanks @benjeffery - I just chatted to @gtsambos and I'm going to look at it now as my top priority
Excellent - I can reproduce on linux - I'll report back once I know what's going on.
Phew! @benjeffery, I'm having some strange things happen when I try to update to the most recent dev version of tskit -- I'll message you on Slack about it
This may be redundant now, but I can confirm that the same behaviour occurs using the code at the current head of the main branch
I think the bug assert must be a different manifestation of the memory corruption (this is where it gets triggered), so I'm going to assume that #1740 fixes that as well.
I got this error message
when I ran the following code:
This code used to work fine, so I assume it's happened because of the recent changes. I'm using the development version of tskit at this commit.