Scott T Small comments

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                                            Scott T Small

lmdb out of memory error on tutorial example

OK, I ran: `with tsinfer.SampleData(path="/scratch365/username/simulation.samples", sequence_length=ts.sequence_length, num_flush_threads=2) as sample_data: for var in ts.variants(): sample_data.add_site(var.site.position, var.genotypes, var.alleles)` Still the same error. I tried absolute path as well. The file system is...

lmdb out of memory error on tutorial example

OK, thanks I will try that. The system has 500G of memory, so that shouldnt be a problem. I will just have to pre-apologize to the other users.

lmdb out of memory error on tutorial example

I tried on my laptop and it worked as expected. It doesnt have enough memory or ram to run my real data. I will contact the sys admins about the...

lmdb out of memory error on tutorial example

Hmm, its telling me that `TypeError: __init__() got an unexpected keyword argument 'max_file_size'` I only see options of: path, sequence_length, num_flush_threads, compressor, chunk_size

lmdb out of memory error on tutorial example

In [9]: tsinfer.__version__ Out[9]: '0.1.4'

lmdb out of memory error on tutorial example

Hi @hyanwong, passing 2**30 to the new version as max_file_size runs the msprime simulation example successfully. With my real data, will I need to estimate the final file size to...

lmdb out of memory error on tutorial example

OK, great. Thanks!

lmdb out of memory error on tutorial example

no, with newer version, meaning same 'Cannot allocate memory' error. It works if I use the max_file_size option.