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GC error (probable corruption) #43567
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Unfortunately this will not be debuggable without reproducer or rr trace. |
I see.
the program just stalls on a non-blocking call:
Could this be by any chance related? |
Perhaps, but the backtrace is of the outside process not where it's actually blocked. Also rr can make things slow, so you may just need to let it run for a while. |
You can also try running with |
I've had a similar problem with 1.7.2. Downgraded to 1.6.6 LTS and it resolved so does appear to be Julia version specific. |
I talked with Aaron out-of-band, and here are some more details on the code he ran: He has a function function gwas_extract_snps(gwas_fh,gwas_keep_fh,keep_snp_set,delim)
# extract keep_snp_set of snps from a gwas file
gwas_io = GZip.open(gwas_fh)
gwas_keep_io = open(gwas_keep_fh,"w")
i = 1
for line in eachline(gwas_io)
snp = split(line,delim)[2]
if in(snp,keep_snp_set)
write(gwas_keep_io,line*"\n")
end
i += 1
if (i % 1000000) == 0
#println(i)
end
end
close(gwas_io)
close(gwas_keep_io)
end And then he has a Distributed for loop of the form: Distributed.@distributed vcat for met in met_arr_keep
#download file from google bucket
#run gwas_extract_snps()
#delete original file
end This table shows whether or not he gets the segfault. ✅ means no segfault. ❌ means he encountered the segfault.
His data cannot be shared publicly, unfortunately, so we don't have an MWE. |
I have a relatively big multithreaded application which runs fine on 1.6.4, but segfaults on 1.7 and 1.7.1.
I will try to create a minimal example which reproduces this segfault, but for now I have console log only:
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