Smartpca memory error
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- Dominant language
- C
- Stars
- 207
- Forks
- 61
- PR merge metrics
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Description
I am running smartpca with 81 million mutations, 2504 samples, .snp, .ind, and .eigenstratgeno input files, and fastmode enabled.
I use the following command to run it:
smartpca -p filepath/parameter_file
After 20 hours, smartpca fails and I get the following error message in my log file:
*** Error in `smartpca': free(): invalid size: 0x00002bbd4662b010 ***
======= Backtrace: =========
...
======= Memory map: ========
...
number of samples used: 2504 number of snps used: 81255192
I am not sure what could be causing this error. Any help is appreciated!
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Research direction
Start with the smartpca entry point and the parameter file used by the reported command, then review the log around the invalid free error. Reproduce with the reported input scale of 81,255,192 SNPs and 2,504 samples if the data is available; done means identifying the cause of the memory failure and confirming a run that completes without the allocator error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- c
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100