Comments (4)
jflot
commented on May 30, 2024
I tried again and it's working now... weird!
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rchikhi
commented on May 30, 2024
hi JF!
The error seems to be :
c++: internal compiler error: Killed (program cc1plus)
which, if I could hasard a guess, could be a memory error? How many threads did you compile with?
Rayan
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jflot
commented on May 30, 2024
Hi Rayan,
I did not specify the number of threads, so I guess that it used all the threads available on the node at that time (i.e. up to 40). But then I tried again a while later and it worked... Perhaps there was something going wrong on the cluster at that time?
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rchikhi
commented on May 30, 2024
If you did make -j then yeah, it uses all threads and could possibly run out of memory.
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Related Issues (20)
- new release soon? HOT 2
- Running bcalm raises error: `cannot create a union-find data structure, too many elements.` HOT 6
- error: 'predecessors' following the 'template' keyword does not refer to a template HOT 8
- Error: libc++abi.dylib: terminating with uncaught exception of type std::out_of_range: basic_string HOT 5
- Compiling bcalm causes trouble when no .git repository is found HOT 1
- Output of bcalm2 similar to minia 3.2.1 unitigs? HOT 2
- Memory error with many reference genomes as input HOT 16
- High frequency of nodes with degree of two with length = 2k-1 HOT 2
- .fa files contain lowercase `km` instead of the documented uppercase `KM` HOT 3
- bcalm 2.2.1 on conda for Mac OS X produces incorrect cDBG (the zombie bug returns!!) HOT 12
- Add better input parsing HOT 1
- Improve error message for bad fasta input HOT 1
- Apparently bcalm crashes with very large k's (4096) HOT 1
- bcalm -version return code 1 to shell
- Glue is too strong, because glue files are not deleted.
- insert unitig disregarding the reverse complement HOT 1
- Option `-out-dir` is not used ? HOT 1
- bug report on a metagenomics dataset HOT 3
- Add header description with `-all-abundance-counts` HOT 2
- Is the output file reproducible? HOT 2
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