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bioinfologics / satsuma2

FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing
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Segmentation fault (core dumped) on test data during KMatch #11

Closed conte1 closed 6 years ago

conte1 commented 6 years ago

Hi,

I'm trying to run satsuma2 using the "test_SatsumaSynteny2" script provided.

I'm getting a seg fault in the KMatch step. The "KM11.log" file shows: /export/software/slurm/spool/slurmd/job11727436/slurm_script: line 2: 8343 Segmentation fault (core dumped) ./bin/KMatch samples/human.X.part.fasta samples/dog.X.part.fasta 13 xcorr_sample_synt/kmat ch_results.k13 13 12 1

And if I try to run that KMatch command by itself, I get: Segmentation fault (core dumped)

Any ideas?

Thanks, Matt

jonwright99 commented 6 years ago

Hi Matt,

Which version of GCC have you used to compile satsuma2?

Thanks, Jon

conte1 commented 6 years ago

I'm using GCC 6.1.0 (and cmake 3.9.1).

jonwright99 commented 6 years ago

We've seen this before and we traced it to a bug in GCC v6. I think the optimisation -O3 in the CMakeList.txt is the cause. If you use -O0 with gcc6 it works, ie. set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -lpthread -std=c++14 -O0 -w")

Or you can use GCC v5.

conte1 commented 6 years ago

Changing to "-O0" and recompiling with gcc6 fixed the issue, thanks.