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iqtree / iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
GNU General Public License v2.0
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Memory issue? #321

Closed brmagalis closed 6 days ago

brmagalis commented 1 week ago

When running lmap, I was able to get to the quartet likelihoods (for which I chose all), but I'm guessing I ran into a memory issue (see below)? %iqtree_44855174.txt

Performing likelihood mapping with all quartets... Computing 42625820447210 quartet likelihoods (one dot represents 100 quartets).

terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc ERROR: STACK TRACE FOR DEBUGGING: ERROR: 1 funcAbort() ERROR: 2 () ERROR: 3 gsignal() ERROR: 4 abort() ERROR: 5 __gnu_cxx::verbose_terminate_handler() ERROR: 6 () ERROR: 7 () ERROR: 8 cxa_rethrow() ERROR: 9 operator new(unsigned long) ERROR: 10 std::vector<QuartetInfo, std::allocator >::_M_default_append(unsigned long) ERROR: 11 PhyloTree::computeQuartetLikelihoods(std::vector<QuartetInfo, std::allocator >&, QuartetGroups&) ERROR: 12 PhyloTree::doLikelihoodMapping() ERROR: 13 runTreeReconstruction(Params&, IQTree&) ERROR: 14 runPhyloAnalysis(Params&, Checkpoint, IQTree&, Alignment&) ERROR: 15 runPhyloAnalysis(Params&, Checkpoint*) ERROR: 16 main() ERROR: 17 __libc_start_main() ERROR: 18 () ERROR: ERROR: IQ-TREE CRASHES WITH SIGNAL ABORTED ERROR: For bug report please send to developers: ERROR: Log file: HG02_gp120.fa.log ERROR: Alignment files (if possible) /tmp/slurmd/job44855174/slurm_script: line 24: 3351709 Aborted (core dumped) iqtree2 -s $file -lmap all

thomaskf commented 6 days ago

Yes, it is out of the memory. From your log file, IQTREE is computing 42625820447210 quartet likelihoods. It needs around 3K TB memory! We will add a message to show the memory usage for this step in our future release. Thank you for reporting the issue.

brmagalis commented 5 days ago

Indeed I did choose all (not thinking), so I reduced that to 25x seq number and no issues. Thanks so much!

From: Thomas Wong @.> Date: Monday, September 23, 2024 at 8:23 PM To: iqtree/iqtree2 @.> Cc: Brittany Rife Magalis @.>, Author @.> Subject: Re: [iqtree/iqtree2] Memory issue? (Issue #321)

Yes, it is out of the memory. From your log file, IQTREE is computing 42625820447210 quartet likelihoods. It needs around 3K TB memory! We will add a message to show the memory usage for this step in our future release. Thank you for reporting the issue.

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