Baliphy seg fault and/or memory errors

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darren...@googlemail.com

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Jan 21, 2019, 9:05:34 AM1/21/19
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Hi,

I'm trying to analyse around 50 sequences of roughly 250 AA's with two constraints. (file attached, ignoring the constraints at the moment). 

This file causes baliphy to either segfault or to throw a lot of errors that look array-size related. I have tried cutting it into smaller datasets to see if it's one sequence in particular, but it appears not as it will run with either half of the sequences. 

I'm therefore left guessing that it may be something about the size of the file, perhaps leading to a zero initial state?

 

bali-phy --version

VERSION: 3.4

BUILD: Jan 21 2019 09:51:59

ARCH: linux x86_64

COMPILER: gcc 7.3.1 x86_64


and simply using the command:  

bali-phy BaliPhy_StartAlignment.fas to minimise any complexity at this stage.

Any suggestions would be gratefully received.


Best wishes


Darren



Some example failures are pasted below the precise failure is often different):

 

------------------------- example 1 -----------------------------------------------------

 

bali-phy: Error!  move = pre-burnin

   submove = NNI_and_lengths

 [single] move = NNI_and_lengths

evaluating reg # 4997 (unchangeable): Array:getIndex <4809> <5875>

 

evaluating reg # 4660 (unchangeable): SModel:calc_root_probability <24737> <6588> <411> <6574> <410> <31843> <5869>

 

evaluating reg # 24737 (unchangeable): Array:getIndex <37623> <24840>

 

evaluating reg # 37296 (unchangeable): case <12108> of {[] -> SModel:peel_leaf_branch (Array:getIndex <5269> <409>) (Array:getIndex <5177> <409>) 'Amino-Acids' (Array:getIndex <5589> 72),n:o -> case o of {p:q -> case q of {[] -> SModel:peel_internal_branch (Array:getIndex <37623> n) (Array:getIndex <37623> p) (Array:getIndex <5268> n) (Array:getIndex <5268> p) (Array:getIndex <5589> 72) <5869>,_ -> <2613>},_ -> <2613>},_ -> <2613>}

 

evaluating reg # 34569 (unchangeable): SModel:peel_internal_branch <24848> <3125> <6201> <4042> <4064> <5869>

 

evaluating reg # 3125 (unchangeable): Array:getIndex <37623> <26351>

 

evaluating reg # 9828 (unchangeable): SModel:peel_internal_branch <13813> <13814> <13815> <6179> <6176> <5869>

 

evaluating reg # 10488 (unchangeable): SModel:peel_internal_branch <10494> <10492> <10491> <10490> <34182> <5869>

 

evaluating reg # 17952 (unchangeable): SModel:peel_internal_branch <24869> <6271> <16999> <31976> <17951> <5869>

 

evaluating reg # 18150 (unchangeable): SModel:peel_internal_branch <1698> <15710> <24968> <26672> <18151> <5869>

 

evaluating reg # 22092 (unchangeable): SModel:peel_internal_branch <22088> <19929> <22082> <22089> <22090> <5869>

 

evaluating reg # 22710 (unchangeable): SModel:peel_internal_branch <22698> <22705> <22706> <22708> <22709> <5869>

 

evaluating reg # 6311 (unchangeable): SModel:peel_internal_branch <6308> <26615> <26617> <26618> <26619> <5869>

 

evaluating reg # 6194 (unchangeable): SModel:peel_internal_branch <29788> <29787> <3439> <18858> <18875> <5869>

 

evaluating reg # 34170 (unchangeable): Prelude:vector_from_list <24326>

 

evaluating reg # 8917 (unchangeable): SModel:lExp <32328> <32333> <8303>

 

evaluating reg # 8303 (unchangeable): Prelude:multiply <9198> 1.0

 

Multiply: object 'unprintable[Likelihood_Cache_Branch] 0x2f6adc0' is not double, int, log_double, or char'

 

 

 

-------------------------- example 2 ---------------------------------------------

 

*** Error in `bali-phy': free(): invalid next size (normal): 0x00000000048c39c0 ***

======= Backtrace: =========

/lib64/libc.so.6(+0x81429)[0x7f8b6ae3c429]

bali-phy(_ZN23Likelihood_Cache_BranchD0Ev+0x19)[0x531079]

bali-phy(_ZN7closure5clearEv+0x34)[0x78dd64]

bali-phy(_ZN8reg_heap12reclaim_usedEi+0x76)[0x738f36]

bali-phy(_ZN8reg_heap33destroy_all_computations_in_tokenEi+0x17b)[0x72b2cb]

bali-phy(_ZN8reg_heap15release_contextEi+0xe6)[0x72d936]

bali-phy(_ZN7contextD1Ev+0x17)[0x7871c7]

bali-phy(_Z25three_way_topology_sampleR9owned_ptrI5ModelERN4MCMC9MoveStatsEi+0xa31)[0x616391]

bali-phy(_Z39walk_tree_sample_NNI_and_branch_lengthsR9owned_ptrI5ModelERN4MCMC9MoveStatsE+0x12c)[0x54494c]

bali-phy(_ZN4MCMC10SingleMove7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x38)[0x588708]

bali-phy(_ZN4MCMC9MoveGroup7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x4a)[0x58851a]

bali-phy(_ZN4MCMC9MoveGroup7iterateER9owned_ptrI5ModelERNS_9MoveStatsE+0x47)[0x583f37]

bali-phy(_Z13do_pre_burninRKN5boost15program_options13variables_mapER9owned_ptrI5ModelERSoS8_+0x17fa)[0x6d17fa]

bali-phy(main+0x2d61)[0x4bcda1]

/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f8b6addd3d5]

 

 

-----------------------------example 3 --------------------------------

 

 

bali-phy: Error!  move = pre-burnin

   submove = NNI_and_lengths

 [single] move = NNI_and_lengths

Treating 'unprintable[pairwise_alignment_t] 0x4596540' as int!

 

BaliPhy_StartAlignment.fas

Benjamin Redelings

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Jan 21, 2019, 11:20:18 AM1/21/19
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Hi Darren,

    I'm sorry about that!  Thank for the report.

    I've been able to reproduce the problem, and I think I see what it causing it.  The plan is to fix it, do some more extensive testing to see if there are any more problems, and then release a version 3.4.2 in the next few days.

-BenRI

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Benjamin Redelings

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Jan 21, 2019, 11:52:05 AM1/21/19
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Hi Darren,

    Oh, I didn't realize that you were using the development version!  It looks like the bug was only in unreleased versions on the master branch.  I fixed a bug that was introduced into the development branch on Jan 15, and now the burnin completes with your data set.

    Unfortunately constraints are currently broken :-(  I am working on a replacement that will work much better, but it is not ready yet.  So, in the mean time, please don't use them.  Sorry about that!

    If you experience any more problem (with released versions, or with git HEAD) please let me know!

-BenRI

On 1/21/19 8:11 AM, darren.obbard via bali-phy-users wrote:
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