Baliphy seg fault and/or memory errors
darren...@googlemail.com
bali-phy --version
VERSION: 3.4
BUILD: Jan 21 2019 09:51:59
ARCH: linux x86_64
COMPILER: gcc 7.3.1 x86_64
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!
Benjamin Redelings
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
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
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