0000218: Seg fault in relax

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Date Submitted

Last Update

0000218

Rosetta

[All Projects] Crash

public

2013-03-16 11:27

2013-03-19 17:02

Reporter

kdrew

Assigned To

rmoretti

Priority

normal

Severity

minor

Reproducibility

always

Status

resolved

Resolution

fixed

Platform

x86

OS X

OS Version

10.6

Product Version

Fixed in Version

Trunk

Summary

0000218: Seg fault in relax

Description

The relax application segfaults when only the database option is set.

Steps To Reproduce

Run:

./bin/relax.macosgccrelease -database ../rosetta_database/

Additional Information

Output:
-snip-
fry2:rosetta_source kdrew$ ./bin/relax.macosgccrelease -database ../rosetta_database/
core.init: Mini-Rosetta version d986849300e5772557ea07c7b76044e93e0f8ddf from git@markula.bio.nyu.edu:rosetta-bonneaulab.git
core.init: command: ./bin/relax.macosgccrelease -database ../rosetta_database/
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1416404664 seed_offset=0 real_seed=-1416404664
core.init.random: RandomGenerator:init: Normal mode, seed=-1416404664 RG_type=mt19937
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN6_mem_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN10_mem_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/MembranePotential/memcbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/MembranePotential/mem_pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp
basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4
protocols.relax.FastRelax: ================== Using default script ==================
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
Segmentation fault
-snip-

Tags

No tags attached.

Application(s) Affected

relax

Command Line Used

./bin/relax.macosgccrelease -database ../rosetta_database/

Developer Options

Fixed in SVN Version

54387

Attached Files

Relationships

related to

0000221

new

Crashes on blank command line

Notes
(0000180) smlewis (Administrator) 2013-03-16 12:47	confirmed on linuxclangrelease

(0000186) rmoretti (Attentive Developer) 2013-03-18 19:15	It looks like there's two issues involved here. The first is that Conformation::is_residue_typeset() assumes that the conformation that it's being called upon has at least one residue in it. -- The algorithm for Conformation::is_residue_typeset() is somewhat broken to begin with (it arbitrarily picks two residues in the pose and assumes that their residue type sets are representative of the entire pose). The other issue is that jd2 looks to be feeding an empty pose to the mover in the case where there's no input flags on the command line. Is this behavior the desired one? I notice there's a default for GenericJobInputter if no other input type is specified, with the comment that it's used for abinitio and the like.

Issue History
Date Modified	Username	Field	Change
2013-03-16 11:27	kdrew	New Issue
2013-03-16 12:47	smlewis	Note Added: 0000180
2013-03-16 12:47	smlewis	Status	new => confirmed
2013-03-18 19:15	rmoretti	Note Added: 0000186
2013-03-19 16:46	rmoretti	Fixed in SVN Version	=> 54387
2013-03-19 16:46	rmoretti	Assigned To	=> rmoretti
2013-03-19 16:46	rmoretti	Resolution	open => fixed
2013-03-19 16:46	rmoretti	Fixed in Version	=> Trunk
2013-03-19 16:46	rmoretti	Steps to Reproduce Updated	View Revisions
2013-03-19 16:47	rmoretti	Status	confirmed => resolved
2013-03-19 17:02	rmoretti	Relationship added	related to 0000221