MantisBT - Rosetta
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IDProjectCategoryView StatusDate SubmittedLast Update
0000218Rosetta[All Projects] Crashpublic2013-03-16 11:272013-03-19 17:02
Reporterkdrew 
Assigned Tormoretti 
PrioritynormalSeverityminorReproducibilityalways
StatusresolvedResolutionfixed 
Platformx86OSOS XOS Version10.6
Product Version 
Fixed in VersionTrunk 
Application(s) Affectedrelax
Command Line Used./bin/relax.macosgccrelease -database ../rosetta_database/
Developer Options
Fixed in SVN Version54387
Summary0000218: Seg fault in relax
DescriptionThe relax application segfaults when only the database option is set.
Steps To ReproduceRun:

./bin/relax.macosgccrelease -database ../rosetta_database/
Additional InformationOutput:
-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-
TagsNo tags attached.
Relationships
related to 0000221new  Crashes on blank command line 
Attached Files
Issue History
Date ModifiedUsernameFieldChange
2013-03-16 11:27kdrewNew Issue
2013-03-16 12:47smlewisNote Added: 0000180
2013-03-16 12:47smlewisStatusnew => confirmed
2013-03-18 19:15rmorettiNote Added: 0000186
2013-03-19 16:46rmorettiFixed in SVN Version => 54387
2013-03-19 16:46rmorettiAssigned To => rmoretti
2013-03-19 16:46rmorettiResolutionopen => fixed
2013-03-19 16:46rmorettiFixed in Version => Trunk
2013-03-19 16:46rmorettiSteps to Reproduce Updatedbug_revision_view_page.php?rev_id=59#r59
2013-03-19 16:47rmorettiStatusconfirmed => resolved
2013-03-19 17:02rmorettiRelationship addedrelated to 0000221

Notes
(0000180)
smlewis   
2013-03-16 12:47   
confirmed on linuxclangrelease
(0000186)
rmoretti   
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.