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ID | Project | Category | View Status | 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 | 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 | ||||||
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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 |
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