Posts by mrwizer

1) Message boards : Number crunching : Report stuck WU -Stretching messages (Message 7930)
Posted 29 Dec 2005 by mrwizer
Post:
NO_MORE_RELAX_CYCLES_1hz6_224_2007_0

Stuck at 1% for 13 hours now.

A sample of the STDOUT.txt file (I have also saved it, if the proj admins or developers need me to email it)
_______________________________________________


[2005-12-29 01:15:27] :: BOINC :: boinc_init()
command executed: projects/boinc.bakerlab.org_rosetta/rosetta_4.81_windows_intelx86.exe aa 1hz6 A -abrelax -stringent_relax -relax_score_filter -output_chi_silent -vary_omega -sim_aneal -rand_envpair_res_wt -rand_SS_wt -farlx -ex1 -ex2 -silent -barcode_from_fragments -barcode_from_fragments_length 10 -ssblocks -barcode_mode 3 -omega_weight 0.5 -jitter_frag -jitter_variation gauss -max_frags 400 -output_silent_gz -paths frags400.txt -filter1 -105 -filter2 -135 -nstruct 10
[STR OPT]New value for [-paths] frags400.txt.
[T/F OPT]Default FALSE value for [-unix_paths]
[T/F OPT]Default FALSE value for [-version]
[T/F OPT]Default FALSE value for [-score]
[T/F OPT]Default FALSE value for [-abinitio]
[T/F OPT]Default FALSE value for [-refine]
[T/F OPT]Default FALSE value for [-assemble]
[T/F OPT]Default FALSE value for [-idealize]
[T/F OPT]Default FALSE value for [-relax]
[T/F OPT]Default FALSE value for [-abrelax_mode]
[T/F OPT]New TRUE value for [-abrelax]
[T/F OPT]New TRUE value for [-sim_aneal]
[T/F OPT]Default FALSE value for [-cenrlx]
[T/F OPT]Default FALSE value for [-force_expand]
[T/F OPT]Default FALSE value for [-minimize]
Rosetta mode: abrelax
[T/F OPT]Default FALSE value for [-chain]
[T/F OPT]Default FALSE value for [-protein]
[T/F OPT]Default FALSE value for [-series]
series_code = aa :: protein_name is 1hz6:: chain_id is A.
[INT OPT]New value for [-nstruct] 10
[T/F OPT]Default FALSE value for [-use_pdbseq]
[T/F OPT]Default FALSE value for [-read_all_chains]
[T/F OPT]Default FALSE value for [-use_pdb_numbering]
[T/F OPT]Default FALSE value for [-fa_input]
[T/F OPT]Default FALSE value for [-overwrite]
[T/F OPT]Default FALSE value for [-output_pdb_gz]
[T/F OPT]New TRUE value for [-output_silent_gz]
[T/F OPT]Default FALSE value for [-output_scorefile_gz]
[T/F OPT]Default FALSE value for [-termini]
[T/F OPT]Default FALSE value for [-Nterminus]
[T/F OPT]Default FALSE value for [-Cterminus]
[T/F OPT]Default FALSE value for [-use_trie]
[T/F OPT]Default FALSE value for [-no_trie]
[T/F OPT]Default FALSE value for [-trials_trie]
[T/F OPT]Default FALSE value for [-no_trials_trie]
[T/F OPT]Default FALSE value for [-read_interaction_graph]
[T/F OPT]Default FALSE value for [-write_interaction_graph]
[STR OPT]Default value for [-ig_file] .
[T/F OPT]Default FALSE value for [-silent_input]
[T/F OPT]New TRUE value for [-output_chi_silent]
[T/F OPT]Default FALSE value for [-timer]
[T/F OPT]Default FALSE value for [-count_attempts]
[T/F OPT]Default FALSE value for [-status]
[T/F OPT]Default FALSE value for [-ise_movie]
[T/F OPT]Default FALSE value for [-output_all]
[T/F OPT]Default FALSE value for [-skip_missing_residues]
[STR OPT]Default value for [-cst] cst.
[STR OPT]Default value for [-dpl] dpl.
[STR OPT]Default value for [-resfile] none.
[T/F OPT]Default FALSE value for [-auto_resfile]
[T/F OPT]Default FALSE value for [-chain_inc]
[T/F OPT]Default FALSE value for [-full_filename]
[T/F OPT]Default FALSE value for [-map_sequence]
[INT OPT]New value for [-max_frags] 400
[T/F OPT]Default FALSE value for [-enable_dna]
[T/F OPT]Default FALSE value for [-loops]
[T/F OPT]Default FALSE value for [-taboo]
[T/F OPT]Default FALSE value for [-multi_chain]
[T/F OPT]New TRUE value for [-ex1]
[T/F OPT]New TRUE value for [-ex2]
[T/F OPT]Default FALSE value for [-ex3]
[T/F OPT]Default FALSE value for [-ex4]
[T/F OPT]Default FALSE value for [-ex1aro]
[T/F OPT]Default FALSE value for [-ex1aro_half]
[T/F OPT]Default FALSE value for [-ex2aro_only]
[INT OPT]Default value for [-extrachi_cutoff] 18
[T/F OPT]Default FALSE value for [-rot_pert]
[T/F OPT]Default FALSE value for [-rot_pert_input]
[T/F OPT]Default FALSE value for [-exdb]
[T/F OPT]Default FALSE value for [-use_electrostatic_repulsion]
[T/F OPT]Default FALSE value for [-explicit_h2o]
[T/F OPT]Default FALSE value for [-solvate]
[T/F OPT]Default FALSE value for [-try_both_his_tautomers]
[T/F OPT]Default FALSE value for [-minimize_rot]
[T/F OPT]Default FALSE value for [-read_hetero_h2o]
[T/F OPT]Default FALSE value for [-Wint_score_only]
[T/F OPT]Default FALSE value for [-Wint_repack_only]
[T/F OPT]Default FALSE value for [-ligand]
[T/F OPT]Default FALSE value for [-enzyme_design]
[T/F OPT]Default FALSE value for [-score_contact_flag]
[T/F OPT]Default FALSE value for [-score_contact_weight]
[T/F OPT]Default FALSE value for [-score_contact_threshold]
[T/F OPT]Default FALSE value for [-scorefxn]
default centroid scorefxn: 4
default fullatom scorefxn: 12
[INT OPT]Default value for [-run_level] 0
[T/F OPT]New TRUE value for [-silent]
run level: -4
[T/F OPT]Default FALSE value for [-benchmark]
[T/F OPT]Default FALSE value for [-debug]
[STR OPT]Default value for [-s] none.
[STR OPT]Default value for [-l] none.
Reading .Rama_smooth_dyn.dat_ss_6.4.gz
Reading .phi.theta.36.HS.resmooth.gz
Reading .phi.theta.36.SS.resmooth.gz
[STR OPT]Default value for [-atom_vdw_set] default.
[T/F OPT]Default FALSE value for [-IUPAC]
Atom_mode set to all
Reading .paircutoffs.gz
[T/F OPT]Default FALSE value for [-decoystats]
set_decoystats_flag: from,to F F
[T/F OPT]Default FALSE value for [-decoyfeatures]
BOINC :: [2005-12-29 01:15:28] :: Total iterations: 10 :: mode: abrelax :: nstartnm: 1 :: number_of_output: 10 :: num_decoys: 0 :: percent complete: 0.01
Searching for dat file: .1hz6.dat
Searching for dat file: .1hz6.dat
WARNING!! .dat file not found!
Looking for fasta file: .1hz6A.fasta
[T/F OPT]Default FALSE value for [-find_disulf]
[T/F OPT]Default FALSE value for [-fix_disulf]
Looking for psipred file: .1hz6A.psipred_ss2
Protein type: alpha/beta Fraction beta: 0.617021263
disabling rg filter
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
WARNING: CONSTRAINT FILE NOT FOUND
Searched for: .1hz6A.cst
Running without distance constraints
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
WARNING: DIPOLAR CONSTRAINT FILE NOT FOUND
Searched for: .1hz6A.dpl
Dipolar constraints will not be used
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
fragment file: .aa1hz6A03_05.400_v1_3.gz
Total Residue 61
frag size: 3 frags/residue: 400
fragment file: .aa1hz6A09_05.400_v1_3.gz
Total Residue 61
frag size: 9 frags/residue: 400
generating 1mer library from 3mer library
[T/F OPT]New TRUE value for [-ssblocks]
1 0.0149999997 0.430000007 -1.8363593E+00900
2 0.0299999993 0.792500019 0.17749999521
3 0.0175000001 0.792500019 0.18999999821
4 0.0524999984 0.732500017 0.21500000421
5 0.0425000004 0.747500002 2.25586629E+01621
6 0.0225000009 0.839999974 -1.83370777E+01721
7 0.00749999983 0.977500021 0.014999999721
8 0.00249999994 0.980000019 35160310421
9 0.0199999996 0.764999986 0.21500000421
10 0.0399999991 0.234999999 14394196800
11 0.0199999996 0.0399999991 -1.60733267E+01600
12 0.00999999978 0.0149999997 0.97500002400
13 0.057500001 0.197500005 -0.73306000200
14 0.132499993 0.425000012 -4.23690928E+02400
15 0.132499993 0.402500004 638593800
16 0.234999999 0.297500014 0.46750000100
17 0.479999989 0.224999994 2.86595359E+01000
18 0.540000021 0.194999993 0.26175373800
19 0.465000004 0.142499998 0.39250001300
20 0.337500006 0.0649999976 128172.64100
21 0.469999999 0.0125000002 -7.16588273E+02300
22 0.725000024 0.00999999978 0.26499998611
23 0.935000002 0.00249999994 0.062511
24 0.972500026 0 -0.81595522211
25 0.997500002 0.00249999994 -7.96294774E-01611
26 0.897499979 0.00749999983 2.37414636E+03511
27 0.944999993 0.00249999994 2.04763381E+02311
28 0.972500026 0.00249999994 -26.966951411
29 0.959999979 0.00749999983 -2207171.511
30 0.967499971 0.00749999983 1.39577531E+03511
31 0.967499971 0.0125000002 1.#QNAN11
32 0.935000002 0.0175000001 0.047499999411
33 0.959999979 0.00499999989 1893.1519811
34 0.957499981 0.0149999997 2.11673764E+01011
35 0.925000012 0.0149999997 0.059999998711
36 0.772499979 0.109999999 -6.08110321E+02311
37 0.730000019 0.132499993 1.9630264E+03411
38 0.479999989 0.232500002 0.28749346700
39 0.185000002 0.170000002 3.95917468E+03500
40 0.0775000006 0.129999995 0.79691147800
41 0.0175000001 0.0524999984 -1.81152543E+01000
42 0.00999999978 0.104999997 8.2244322E+01400
43 0.0199999996 0.620000005 0.36000001400
44 0.0225000009 0.872500002 0.10499999721
45 0.0175000001 0.922500014 0.059999998721
46 0.0225000009 0.899999976 0.077500000621
47 0.0625 0.74000001 0.19750000521
48 0.0524999984 0.622500002 -1.15750527E+02800
49 0.057500001 0.167500004 0.77499997600
50 0.0474999994 0.0350000001 -4.39199683E+02500
51 0.0149999997 0.102499999 0.88249999300
52 0.00999999978 0.529999971 373089400
53 0.0125000002 0.842499971 -6.21198231E+01721
54 0.0125000002 0.949999988 0.037500001521
55 0.0149999997 0.972500026 0.012500000221
56 0.0175000001 0.944999993 1.25936928E+01721
57 0.0799999982 0.839999974 0.079999998221
58 0.075000003 0.855000019 -2.63520977E+02721
59 0.0724999979 0.754999995 1.65152136E+01321
60 0.0324999988 0.319999993 0.64817297500
61 0.00999999978 0.0974999964 -7.014964E+01200
1 2 9 0.828437507
2 23 36 0.940357208
3 44 47 0.858750045
4 53 59 0.880000055
[T/F OPT]Default FALSE value for [-check_homs]
calculating fragment_diversity...
[T/F OPT]New TRUE value for [-barcode_mode]
[INT OPT]New value for [-barcode_mode] 3
[T/F OPT]Default FALSE value for [-increment_barcode]
[T/F OPT]Default FALSE value for [-barcode_file]
[T/F OPT]New TRUE value for [-barcode_from_fragments]
feature_set::analyze_fragments: analyzing fragments to generate consistent sampling barcode
res_num = 1 H=17 E=120 L=263 A=36 G=0 O=0 B=364 EE=0
res_num = 2 H=35 E=619 L=146 A=79 G=0 O=0 B=721 EE=0
res_num = 3 H=68 E=982 L=150 A=123 G=0 O=0 B=1077 EE=0
res_num = 4 H=58 E=956 L=186 A=170 G=7 O=0 B=1023 EE=0
res_num = 5 H=65 E=914 L=221 A=165 G=16 O=0 B=1017 EE=2
res_num = 6 H=43 E=782 L=375 A=191 G=103 O=0 B=905 EE=1
res_num = 7 H=48 E=1074 L=78 A=94 G=3 O=0 B=1103 EE=0
res_num = 8 H=53 E=1103 L=44 A=130 G=0 O=0 B=1070 EE=0
res_num = 9 H=57 E=1052 L=91 A=113 G=5 O=0 B=1080 EE=2
res_num = 10 H=41 E=759 L=400 A=291 G=16 O=0 B=892 EE=1
res_num = 11 H=23 E=190 L=987 A=537 G=188 O=0 B=471 EE=4
res_num = 12 H=23 E=38 L=1139 A=104 G=744 O=0 B=160 EE=192
res_num = 13 H=64 E=172 L=964 A=346 G=27 O=0 B=825 EE=2
res_num = 14 H=105 E=551 L=544 A=344 G=1 O=0 B=853 EE=2
res_num = 15 H=145 E=525 L=530 A=386 G=46 O=0 B=764 EE=4
res_num = 16 H=149 E=535 L=516 A=364 G=8 O=0 B=828 EE=0
res_num = 17 H=311 E=553 L=336 A=436 G=17 O=0 B=745 EE=2
res_num = 18 H=372 E=557 L=271 A=488 G=15 O=0 B=694 EE=3
res_num = 19 H=422 E=492 L=286 A=500 G=24 O=0 B=673 EE=3
res_num = 20 H=370 E=323 L=507 A=559 G=36 O=0 B=602 EE=3
res_num = 21 H=243 E=157 L=800 A=320 G=366 O=0 B=260 EE=254
res_num = 22 H=394 E=172 L=634 A=580 G=1 O=0 B=617 EE=2
res_num = 23 H=831 E=143 L=226 A=919 G=9 O=0 B=272 EE=0
res_num = 24 H=977 E=83 L=140 A=1046 G=6 O=0 B=148 EE=0
res_num = 25 H=1050 E=52 L=98 A=1102 G=8 O=0 B=90 EE=0
res_num = 26 H=1009 E=37 L=154 A=1090 G=5 O=0 B=103 EE=2
res_num = 27 H=973 E=36 L=191 A=1046 G=1 O=0 B=150 EE=3
res_num = 28 H=1059 E=22 L=119 A=1091 G=2 O=0 B=107 EE=0
res_num = 29 H=1140 E=12 L=48 A=1163 G=8 O=0 B=29 EE=0
res_num = 30 H=1141 E=18 L=41 A=1167 G=1 O=0 B=32 EE=0
res_num = 31 H=1070 E=49 L=81 A=1109 G=2 O=0 B=89 EE=0
res_num = 32 H=1043 E=74 L=83 A=1098 G=1 O=0 B=101 EE=0
res_num = 33 H=978 E=89 L=133 A=1039 G=4 O=0 B=157 EE=0
res_num = 34 H=1028 E=70 L=102 A=1080 G=1 O=0 B=119 EE=0
res_num = 35 H=1005 E=39 L=156 A=1077 G=15 O=0 B=108 EE=0
res_num = 36 H=887 E=60 L=253 A=1027 G=1 O=0 B=172 EE=0
res_num = 37 H=906 E=82 L=212 A=992 G=6 O=0 B=202 EE=0
res_num = 38 H=680 E=80 L=440 A=927 G=22 O=0 B=248 EE=3
res_num = 39 H=584 E=85 L=531 A=864 G=26 O=0 B=310 EE=0
res_num = 40 H=342 E=68 L=790 A=742 G=49 O=0 B=404 EE=5
res_num = 41 H=77 E=26 L=1097 A=634 G=209 O=0 B=352 EE=5
res_num = 42 H=28 E=48 L=1124 A=97 G=733 O=0 B=191 EE=179
res_num = 43 H=60 E=467 L=673 A=264 G=12 O=0 B=921 EE=3
res_num = 44 H=55 E=945 L=200 A=113 G=15 O=0 B=1071 EE=1
res_num = 45 H=50 E=1035 L=115 A=92 G=1 O=0 B=1105 EE=2
res_num = 46 H=81 E=1026 L=93 A=145 G=0 O=0 B=1055 EE=0
res_num = 47 H=81 E=964 L=155 A=160 G=22 O=0 B=1014 EE=4
res_num = 48 H=140 E=701 L=359 A=369 G=0 O=0 B=831 EE=0
res_num = 49 H=146 E=449 L=605 A=461 G=7 O=0 B=732 EE=0
res_num = 50 H=92 E=64 L=1044 A=555 G=92 O=0 B=537 EE=16
res_num = 51 H=52 E=54 L=1094 A=611 G=191 O=0 B=390 EE=8
res_num = 52 H=41 E=499 L=660 A=113 G=335 O=0 B=461 EE=291
res_num = 53 H=47 E=937 L=216 A=112 G=3 O=0 B=1085 EE=0
res_num = 54 H=45 E=1071 L=84 A=91 G=0 O=0 B=1109 EE=0
res_num = 55 H=57 E=1029 L=114 A=131 G=10 O=0 B=1059 EE=0
res_num = 56 H=62 E=958 L=180 A=116 G=93 O=0 B=990 EE=1
res_num = 57 H=75 E=1027 L=98 A=125 G=0 O=0 B=1075 EE=0
res_num = 58 H=77 E=983 L=140 A=167 G=5 O=0 B=1028 EE=0
res_num = 59 H=91 E=906 L=203 A=166 G=9 O=0 B=1023 EE=2
res_num = 60 H=52 E=326 L=422 A=219 G=66 O=0 B=514 EE=1
res_num = 61 H=8 E=39 L=353 A=49 G=142 O=5 B=111 EE=93
[INT OPT]New value for [-barcode_from_fragments_length] 10
Feature: bff_000
Flavor 8.65039e-008
Flavor 0.002125
barcode_cst: torsion= 14 residue= 1 cval= H ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.015
barcode_cst: torsion= 14 residue= 1 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.032875
barcode_cst: torsion= 14 residue= 1 cval= L ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0045
barcode_cst: torsion= 13 residue= 1 cval= A ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0455
barcode_cst: torsion= 13 residue= 1 cval= B ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0021875
barcode_cst: torsion= 14 residue= 2 cval= H ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0386875
barcode_cst: torsion= 14 residue= 2 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.009125
barcode_cst: torsion= 14 residue= 2 cval= L ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0049375
barcode_cst: torsion= 13 residue= 2 cval= A ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0450625
barcode_cst: torsion= 13 residue= 2 cval= B ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00283333
barcode_cst: torsion= 14 residue= 3 cval= H ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0409167
barcode_cst: torsion= 14 residue= 3 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00625
barcode_cst: torsion= 14 residue= 3 cval= L ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.005125
barcode_cst: torsion= 13 residue= 3 cval= A ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.044875
barcode_cst: torsion= 13 residue= 3 cval= B ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00241667
barcode_cst: torsion= 14 residue= 4 cval= H ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0398333
barcode_cst: torsion= 14 residue= 4 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00775
barcode_cst: torsion= 14 residue= 4 cval= L ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00708333
barcode_cst: torsion= 13 residue= 4 cval= A ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.042625
barcode_cst: torsion= 13 residue= 4 cval= B ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.000291667
barcode_cst: torsion= 13 residue= 4 cval= G ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00270833
barcode_cst: torsion= 14 residue= 5 cval= H ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0380833
barcode_cst: torsion= 14 residue= 5 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00920833
barcode_cst: torsion= 14 residue= 5 cval= L ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.006875
barcode_cst: torsion= 13 residue= 5 cval= A ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.042375
barcode_cst: torsion= 13 residue= 5 cval= B ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.000666667
barcode_cst: torsion= 13 residue= 5 cval= G ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 8.33333e-005
barcode_cst: torsion= 13 residue= 5 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00179167
barcode_cst: torsion= 14 residue= 6 cval= H ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0325833
barcode_cst: torsion= 14 residue= 6 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.015625
barcode_cst: torsion= 14 residue= 6 cval= L ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00795833
barcode_cst: torsion= 13 residue= 6 cval= A ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0377083
barcode_cst: torsion= 13 residue= 6 cval= B ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00429167
barcode_cst: torsion= 13 residue= 6 cval= G ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 4.16667e-005
barcode_cst: torsion= 13 residue= 6 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.002
barcode_cst: torsion= 14 residue= 7 cval= H ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.04475
barcode_cst: torsion= 14 residue= 7 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00325
barcode_cst: torsion= 14 residue= 7 cval= L ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00391667
barcode_cst: torsion= 13 residue= 7 cval= A ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0459583
barcode_cst: torsion= 13 residue= 7 cval= B ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.000125
barcode_cst: torsion= 13 residue= 7 cval= G ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00220833
barcode_cst: torsion= 14 residue= 8 cval= H ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0459583
barcode_cst: torsion= 14 residue= 8 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00183333
barcode_cst: torsion= 14 residue= 8 cval= L ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00541667
barcode_cst: torsion= 13 residue= 8 cval= A ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0445833
barcode_cst: torsion= 13 residue= 8 cval= B ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.002375
barcode_cst: torsion= 14 residue= 9 cval= H ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0438333
barcode_cst: torsion= 14 residue= 9 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00379167
barcode_cst: torsion= 14 residue= 9 cval= L ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00470833
barcode_cst: torsion= 13 residue= 9 cval= A ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.045
barcode_cst: torsion= 13 residue= 9 cval= B ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.000208333
barcode_cst: torsion= 13 residue= 9 cval= G ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 8.33333e-005
barcode_cst: torsion= 13 residue= 9 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00170833
barcode_cst: torsion= 14 residue= 10 cval= H ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.031625
barcode_cst: torsion= 14 residue= 10 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0166667
barcode_cst: torsion= 14 residue= 10 cval= L ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.012125
barcode_cst: torsion= 13 residue= 10 cval= A ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0371667
barcode_cst: torsion= 13 residue= 10 cval= B ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.000666667
barcode_cst: torsion= 13 residue= 10 cval= G ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 4.16667e-005
barcode_cst: torsion= 13 residue= 10 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Feature: bff_001
Flavor -5.07425e-008
Flavor 0.000958333
barcode_cst: torsion= 14 residue= 11 cval= H ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00791667
barcode_cst: torsion= 14 residue= 11 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.041125
barcode_cst: torsion= 14 residue= 11 cval= L ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.022375
barcode_cst: torsion= 13 residue= 11 cval= A ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.019625
barcode_cst: torsion= 13 residue= 11 cval= B ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00783333
barcode_cst: torsion= 13 residue= 11 cval= G ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.000166667
barcode_cst: torsion= 13 residue= 11 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.000958333
barcode_cst: torsion= 14 residue= 12 cval= H ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00158333
barcode_cst: torsion= 14 residue= 12 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0474583
barcode_cst: torsion= 14 residue= 12 cval= L ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00433333
barcode_cst: torsion= 13 residue= 12 cval= A ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00666667
barcode_cst: torsion= 13 residue= 12 cval= B ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.031
barcode_cst: torsion= 13 residue= 12 cval= G ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.008
barcode_cst: torsion= 13 residue= 12 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00266667
barcode_cst: torsion= 14 residue= 13 cval= H ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00716667
barcode_cst: torsion= 14 residue= 13 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0401667
barcode_cst: torsion= 14 residue= 13 cval= L ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0144167
barcode_cst: torsion= 13 residue= 13 cval= A ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.034375
barcode_cst: torsion= 13 residue= 13 cval= B ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.001125
barcode_cst: torsion= 13 residue= 13 cval= G ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 8.33333e-005
barcode_cst: torsion= 13 residue= 13 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.004375
barcode_cst: torsion= 14 residue= 14 cval= H ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0229583
barcode_cst: torsion= 14 residue= 14 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0226667
barcode_cst: torsion= 14 residue= 14 cval= L ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0143333
barcode_cst: torsion= 13 residue= 14 cval= A ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0355417
barcode_cst: torsion= 13 residue= 14 cval= B ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 4.16667e-005
barcode_cst: torsion= 13 residue= 14 cval= G ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 8.33333e-005
barcode_cst: torsion= 13 residue= 14 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.00604167
barcode_cst: torsion= 14 residue= 15 cval= H ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.021875
barcode_cst: torsion= 14 residue= 15 cval= E ival= 0 fval= 0 fval1= 0 fval2= 0 fval3= 0
Flavor 0.0220833
2) Message boards : Number crunching : App 4.78 (Message 1677)
Posted 24 Oct 2005 by mrwizer
Post:
Memory usage of the Rosetta application. although realted to the WU type, it can also be affected by the application. For instance, 4.75 had a much larger memory usage.
3) Message boards : Number crunching : App 4.78 (Message 1673)
Posted 24 Oct 2005 by mrwizer
Post:
David (or anyone else that knows), what exactly was changed in 4.78? I know the memory foot print was reduced, and OS X 10.3.9 is now supported. But has anything been added for WU hangs or errors?

Not a push, just trying to get a grasp on what was modified. And if there is a change log, etc., just point me in the right direction. Thanks.
4) Message boards : Number crunching : 1% for 37 hours (Message 1548)
Posted 20 Oct 2005 by mrwizer
Post:
Personally, I have had the 1% hang on AMD and Intel boxes, with or without HT, and on Win2000 and WinXP. Just had two more this morning. All running BOINC 4.45.

Oh, and all currently only run Rosetta.
5) Message boards : Number crunching : 1% for 37 hours (Message 1508)
Posted 19 Oct 2005 by mrwizer
Post:
This thread has more info...

http://boinc.bakerlab.org/rosetta/forum_thread.php?id=78

You can try restarting BOINC manager, or the WU. I have had a WU stay frozen after this though, so aborting may be the last option.
6) Message boards : Number crunching : Would people be interested in being able to see the result plots of users, computers, and teams from the leader lists? (Message 1507)
Posted 19 Oct 2005 by mrwizer
Post:
Idea sounds good to me too.
7) Message boards : Number crunching : New Top Predictions (Message 1329)
Posted 14 Oct 2005 by mrwizer
Post:
Congrats koerni and j2satx.

Thanks for the heads up Ethan.
8) Message boards : Number crunching : can it really be so slow ? (Message 1321)
Posted 13 Oct 2005 by mrwizer
Post:
Anyone else getting more of these lately? I have gotten at least four WU's in the past day that have gotten stuck on 1%. And on different machines...
9) Message boards : Number crunching : can it really be so slow ? (Message 1266)
Posted 11 Oct 2005 by mrwizer
Post:
Sent.
10) Message boards : Number crunching : can it really be so slow ? (Message 1262)
Posted 11 Oct 2005 by mrwizer
Post:
David, do you still need the read outs on this problem? I have one that was stuck on 1% after 53 hours. I have the stdout.txt file.
11) Message boards : Number crunching : A few things about RAC (Message 661)
Posted 27 Sep 2005 by mrwizer
Post:
You definitely need three, otherwise how can you determine which result is correct?


In a previous message the scientists stated that they are able to tell if a scientific result is 'bogus'. They are able to tell if it's correct outside of duplicating work units. . So implementing redundancy sounds like it would only be to 'fix' RAC calculations. . . which would be sad that a small number of participants cause the computing power of the grid to be cut in half or a third so their name is at the top of a list.


Not correct in the sense of real science, rather correct from the standpoint or credit given. If you have two results each claiming very different credit amounts, which one do you give? The high or low. This is why you would need three to average or knock out the extreme request.
12) Message boards : Number crunching : A few things about RAC (Message 657)
Posted 27 Sep 2005 by mrwizer
Post:


There's at least two issues in there.

One is that RAC is junk, and bears no resemblance to average work being done.

Credit is also being granted incorrectly without the quorum procedure in place.
Reduncancy is more that just credit validation also - it should also compare the work output to make sure folks are no returning junk.

I'm not sure how a 2 user quorum would work - average the two scores?

The 3 or more quorum enables ridiculously high and/or low claimed credit to be thrown out.



You definitely need three, otherwise how can you determine which result is correct?
13) Message boards : Number crunching : can it really be so slow ? (Message 639)
Posted 27 Sep 2005 by mrwizer
Post:


As an additional, I had one work unit get stuck at at 1%. A simple restart of BOINC fixed it, and the work unit finished fine.


I have also had a WU stick at 1%. Normally I get WU done in a bit over 2 hours, but one was stuck on 1% after 3 hours.
14) Message boards : Number crunching : Error report (Message 505)
Posted 26 Sep 2005 by mrwizer
Post:
Look Here


OK, but the Rosetta application does not crash. So unless backups are made all the time, the error will still occur.

And is this something that can be fixed by different coding in the application? I just find it wierd that it only happens on one of my machines...
15) Message boards : Number crunching : Error report (Message 502)
Posted 26 Sep 2005 by mrwizer
Post:
9/25/2005 4:48:12 PM|rosetta@home|Unrecoverable error for result 1pvaA_abrelax_14956_2 ( - exit code -1073741819 (0xc0000005))

R@H app 4.77
BOINC app 4.45
WinXP Pro
1.8 P4 M
16) Message boards : Number crunching : Optimized Windows Application (Message 442)
Posted 25 Sep 2005 by mrwizer
Post:
I am still having a few issues on loosing CPU time when BOINC switches from other projects such as Einstein. I just went from 4:49 to 4:09, switched from Seti this time. This is with 4.77, BOINC version 4.45.
17) Message boards : Cafe Rosetta : Congrats to Travis Tuck and PCZ (Message 431)
Posted 24 Sep 2005 by mrwizer
Post:
It is very impressive to see feedback from the project already!

And congrats Travis and PCZ.
18) Message boards : Number crunching : Optimized Windows Application (Message 347)
Posted 22 Sep 2005 by mrwizer
Post:
Thanks David. I am up and running now. It is wonderful to have such a responsive group behind the project.
19) Message boards : Number crunching : Optimized Windows Application (Message 343)
Posted 22 Sep 2005 by mrwizer
Post:
With the new Windows app, I cannot get any WU's to start with one machine.

9/22/2005 3:02:50 PM|rosetta@home|Unrecoverable error for result 1pvaA_abrelax_5084_5 (CreateProcess() failed - The process cannot access the file because it is being used by another process. (0x20))

What other process??? Is this my issue or an issue with the new Windows app?
20) Message boards : Number crunching : CPU type (Message 266)
Posted 21 Sep 2005 by mrwizer
Post:
Has anyone noticed if the Rosetta application favors AMD or Intel (or even PowerPC)? I know with some other BOINC projects, one type seems to be preferable, whether the cause is specific optimizations or cache size, etc. Thanks...


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