Same box again, result 1ogw__topology_sample_123786_1.

This is also the same box that had download errors as I reported in this message in an earlier thread. Bad luck, or significant?

This result ran for 3222sec without checkpoint and with fraction done = 0.01 throughout, and then I stopped it. Before aborting, I'd monitored stdout for about 10min using tail -f and nothing had been appended.

I've given you a little more of stdout than you asked, as there are a couple of files it says are missing, and I don't know enouugh about your app to know if that is expceted or not. Deleted ranges of lines shown as [[...]]


stderr.txt

# =====================================
# random seed: 1148861
# =====================================

stdout.txt

BOINC :: 2005-12-16 15:56:28 :: boinc_init()
command executed: rosetta_4.79_i686-pc-linux-gnu aa 1ogw _ -abrelax_mode -stringent_relax -more_relax_cycles -relax_score_filter -filter1 -105 -filter2 -145 -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 -barcode_file 1ogw.top7_lowenergy.cst -jitter_frag -jitter_variation gauss -output_silent_gz -nstruct 10
[STR  OPT]Default value for [-paths] paths.txt.
--------------------------------------------
WARNING::  paths.txt file not found!!
           Setting all paths to ./
           Using default fragment file names:
             aa*****03_05.200_v1_3
             aa*****03_05.200_v1_3
--------------------------------------------
[T/F  OPT]Default FALSE value for [-version]
[T/F  OPT]Default FALSE value for [-abrelax]
[T/F  OPT]Default FALSE value for [-score]

[[...]]

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 :: 2005-12-16 15:56:29 :: Total iterations: 10 :: mode: abrelax :: nstartnm: 1 :: number_of_output: 10 :: num_decoys: 0 :: percent complete: 0.01
Searching for dat file: ./1ogw.dat
Searching for dat file: ./1ogw.dat
WARNING!! .dat file not found!
Looking for fasta file: ./1ogw_.fasta
[T/F  OPT]Default FALSE value for [-find_disulf]
[T/F  OPT]Default FALSE value for [-fix_disulf]
Looking for psipred file: ./1ogw_.psipred_ss2
Protein type: alpha/beta  Fraction beta:   0.543478251
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
WARNING: CONSTRAINT FILE NOT FOUND
Searched for: ./1ogw_.cst
Running without distance constraints
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
WARNING: DIPOLAR CONSTRAINT FILE NOT FOUND
 Searched for: ./1ogw_.dpl
 Dipolar constraints will not be used
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
fragment file: ./aa1ogw_03_05.200_v1_3.gz
Total Residue 76
frag size: 3    frags/residue: 200
fragment file: ./aa1ogw_09_05.200_v1_3.gz
Total Residue 76
frag size: 9    frags/residue: 200
generating 1mer library from 3mer library
[T/F  OPT]New TRUE value for [-ssblocks]
 1  0.00499999989  0.354999989  0.63999998600
 2  0.0199999996  0.800000012  2415.8430221

[[...]]

Starting score3 moves...
kk,score3,low_score,rms_err,low_rms,rms_min,naccept
  0   15.337   15.337    9.554    9.554    8.225 1082
  1   25.891   15.337    8.148    9.554    7.765 1275
pre-computing chuck/gunn move set for frag length 3
  2   38.884   12.257    9.662    9.424    7.765 1466
  3   28.377   12.257    7.742    9.424    7.401 1735
smooth                         trials: 8000 accepts: 460 %: 5.75
standard                       trials: 4000 accepts: 193 %: 4.825
-----------------------------------------------------
-----------------------------------------------------
[T/F  OPT]New TRUE value for [-stringent_relax]
CYCLES::number is  1 x total_residue: 76
[T/F  OPT]New TRUE value for [-more_relax_cycles]
initializing full atom coordinates
starting score  1927.85217 rms  9.42364883
starting full atom minimization
[T/F  OPT]New TRUE value for [-relax_score_filter]
[T/F  OPT]New TRUE value for [-filter1]
[T/F  OPT]New TRUE value for [-filter1]
[REAL OPT]New value for [-filter1]  -105
[T/F  OPT]New TRUE value for [-filter2]
[REAL OPT]New value for [-filter2]  -145
CYCLES::number is  1 x total_residue: 228
starting score -110.235764 rms  11.6548042
starting full atom simulated anealing
pre-computing chuck/gunn move set for frag length 1

Same box, result = 1n0u__topology_sample_128114_0

Aborted after 1700sec, fraction done = 0.01, no checkpoint, nothing written to stdout for over ten minutes.

[edit begins]
Followijng this I detached the box and attached again as this new host, the downloads worked fine, and the first result had checkpointed twice in the first 486 seconds.

Is it possible that after some problem with downloads, one or more files is missing or corrupt and this is not corrected? Or is this a complete red herring?
[edit ends]

stdout contained the same warnings about those 2 missing files, but I havent posted them this time. I have kept stdout & stderr from this and previous aborted result in case you'd like them emailing to you.

$ cat stderr.txt
# =====================================
# random seed: 1217781
# =====================================


$ head stdout.txt

BOINC :: 2005-12-16 16:54:07 :: boinc_init()
command executed: rosetta_4.79_i686-pc-linux-gnu aa 1n0u _ -relax_score_filter -filter1 -100 -filter2 -140 -abrelax_mode -stringent_relax -more_relax_cycles -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 -barcode_file 1n0u.top7_lowenergy.cst -jitter_frag -jitter_variation gauss -output_silent_gz -nstruct 10
[STR  OPT]Default value for [-paths] paths.txt.
--------------------------------------------
WARNING::  paths.txt file not found!!
           Setting all paths to ./
           Using default fragment file names:
             aa*****03_05.200_v1_3
             aa*****03_05.200_v1_3
--------------------------------------------


$ tail stdout.txt

[T/F  OPT]New TRUE value for [-relax_score_filter]
[T/F  OPT]New TRUE value for [-filter1]
[T/F  OPT]New TRUE value for [-filter1]
[REAL OPT]New value for [-filter1]  -100
[T/F  OPT]New TRUE value for [-filter2]
[REAL OPT]New value for [-filter2]  -140
CYCLES::number is  1 x total_residue: 207
starting score -114.071526 rms  9.88577175
starting full atom simulated anealing
pre-computing chuck/gunn move set for frag length 1

temporary storage, please don't add to this thread...

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