Posts by caesar1987

1) Message boards : Number crunching : Rosetta Mini with new score terms bug thread (Message 56860)
Posted 11 Nov 2008 by Profile caesar1987
Post:
memory usage is realy verry enormous

now is it by me 290MB in ram and 500MB in VM!

with minirosetta 1.40 is my computer unusable.
2) Message boards : Number crunching : Minirosetta v1.40 bug thread (Message 56804)
Posted 10 Nov 2008 by Profile caesar1987
Post:

Last night, it had accumulated about 6 CPU hours and claimed that it would finish in another 10 CPU minutes. This morning, it has accumulated over 12 CPU hours and claims that it will finish in another 9 CPU minutes and 56 seconds.

Also, it's currently the most memory hungry process on my machine. The Windows Task Manager recently said it was using over 256,000K of memory - over 10 times as much as the next process - but then dropped that to a little over 200,000K and is now 223,132K.
same by me
it say that it will finish in 9minuter and 51 sec. But by me is accumulates only 5 hour 5 min, but las hour it is the same.

"mini"rosetta mem usage -cca 290,000 K, VMsize - 320,000 K!!!
whats on this mini?
3) Message boards : Number crunching : Minirosetta v1.39 bug thread (Message 56707)
Posted 4 Nov 2008 by Profile caesar1987
Post:
<core_client_version>6.2.19</core_client_version>
<![CDATA[
<message>
CreateProcess() failed - Access is denied. (0x5)
</message>
]]>


205025484
204992187
4) Message boards : Number crunching : Rosetta Mini with new score terms 1.02 (Message 56565)
Posted 31 Oct 2008 by Profile caesar1987
Post:
203584512


<core_client_version>6.2.19</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>

ERROR: in::file::zip minirosetta_database.zip does not exist!
ERROR:: Exit from: ....srcappspublicboincminirosetta.cc line: 74
called boinc_finish

</stderr_txt>
]]>

//edit

the same
203727917
203727919

//edit2

the same by another 2.
i stop rosetta for 1 day and wait for another tasks.
5) Message boards : Number crunching : Minirosetta v1.28 bug thread (Message 53646)
Posted 12 Jun 2008 by Profile caesar1987
Post:
Bug in grapnic

http://caesar1987.px2.biz/subfolder/mix/imagebug.jpg
http://caesar1987.px2.biz/subfolder/mix/imagebug2.jpg
http://caesar1987.px2.biz/subfolder/mix/imagebug3.jpg
6) Message boards : Number crunching : Problems with version 5.96 (Message 53418)
Posted 28 May 2008 by Profile caesar1987
Post:
error

http://boinc.bakerlab.org/rosetta/result.php?resultid=167013698
7) Message boards : Number crunching : minirosetta v1.19 bug thread (Message 53048)
Posted 14 May 2008 by Profile caesar1987
Post:
http://boinc.bakerlab.org/rosetta/result.php?resultid=162352303
8) Message boards : Number crunching : Problems with minirosetta version 1.+ (Message 51822)
Posted 5 Mar 2008 by Profile caesar1987
Post:
Try this explanation

From the above link

the new version of rosetta is extremely powerful, but as it is very new, there are still some rare problems surfacing, and some of the bells and whistles, such as the screensaver, are not yet in place.

Other "older" applications (Rosetta Beta 5.93 / Rosetta 5.82) are still in the mix so just abort the mini's or just let them run through to completion, your choice.
thx... =)
9) Message boards : Number crunching : Problems with minirosetta version 1.+ (Message 51820)
Posted 5 Mar 2008 by Profile caesar1987
Post:
today my boinc get to monirosetta.. but i cant see graphics (by screensaver i have only boinc logo and text runing rosetta...) how can i go back to old rosetta?
10) Message boards : Number crunching : New work which I never received (Message 37030)
Posted 20 Feb 2007 by Profile caesar1987
Post:
why show me server in

http://boinc.bakerlab.org/rosetta/results.php?userid=131900

work 56285310

which i havent newer downloaded???
11) Message boards : Number crunching : Problem with view structure predictions (Message 36223)
Posted 6 Feb 2007 by Profile caesar1987
Post:
you can either remove the file or edit it by changing 54 to 0.

Then try extracting the models. What particular work unit are you trying to extract from?

Oooo
I channged 54 to 0.
And it is all ok..
After each extract is the number higher by 1.
So, somewhere in the program is a bug...

And i try it with cca 10 out files and all is ok...

thanx a lot...
12) Message boards : Number crunching : Problem with view structure predictions (Message 36220)
Posted 6 Feb 2007 by Profile caesar1987
Post:
You have to remove the rosetta_init_cnt.txt file. You also may need to add -termini in the arguments for some work units. We'll modify the app in the next release so you will no longer have to remove the init_cnt file if running in standalone mode. The file prevents the app from restarting over and over again without producing any results.


rosetta_init_cnt.txt is in the folder.

***rosetta_init_cnt.txt***
54 0

and when will be the next release???
13) Message boards : Number crunching : Problem with view structure predictions (Message 36183)
Posted 6 Feb 2007 by Profile caesar1987
Post:
when i do that, what is here
http://boinc.bakerlab.org/rosetta/rah_view_predictions.php
the file S_XXXX_XXXX.pdb or F_XXXX_XXXX.pdb will not be created

here are logs

****stderr.txt****
Can't set up shared mem: -1
Will run in standalone mode.
# cpu_run_time_pref: 7200
Too many restarts with no progress. Keep application in memory while preempted.
======================================================
DONE :: 1 starting structures built 10 (nstruct) times
This process generated 0 decoys from 0 attempts
======================================================


BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down...

****stdout.txt****
[STR OPT]Default value for [-description_file] rosetta_description.txt.
[REAL OPT]Default value for [-cpu_frac] 10
[REAL OPT]Default value for [-frame_rate] 10
[INT OPT]Default value for [-cpu_run_time] 28800
command executed: rosetta_5.45_windows_intelx86.exe -extract -all -s aaz029.out
[T/F OPT]Default FALSE value for [-args_file]
[STR OPT]Default value for [-paths] paths.txt.
[T/F OPT]Default FALSE value for [-unix_paths]
--------------------------------------------
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 [-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]
[T/F OPT]Default FALSE value for [-abrelax_mode]
[T/F OPT]Default FALSE value for [-design]
[T/F OPT]Default FALSE value for [-dock]
[T/F OPT]Default FALSE value for [-membrane]
[T/F OPT]Default FALSE value for [-loops]
[T/F OPT]Default FALSE value for [-pdbstats]
[T/F OPT]Default FALSE value for [-interface]
[T/F OPT]Default FALSE value for [-barcode_stats]
[T/F OPT]Default FALSE value for [-pKa]
[T/F OPT]Default FALSE value for [-pose_looping]
[T/F OPT]Default FALSE value for [-domain_insertion]
[T/F OPT]Default FALSE value for [-pose1]
[T/F OPT]Default FALSE value for [-bk_min]
[T/F OPT]Default FALSE value for [-adna]
[T/F OPT]Default FALSE value for [-pdna]
[T/F OPT]Default FALSE value for [-prna]
[T/F OPT]Default FALSE value for [-jumping]
[T/F OPT]Default FALSE value for [-pose_abinitio]
[T/F OPT]Default FALSE value for [-pose_rhiju]
[T/F OPT]New TRUE value for [-extract]
[T/F OPT]Default FALSE value for [-jump_relax]
[T/F OPT]Default FALSE value for [-cst_mode]
[T/F OPT]Default FALSE value for [-mj_min]
Rosetta mode: pose1
[T/F OPT]Default FALSE value for [-chain]
[T/F OPT]Default FALSE value for [-protein]
[T/F OPT]Default FALSE value for [-series]
[INT OPT]Default value for [-nstruct] 10
[T/F OPT]Default FALSE value for [-read_all_chains]
[T/F OPT]Default FALSE value for [-preserve_header]
[T/F OPT]Default FALSE value for [-use_pdb_numbering]
[T/F OPT]Default FALSE value for [-flip_symmetric_sidechains]
[T/F OPT]Default FALSE value for [-fa_input]
[T/F OPT]Default FALSE value for [-overwrite]
[T/F OPT]Default FALSE value for [-no_filters]
[T/F OPT]Default FALSE value for [-output_pdb_gz]
[T/F OPT]Default FALSE value for [-output_silent_gz]
[T/F OPT]Default FALSE value for [-output_scorefile_gz]
[T/F OPT]Default FALSE value for [-pose_silent_out]
[T/F OPT]Default FALSE value for [-sasapack_bvalues]
[T/F OPT]Default FALSE value for [-cenlist_values]
[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 [-use_conformer]
[T/F OPT]Default FALSE value for [-use_bbind_conformer]
[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 [-pose_relax]
[T/F OPT]Default FALSE value for [-output_interaction_graph_memory_usage]
[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 [-packer_precompute_only]
[T/F OPT]Default FALSE value for [-tight_memory_restrictions]
[T/F OPT]Default FALSE value for [-lazy_ig]
[T/F OPT]Default FALSE value for [-linmem_ig]
[T/F OPT]Default FALSE value for [-minimalist_ig]
[T/F OPT]Default FALSE value for [-use_sasa_pack_score]
[T/F OPT]Default FALSE value for [-output_dot_kinemage]
[T/F OPT]Default FALSE value for [-pack_low_temp_annealing]
[T/F OPT]Default FALSE value for [-multi_cool_annealer]
[T/F OPT]Default FALSE value for [-no_his_his_pairE]
[T/F OPT]Default FALSE value for [-silent_input]
[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 [-decoy_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 [-output_chi_silent]
[T/F OPT]Default FALSE value for [-accept_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.
[STR OPT]Default value for [-equiv_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]Default value for [-max_frags] 200
[T/F OPT]Default FALSE value for [-output_centroids]
[STR OPT]Default value for [-protein_name_prefix] .
[STR OPT]Default value for [-frags_name_prefix] .
[T/F OPT]Default FALSE value for [-protein_name_prefix_homolog]
[T/F OPT]Default FALSE value for [-use_homolog_env_stats]
[T/F OPT]Default FALSE value for [-use_homolog_pair_stats]
[T/F OPT]Default FALSE value for [-use_homolog_env_stats_in_farlx]
[T/F OPT]Default FALSE value for [-use_homolog_pair_stats_in_farlx]
[T/F OPT]Default FALSE value for [-output_hbond_info]
[REAL OPT]Default value for [-vdw_reweight] 1
[REAL OPT]Default value for [-env_reweight] 1
[REAL OPT]Default value for [-pair_reweight] 1
[REAL OPT]Default value for [-cb_reweight] 1
[REAL OPT]Default value for [-sheet_reweight] 1
[REAL OPT]Default value for [-ss_reweight] 1
[REAL OPT]Default value for [-hs_reweight] 1
[REAL OPT]Default value for [-rsigma_reweight] 1
[REAL OPT]Default value for [-rg_reweight] 1
[REAL OPT]Default value for [-pc_reweight] 1
[REAL OPT]Default value for [-fa_atr_reweight] 1
[REAL OPT]Default value for [-fa_rep_reweight] 1
[REAL OPT]Default value for [-fa_dun_reweight ] 1
[REAL OPT]Default value for [-fa_pair_reweight] 1
[REAL OPT]Default value for [-fa_plane_reweight] 1
[REAL OPT]Default value for [-fa_solv_reweight] 1
[REAL OPT]Default value for [-fa_ref_reweight ] 1
[REAL OPT]Default value for [-fa_pH_reweight] 1
[REAL OPT]Default value for [-fa_h2o_reweight] 1
[REAL OPT]Default value for [-fa_prob1b_reweight] 1
[REAL OPT]Default value for [-fa_gb_elec_reweigh] 1
[REAL OPT]Default value for [-hb_srbb_reweight] 1
[REAL OPT]Default value for [-hb_lrbb_reweight] 1
[REAL OPT]Default value for [-hb_sc_reweight] 1
[REAL OPT]Default value for [-chainbreak_reweight] 1
[REAL OPT]Default value for [-dummy_model_reweight] 1
[REAL OPT]Default value for [-saxs_model_reweight] 1
[REAL OPT]Default value for [-Wplane_total] 0
[T/F OPT]Default FALSE value for [-fa_max_dis]
[T/F OPT]Default FALSE value for [-hydrogen_interaction_cutoff]
[T/F OPT]Default FALSE value for [-find_disulf]
[T/F OPT]Default FALSE value for [-fix_disulf]
[T/F OPT]Default FALSE value for [-enable_dna]
[T/F OPT]Default FALSE value for [-enable_rna]
[T/F OPT]Default FALSE value for [-dna_interface]
[T/F OPT]Default FALSE value for [-enable_ligand_aa]
[T/F OPT]Default FALSE value for [-phospho_ser]
[T/F OPT]Default FALSE value for [-surface]
[T/F OPT]Default FALSE value for [-loops]
[T/F OPT]Default FALSE value for [-taboo]
[T/F OPT]Default FALSE value for [-vary_omega]
[T/F OPT]Default FALSE value for [-fine_hb_categories]
[T/F OPT]Default FALSE value for [-geometric_sol]
[T/F OPT]Default FALSE value for [-multi_chain]
[T/F OPT]Default FALSE value for [-ex1]
[T/F OPT]Default FALSE 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]
[T/F OPT]Default FALSE value for [-exOH]
[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 [-pH]
[T/F OPT]Default FALSE value for [-try_both_his_tautomers]
[T/F OPT]Default FALSE value for [-hydrate_dna]
[T/F OPT]Default FALSE value for [-ex_dna_waters]
[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]Default FALSE value for [-silent]
[T/F OPT]Default FALSE value for [-output_silent_gz]
[T/F OPT]Default FALSE value for [-verbose]
[T/F OPT]Default FALSE value for [-gush]
[T/F OPT]Default FALSE value for [-yap]
[T/F OPT]Default FALSE value for [-chat]
[T/F OPT]Default FALSE value for [-inform]
[T/F OPT]Default FALSE value for [-quiet]
run level: 0
[T/F OPT]Default FALSE value for [-benchmark]
[T/F OPT]Default FALSE value for [-debug]
[INT OPT]Default value for [-sym_des_units] 1
[T/F OPT]Default FALSE value for [-mj_min]
[REAL OPT]Default value for [-mod_hhrep_height] 1
[REAL OPT]Default value for [-mod_hhrep_width] 1
[REAL OPT]Default value for [-mod_hhrep_center] 2.79999995
[REAL OPT]Default value for [-mod_hhrep_exponent] 4
[REAL OPT]Default value for [-smooth_etable_ljweight] 1.15999997
[REAL OPT]Default value for [-smooth_etable_solvweight] 1.5
[STR OPT]New value for [-s] aaz029.out.
Starting structure: aaz029.out
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 [-interface_ds]
[T/F OPT]Default FALSE value for [-decoystats]
set_decoystats_flag: from,to F F
[T/F OPT]Default FALSE value for [-decoyfeatures]
[T/F OPT]Default FALSE value for [-evolution]
[T/F OPT]Default FALSE value for [-evol_recomb]
[T/F OPT]Default FALSE value for [-profile]
BOINC :: [2007-02-06 04:02:10] :: mode: pose1 :: nstartnum: 1 :: number_of_output: 10 :: num_decoys: 0 :: pct_complete: 0.01
======================================================
DONE :: 1 starting structures built 10 (nstruct) times
This process generated 0 decoys from 0 attempts
======================================================

thanx for help






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