Posts by Nikolay A. Saharov

1) Message boards : Number crunching : UP, DOWN, CPU WU ERRORS (Message 2105)
Posted 12 Jan 2010 by Profile Nikolay A. Saharov
Post:
Hi

In job.xml file for this result 1659448 I've found this subtask:
<task>
        <application>autogrid</application>
        <stdout_filename>stdout</stdout_filename>
        <stderr_filename>stderr</stderr_filename>
        <command_line> -p receptor_4.gpf -l out_4.glg </command_line>
        <weight>1</weight>
    </task>    


It seems there is a wrong cmd line parameter "-l out_4.glg". In all other autogrid subtasks this parameter is "-l out.glg" (without _4).

Is this correct?
2) Message boards : Number crunching : UP, DOWN, CPU WU ERRORS (Message 2103)
Posted 10 Jan 2010 by Profile Nikolay A. Saharov
Post:
21:12:12 (1888): wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/summarize_docking.py" -l out_7.dlg -r receptor_7.pdbqt -o summary_7.txt)
21:12:24 (1888): wrapper: running ./Python25/python.exe ("./top_summary.py" summary_1.txt summary_2.txt summary_3.txt summary_4.txt summary_5.txt summary_6.txt summary_7.txt)
app exit status: 0x1
21:12:37 (1888): called boinc_finish



I think python can't find this top_summary.py script. I also can't find it neither in MGLToolsPckgs archive nor DD@H project directory.

3) Message boards : Number crunching : Security flaw ? (Message 2015)
Posted 25 Dec 2009 by Profile Nikolay A. Saharov
Post:
Try to add all BOINC directories to NIS ignore list.
4) Message boards : Number crunching : mdrun 7.01/14 runtime (Message 1498)
Posted 9 Oct 2009 by Profile Nikolay A. Saharov
Post:
No problem with this. DCF is 68 :)

Which is still too high. You'd want it to be a lot lower, with a maximum of perhaps 5.

But that said, I suspect the fpops estimate on these tasks to be way off. Can you open your client_state.xml file, find Drug Discovery, find one of the tasks for the mdrun application and post the lines for <rsc_fpops_est> and <rsc_fpops_bound>, please?

Make sure to just close client_state.xml, if you get the question to save changes, click No.


No, these WUs were aborted because of exceeded disk limit error, see my previous post. And I have 48 Gb of free disk space.

Ok, I've reset the project to initialize DCF and download a new tasks because LTD was also very big negative value.
5) Message boards : Number crunching : mdrun 7.01/14 runtime (Message 1480)
Posted 9 Oct 2009 by Profile Nikolay A. Saharov
Post:
Check your Task Duration Correction Factor (TDCF). It may well be at 100, throwing off a more coherent ETC. To reset the TDCF to 1, reset the project, or if you know how and are comfortable with that, manually change its number in client_state.xml

No problem with this. DCF is 68 :)

What is bad, these WUs are finished with errors (exceeded disk limit: 958.22MB > 953.67MB):

09.10.2009 2:28:08	DrugDiscovery	Aborting task asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36717_ChemDiv_E511-3733_1254856773510751281_1254972686336430239_3910_1254973412_1: exceeded disk limit: 958.22MB > 953.67MB
09.10.2009 2:28:08	DrugDiscovery	[task_debug] task_state=ABORT_PENDING for asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36717_ChemDiv_E511-3733_1254856773510751281_1254972686336430239_3910_1254973412_1 from abort_task
09.10.2009 2:28:08	DrugDiscovery	[task_debug] result state=COMPUTE_ERROR for asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36717_ChemDiv_E511-3733_1254856773510751281_1254972686336430239_3910_1254973412_1 from CS::report_result_error
09.10.2009 2:28:08	DrugDiscovery	[task_debug] result state=ABORTED for asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36717_ChemDiv_E511-3733_1254856773510751281_1254972686336430239_3910_1254973412_1 from abort_task
09.10.2009 2:29:09	DrugDiscovery	[task_debug] task_state=ABORTED for asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36717_ChemDiv_E511-3733_1254856773510751281_1254972686336430239_3910_1254973412_1 from kill_task
09.10.2009 2:29:09	DrugDiscovery	Computation for task asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36717_ChemDiv_E511-3733_1254856773510751281_1254972686336430239_3910_1254973412_1 finished
09.10.2009 2:29:09	DrugDiscovery	[task_debug] result state=COMPUTE_ERROR for asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36717_ChemDiv_E511-3733_1254856773510751281_1254972686336430239_3910_1254973412_1 from CS::app_finished
09.10.2009 2:53:12	DrugDiscovery	Aborting task asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36735_ChemDiv_C614-0998_1254856788637608611_1254972534674566603_3910_1254973411_0: exceeded disk limit: 953.69MB > 953.67MB
09.10.2009 2:53:12	DrugDiscovery	[task_debug] task_state=ABORT_PENDING for asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36735_ChemDiv_C614-0998_1254856788637608611_1254972534674566603_3910_1254973411_0 from abort_task
09.10.2009 2:53:12	DrugDiscovery	[task_debug] result state=COMPUTE_ERROR for asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36735_ChemDiv_C614-0998_1254856788637608611_1254972534674566603_3910_1254973411_0 from CS::report_result_error
09.10.2009 2:53:12	DrugDiscovery	[task_debug] result state=ABORTED for asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36735_ChemDiv_C614-0998_1254856788637608611_1254972534674566603_3910_1254973411_0 from abort_task
09.10.2009 2:54:12	DrugDiscovery	[task_debug] task_state=ABORTED for asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36735_ChemDiv_C614-0998_1254856788637608611_1254972534674566603_3910_1254973411_0 from kill_task
09.10.2009 2:54:12	DrugDiscovery	Computation for task asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36735_ChemDiv_C614-0998_1254856788637608611_1254972534674566603_3910_1254973411_0 finished
09.10.2009 2:54:12	DrugDiscovery	[task_debug] result state=COMPUTE_ERROR for asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36735_ChemDiv_C614-0998_1254856788637608611_1254972534674566603_3910_1254973411_0 from CS::app_finished
09.10.2009 3:03:13	DrugDiscovery	Aborting task asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36788_ChemDiv_C301-4871_1254856839984565851_1254972825392505003_3910_1254973412_2: exceeded disk limit: 954.13MB > 953.67MB
09.10.2009 3:03:13	DrugDiscovery	[task_debug] task_state=ABORT_PENDING for asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36788_ChemDiv_C301-4871_1254856839984565851_1254972825392505003_3910_1254973412_2 from abort_task
09.10.2009 3:03:13	DrugDiscovery	[task_debug] result state=COMPUTE_ERROR for asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36788_ChemDiv_C301-4871_1254856839984565851_1254972825392505003_3910_1254973412_2 from CS::report_result_error
09.10.2009 3:03:13	DrugDiscovery	[task_debug] result state=ABORTED for asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36788_ChemDiv_C301-4871_1254856839984565851_1254972825392505003_3910_1254973412_2 from abort_task
09.10.2009 3:04:13	DrugDiscovery	[task_debug] task_state=ABORTED for asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36788_ChemDiv_C301-4871_1254856839984565851_1254972825392505003_3910_1254973412_2 from kill_task
09.10.2009 3:04:13	DrugDiscovery	Computation for task asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36788_ChemDiv_C301-4871_1254856839984565851_1254972825392505003_3910_1254973412_2 finished
09.10.2009 3:04:13	DrugDiscovery	[task_debug] result state=COMPUTE_ERROR for asgn_md_5000000_steps_P10_TYR52_LEU33_GLN56_36788_ChemDiv_C301-4871_1254856839984565851_1254972825392505003_3910_1254973412_2 from CS::app_finished
6) Message boards : Number crunching : mdrun 7.01/14 runtime (Message 1471)
Posted 8 Oct 2009 by Profile Nikolay A. Saharov
Post:
Hello,

I have 3 WUs of mdrun 7.14 with deadline 10.05.2011 (results 877458, 877459, 877460).
The time to completion is 87600 hours for each WU and it is not changing.
The current progress is 3.5% and 13 hours of CPU time.
All these WUs are in EDF mode.
7) Message boards : Number crunching : Upload, Download and WU Errors (Message 940)
Posted 31 Jul 2009 by Profile Nikolay A. Saharov
Post:
it seems all my P8_LEU42_* WUs finished with errors:
<message>
 - exit code 195 (0xc3)
</message>
<stderr_txt>
wrapper: starting
wrapper: running ../../projects/boinc.drugdiscoveryathome.com/unzip_1.011_windows_intelx86.exe (-qq -o "./MGLTools*.zip" -d ".")

CreateFile() error 32 when trying set file time

CreateFile() error 32 when trying set file time

CreateFile() error 32 when trying set file time

CreateFile() error 32 when trying set file time
wrapper: running 7za.exe (e ligand.mol2.7z)
wrapper: running ./Python25/python.exe (make_sitecustomize.py ".")
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/Support/sitecustomize.py")
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py" -l ligand.mol2 -o ligand.pdbqt)
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py" -U nphs_lps_waters -r receptor.pdb -o receptor.pdbqt)
close failed: [Errno 9] Bad file descriptor
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_flexreceptor4.py" -r receptor.pdbqt -g receptor_rigid.pdbqt -x receptor_flex.pdbqt -s LEU42_LYS44_ILE46_ASN49_TYR50)
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py" -l ligand.pdbqt -r receptor_rigid.pdbqt -x receptor_flex.pdbqt -p custom_parameter_file=1 -p parameter_file=AD4_parameters.dat)
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_dpf4.py" -l ligand.pdbqt -r receptor_rigid.pdbqt -x receptor_flex.pdbqt -p compute_unbound_extended_flag=0 -p ga_run=1)
wrapper: running ../../projects/boinc.drugdiscoveryathome.com/autogrid_1.011_windows_intelx86.exe (-p receptor_rigid.gpf -l out.glg)
wrapper: running ../../projects/boinc.drugdiscoveryathome.com/autodock_1.011_windows_intelx86.exe (-p ligand_receptor_rigid.dpf -l out.dlg)
app exit status: 0xff
called boinc_finish




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