[phenixbb] problem in rosetta rebuilding

intekhab alam faisaldbg at gmail.com
Sun Jul 31 23:33:58 PDT 2011


Hi, Tom
sorry for the delayed response.
I was abale to fix by running one model.
rosetta is working fine now.

thanks again

Intekhab Alam

On Thu, Jul 21, 2011 at 11:49 PM, Thomas C. Terwilliger <
terwilliger at lanl.gov> wrote:

> Hi Intekhab,
>
> I'm glad the test works at least.  How about trying this:
>
> Run just the job that hangs, but instead of running 100 models...just run
> one single model.  Does that work?
>
> All the best,
> Tom
>
>
> >> Hi Tom
> >> i tried the commnad line and it works well. we also have increased the
> >> memory to 3GB (earlier it was 2GB)
> >> but still the system hangs with no response overnight.
> >> the specifications of my system is as:
> >> Ubuntu 9.04
> >> GCC 4.2
> >> RAM 3GB
> >> Rosetta 3.2
> >> Phenix 1.7.1
> >> the command line test using
> >> "phenix_regression.wizards.test_command_line_rosetta_quick_tests
> >> test_rosetta_rebuild" works well .
> >>
> >> regards
> >> intekhab alam
> >> On Tue, Jul 19, 2011 at 11:31 PM, Thomas C. Terwilliger <
> >> terwilliger at lanl.gov> wrote:
> >>
> >>> Hi Intekhab,
> >>>
> >>> I'm not sure about the part about the machine shutting down...but here
> >>> is
> >>> a little test you can run to make sure that rosetta and phenix are
> >>> working
> >>> properly together in rebuilding a model:
> >>>
> >>>  phenix_regression.wizards.test_command_line_rosetta_quick_tests
> >>> test_rosetta_rebuild
> >>>
> >>> or a more complete set of tests:
> >>>
> >>>  phenix_regression.wizards.test_command_line_rosetta_quick_tests
> >>>
> >>> All the best,
> >>> Tom T
> >>>
> >>>
> >>>
> >>> >> On 07/19/2011 04:49 PM, intekhab alam wrote:
> >>> >>>
> >>> >>> Hi
> >>> >>> i tried to run rosetta on a unix machine (ubuntu 9.04) for my data.
> >>> Upto
> >>> >>> MR step everything goes fine , but during the rebuilding step after
> >>> 20
> >>> >>> cycles the computer shuts down.
> >>> >>
> >>> >> Interesting behavior for a Linux machine.
> >>> >>
> >>> >> Once the machine has rebooted, reading the output
> >>> >> of the dmesg command and looking at events prior to the last boot
> >>> >> may give you some information on why the computer hung.
> >>> >>
> >>> >> My guess is that you went out of memory while using mr_rosetta.
> >>> >>
> >>> >>> i have attached the log file for the autobuilding run of rosetta. i
> >>> am
> >>> >>> using phenix 1.7.1-743 version.
> >>> >>> i will be grateful if some one helps me out
> >>> >>> --
> >>> >>> INTEKHAB ALAM
> >>> >>> LABORATORY OF STRUCTURAL BIOINFORMATICS
> >>> >>> KOREA UNIVERSITY, SEOUL
> >>> >>>
> >>> >>>
> >>> >>>
> >>> >>> _______________________________________________
> >>> >>> phenixbb mailing list
> >>> >>> phenixbb at phenix-online.org
> >>> >>> http://phenix-online.org/mailman/listinfo/phenixbb
> >>> >>
> >>> >> _______________________________________________
> >>> >> phenixbb mailing list
> >>> >> phenixbb at phenix-online.org
> >>> >> http://phenix-online.org/mailman/listinfo/phenixbb
> >>> >>
> >>>
> >>> _______________________________________________
> >>> phenixbb mailing list
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> >>> http://phenix-online.org/mailman/listinfo/phenixbb
> >>>
> >>
> >>
> >>
> >> --
> >> INTEKHAB ALAM
> >> LABORATORY OF STRUCTURAL BIOINFORMATICS
> >> KOREA UNIVERSITY, SEOUL
> >>
>
>


-- 
INTEKHAB ALAM
LABORATORY OF STRUCTURAL BIOINFORMATICS
KOREA UNIVERSITY, SEOUL
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