problem in rosetta rebuilding
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. 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
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
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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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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 < [email protected]> 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
participants (3)
-
Francois Berenger -
intekhab alam -
Thomas C. Terwilliger