MantisBT - MEGA
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0000535MEGA[All Projects] Feedbackpublic2017-09-04 06:472017-09-19 07:51
guest 
gstecher 
normalminorhave not tried
resolvedno change required 
MEGA-CC 11 (command line version) 
 
Nicolas
Cellier
contact@nicolas-cellier.net
contact@nicolas-cellier.net
0000535: Improve cluster run
Hello

I manage a small-scale cluster for numerical analysis and some students have to run analysis with MEGA7-cc. We have some troubles about how this software works.

- the command-line API need GTK. We have to use a virtual Xorg server or X11 forwarding. Is it possible to improve this and remove the need of a graphical server?
- the Model selection take huge amount of memory (50 ~ 70G). Proper blocking algorithm can reduce the impact on the RAM usage. Are such improvement planned?

Thank you
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Issue History
2017-09-04 06:47guestNew Issue
2017-09-19 07:38gstecherNote Deleted: 0000386
2017-09-19 07:51gstecherNote Added: 0003852
2017-09-19 07:51gstecherStatusnew => resolved
2017-09-19 07:51gstecherResolutionopen => no change required
2017-09-19 07:51gstecherAssigned To => gstecher

Notes
(0003852)
gstecher   
2017-09-19 07:51   
Hi Nicolas,

I am writing in response to your questions regarding the MEGA software. MEGA has traditionally been developed as a desktop GUI application and the MEGA-CC version is provided for convenience but it is not optimized to run on clusters or headless machines. Regarding the memory usage of the model selection analysis, that is characteristic of MEGA's likelihood framework in general. However, in future versions there are plans to give users some control over memory allocation, at the expense of computational time.

--
Best regards,

Glen Stecher
Institute for Genomics and Evolutionary Medicine
igem.temple.edu