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| ID | Project | Category | View Status | Date Submitted | Last Update | ||||
| 0003382 | MEGA | [All Projects] Feedback | public | 2022-01-18 03:16 | 2022-02-01 09:44 | ||||
| Reporter | guest | ||||||||
| Assigned To | gstecher | ||||||||
| Priority | normal | Severity | minor | Reproducibility | have not tried | ||||
| Status | resolved | Resolution | won't fix | ||||||
| Platform | OS | ||||||||
| Product Version | MEGA-CC 11 (command line version) | ||||||||
| Target Version | Fixed in Version | ||||||||
| Summary | 0003382: Use of CPU cluster for tree bootstrap | ||||||||
| Description | Hello, I am running a Maximum-Likelihood Tree analysis on a 32 CPU cluster. It comes from 310 nucleotide sequences of around 1.2 kb each. I used the prototype tool. I set the Bootstrap value to 500 and the thread value to 32, since we have a cluster of 32 CPUs. It is that it is running very slow, takes almost a week. It is not using the 32 CPUs but only one. The software can use all because for the Model Selection it did use all 32 CPUs. What can be the issue? | ||||||||
| Tags | No tags attached. | ||||||||
| Attach Tags | (Separate by ",") | ||||||||
| First Name | Diego | ||||||||
| Last Name | Galagovsky | ||||||||
| dgalagovsky@ice.mpg.de | |||||||||
| Confirm Email | dgalagovsky@ice.mpg.de | ||||||||
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(0004792) gstecher (administrator) 2022-02-01 09:44 |
Hi there, I am writing in response to your recent question regarding the MEGA software. The current version of MEGA has limited capacity to use multiple CPUs for its maximum likelihood tree search. It uses a fine-grained approach for multithreading when doing branch swapping. This is different than the model selection analysis which distributes the analysis of different models to different threads. There are plans to improve the maximum likelihood tree search parallelization and optimize it for many CPUs but it will be a while before that will happen . Best regards, Glen Stecher Institute for Genomics and Evolutionary Medicine igem.temple.edu |
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Issue History |
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| Date Modified | Username | Field | Change |
| 2022-01-18 03:16 | guest | New Issue | |
| 2022-02-01 09:44 | gstecher | Note Added: 0004792 | |
| 2022-02-01 09:44 | gstecher | Status | new => resolved |
| 2022-02-01 09:44 | gstecher | Resolution | open => won't fix |
| 2022-02-01 09:44 | gstecher | Assigned To | => gstecher |
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Issue History |
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