Memory usage of 3.6.1 becomes much higher than that of 3.4.1 as the number of taxa increases

Skip to first unread message

Wayne Pfeiffer

Jul 12, 2022, 6:02:36 PM7/12/22
to bali-phy-users

I support the CIPRES gateway where we have made Version 3.4.1 of BAli-Phy available for some time. Recently I installed 3.6.1 on the Expanse supercomputer that we use and was surprised that memory usage of the new version of BAli-Phy becomes much higher than that of the earlier version as the number of taxa increases.

The attached table lists the memory usage by 3.6.1 for 10 representative data sets, mostly from our users. The Slurm memory is what I specified upon job submission, while the sacct memory is the high-water mark reported after the job completed. Usage charges to our users are proportional to the Slurm memory, so the larger jobs are much more expensive. By contrast, the Slurm memory needed by 3.4.1 for all of the data sets listed is only 2 GB. 

I made 3.6.1 runs using both the prebuilt executable from and an executable built from source. Both exhibit the same increase in memory.

Please let me know if you expect this increase in memory and whether there might be a way to reduce it. If not, we could continue to make 3.4.1 available in addition to 3.6.1 for users with large numbers of taxa.

Best regards,  Wayne


Benjamin Redelings

Jul 12, 2022, 6:26:51 PM7/12/22
to, Pfeiffer, Wayne, Miller, Mark

Hi Wayne,

Thanks for the detailed bug report.  I will take a look at what is allocating the extra memory in 3.6.1, but it might take me a little while to track this down.

You received this message because you are subscribed to the Google Groups "bali-phy-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
To view this discussion on the web visit

Pfeiffer, Wayne

Jul 12, 2022, 7:44:20 PM7/12/22
to Benjamin Redelings,, Pfeiffer, Wayne, Miller, Mark
Hi Ben,

Thanks for the prompt reply!

Good luck on tracking down the increase in memory usage :)

Reply all
Reply to author
0 new messages