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Cibiv / IQ-TREE

Efficient phylogenomic software by maximum likelihood
http://www.iqtree.org
GNU General Public License v2.0
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Setting maximum number of CPUs with AUTO #57

Closed sjspielman closed 6 years ago

sjspielman commented 6 years ago

Hi,

I am looking to run iqtree on a cluster and would like to be able to take advantage of -nt AUTO. However, by default, iqtree is detecting the total number of cores on the given compute node, which may or may not match the resource allocation requested. For example, if a node has 64 cores but my job only requested 32, I would like to be able to use AUTO while also specifying "no more than 32". Is this possible with the current version?

Thanks! -Stephanie

bqminh commented 6 years ago

Hi Stephanie, this is a reasonable request, right now there is no option to restrict the max number of cores when doing -nt AUTO. But that should be easy to implement, e.g. with a new -ntmax option.

Minh

On 7 Mar 2018, at 12:50 am, Stephanie notifications@github.com wrote:

Hi,

I am looking to run iqtree on a cluster and would like to be able to take advantage of -nt AUTO. However, by default, iqtree is detecting the total number of cores on the given compute node, which may or may not match the resource allocation requested. For example, if a node has 64 cores but my job only requested 32, I would like to be able to use AUTO while also specifying "no more than 32". Is this possible with the current version?

Thanks! -Stephanie

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Cibiv/IQ-TREE/issues/57, or mute the thread https://github.com/notifications/unsubscribe-auth/AOM303lnlF8Uilx3nYr1XpnbG2ZyWMBbks5tbpQ5gaJpZM4SevUL.

jvollme commented 6 years ago

I was just about to post the same Issue when I noticed it was posted here already. This would be a very important feature for safe usage of iqtree on shared clusters. Really hope that you can implement it in the next release...

bqminh commented 6 years ago

Can you please test beta version /releases/v1.6.2.a ?

It has a new option, for example, -ntmax 10 to restrict the maximum of 10 CPU cores.

sjspielman commented 6 years ago

Hi Minh,

Tested Mac and Linux versions, works as expected! Thanks!

-Stephanie

RaSieb commented 3 years ago

Is this an issue only here locally, or do others also experience that the -ntmax / --max-threads option is ignored in iqtree? I have tested both with iqtree 2.1.2 and 1.6.9 (which is wrongly stated as 1-6-12 in the attached screenshot), and under the Creating fast initial parsimony tree by random order stepwise addition... step, all CPU's of the node are taken when using "AUTO". [edit] I have to note that this was ran with 12k COVID-19 sequences. It seems like there is no issue with around 8k sequences... Screen Shot 2021-01-14 at 11 42 52

bqminh commented 3 years ago

Hi there, please see an answer and solution here:

https://github.com/iqtree/iqtree2/issues/18 https://github.com/iqtree/iqtree2/issues/18

On 14 Jan 2021, at 9:48 pm, RaSi notifications@github.com wrote:

Is this an issue only here locally, or do others also experience that the -ntmax / --max-threads option is ignored in iqtree? I have tested both with iqtree 2.1.2 and 1.6.9 (which is wrongly stated as 1-6-12 in the attached screenshot), and under the Creating fast initial parsimony tree by random order stepwise addition... step, all CPU's of the node are taken when using "AUTO". https://user-images.githubusercontent.com/19334536/104581030-4d603f80-565e-11eb-8aec-3796df0aad2a.png — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/Cibiv/IQ-TREE/issues/57#issuecomment-760116558, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADRTPU23IUV7FEDRYC63YQTSZ3DZXANCNFSM4ET26UFQ.