Dear Andrew,
in general, it should be possible, but there a couple of exceptions.
I'd recommend to just copy all PREFIX.raxml.* files to a new directory, try to restart with a higher
number of threads there, and see what happens :)
Best,
Oleksiy
On 01.03.24 09:22, Andrew ODonnell wrote:
> Dear Alexis,
>
> I've run 20 tree searches on a large data set of 1,600 sequences using 10 threads using raxml-ng, as
> determined by the estimation, by following along with the raxml tutorial. However, we have up to 32
> available cores on our computing cluster, and I'm wondering if the checkpointing described here
> <
https://github.com/amkozlov/raxml-ng/wiki/Advanced-Tutorial> allows me to stop the search, increase
> the number of threads, and then resume from a checkpoint (i.e. can I change a parameter in how raxml
> was called and still benefit from the checkpointing features)? My search is still running, but
> taking a very long time, and I would like to first ask, and then try stopping the run an re-starting
> with more threads selected.
>
> I used the raxml-ng-mpi verion as so, while following along with the raxml-ng tutorial:
>
> *RAxML-NG v. 1.1.0 released on 29.11.2021 by The Exelixis Lab.
> Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
> Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
> Latest version:
https://github.com/amkozlov/raxml-ng
> Questions/problems/suggestions? Please visit:
https://groups.google.com/forum/#!forum/raxml
>
> System: Intel(R) Xeon(R) CPU E5-2683 v4 @ 2.10GHz, 32 cores, 503 GB RAM
>
> RAxML-NG was called at 28-Feb-2024 11:35:02 as follows:
>
> raxml-ng-mpi --msa hits.phy --model JTT+G --prefix T3 --threads 10 --seed 2
>
> Analysis options:
> run mode: ML tree search
> start tree(s): random (10) + parsimony (10)
> random seed: 2
> tip-inner: OFF
> pattern compression: ON
> per-rate scalers: OFF
> site repeats: ON
> fast spr radius: AUTO
> spr subtree cutoff: 1.000000
> branch lengths: proportional (ML estimate, algorithm: NR-FAST)
> SIMD kernels: AVX2
> parallelization: coarse-grained (auto), PTHREADS (10 threads), thread pinning: ON
>
> [00:00:00] Reading alignment from file: hits.phy
> [00:00:00] Loaded alignment with 1637 taxa and 7894 sites*
>
> On Friday, March 16, 2018 at 5:40:44 AM UTC+1 Alexandros Stamatakis wrote:
>
> Hi Tauna,
>
> Restarting from checkpoint with RAxML does not work for the RAxML
> command you are using and it also doesn't work for the hybrid version,
> unfortunately.
>
> You can either split up those 10 ML searches into 10 individual searches
> (10 jobs), but you need to make sure that each search is started with a
> different random number seed (-p option).
>
> Alternatively you can use ExaML (as you said) or RAxML-NG, the new
> better version of RAxML:
>
https://github.com/amkozlov/raxml-ng <
https://github.com/amkozlov/raxml-ng>
> > For more options, visit
https://groups.google.com/d/optout <
https://groups.google.com/d/optout>.
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
>
>
www.exelixis-lab.org <
http://www.exelixis-lab.org>
> To view this discussion on the web visit
>
https://groups.google.com/d/msgid/raxml/c73889db-40ba-4355-a3bb-300e71d1849en%40googlegroups.com
> <
https://groups.google.com/d/msgid/raxml/c73889db-40ba-4355-a3bb-300e71d1849en%40googlegroups.com?utm_medium=email&utm_source=footer>.