HyPhy message board | |
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl
HYPHY Package >> HyPhy bugs >> Multiple threads & MPI evaluation http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1140709612 Message started by Oscar Harari on Feb 23rd, 2006 at 7:46am |
Title: Multiple threads & MPI evaluation Post by Oscar Harari on Feb 23rd, 2006 at 7:46am
Hi,
I've been deploying HyPhy on several platforms and it rocks! My aim is to run it on parallel platforms: - MPI: The linker reports the following error: Linking HYPHYMPI obj_MPI/likefunc.cpp.o(.text+0xf86f): In function `_LikelihoodFunction::Optimize()': : undefined reference to `_hy_mpi_node_rank' collect2: ld returned 1 exit status Emulating the GTK version, I added the following lines to main-unix.cxx: (line 89) int _hy_mpi_node_rank; (line 697) _hy_mpi_node_rank = rank; It linked. Now I don’t know which algorithm execute to test it as a parallel job. - Multiple threads: I was able to compile MP and MP2 versions without problems. When I execute the process (with the command line opcion CPU=4, because I have a 2 dual core processors) I just observe only 1 processor fully loaded, but the others idle. Again I don’t know which algorithms make use of the pthreads facilities. Regards, Oscar Harari |
Title: Re: Multiple threads & MPI evaluation Post by Sergei on Feb 23rd, 2006 at 8:37am
Dear Oscar,
Thanks for the heads-up about missing variable definitions. I was actually updating the GTK version to run in MPI mode and forgot to add the same global variable to main-unix.cxx I'll fix that before I build the next snapshot. Re:pthreads; all likelihood function optimizations use pthreads - the effect is more noticeable when the data sets are large. Since most analyses need likelihood function optimizations, you should see multiple threads spawned and run. You can try to run BatchFiles/speedtest.bf with various numbers of CPUs and see if the speed improves. That dataset is small, so you won't see a 2x (or 4x) speedup, but you should see some. Some more obscure algorithms (e.g. ancestral state sampling) also make use of pthreads. Cheers, Sergei |
Title: Re: Multiple threads & MPI evaluation Post by Oscar Harari on Feb 24th, 2006 at 7:30am
Thank you very much!
I was able to check the speed up executing the MP version. Right now I am testing the MPI version. Basically I am runing MPITest.bf. It seems to exchange messages among the nodes. I would like to know if the algorithm are using all of the available nodes or one should code a batch file to produce a phylogenetic tree. Regards, Oscar |
HyPhy message board » Powered by YaBB 2.5.2! YaBB Forum Software © 2000-2024. All Rights Reserved. |