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HYPHY Package >> HyPhy feedback >> MPI compilation http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1156524882 Message started by tlefebure on Aug 25th, 2006 at 9:54am |
Title: MPI compilation Post by tlefebure on Aug 25th, 2006 at 9:54am
Hello,
I'm now trying to compile with the MPI flag, and obtain this error: Code (] [tristan@babylon HYPHY_Source):
I have lam install (I use it to run mrbayes with MPI, and it works fine). Librairies and binaries seem present: Code (] [tristan@babylon HYPHY_Source):
Is someone knows what's the problem? (I did not found the solution for MP, and thus try to solve the problem using MPI, yes that's not nice...) Thanks, Tristan |
Title: Re: MPI compilation Post by Sergei on Aug 25th, 2006 at 10:15am
Dear Tristan,
Try editing the build.sh file to use 'mpic++' in place of 'g++' as the compiler and see what happens. Also, you may need to add a -I include path for wherever the mpi.h file is. Cheers, Sergei |
Title: Re: MPI compilation Post by tlefebure on Aug 25th, 2006 at 10:59am
thanks Sergei,
I changed "g++" by "mpic++" (lign 6 of build.sh), and I removed "-lmpich" from the lign 148, and the compilation worked. Great. than what I did: [code] echo "localhost cpu=4" > lamhosts lamboot lamhosts mpirun -np 4 ./HYPHYMPI BatchFiles/speedtest.bf [/code] and it worked, the four cpus were used. Nevertheless the time needed is not that good: 31s, which is the same time used by a single cpus (which is already too slow)... |
Title: Re: MPI compilation Post by Sergei on Aug 25th, 2006 at 11:03am
Dear Tristan,
speedtest.bf is not written to take advantage of MPI - only MP (it's actually very difficult to efficiently split up a single likelihood evaluation in a distributed environment). A number of standard analyses are MPI enables though, and you should see speed-ups there. Try to run MPITest.bf to see that the MPI build is working properly. I am still puzzled as to why gcc would produce such poor code for the Xeon - it is even slower than an old Athlon XP running at 1.33 GHz. Does your gcc version have a 'fast' flag? Perhaps try setting that in the MP (or SP) build and see if CPU specific tweaking will help. Cheers, Sergei |
Title: Re: MPI compilation Post by tlefebure on Aug 25th, 2006 at 12:49pm
Here is the results with MPITest.bf:
Code (][tristan@babylon HYPHY_Source):
Then I tried to compile with SP with the -fast and -m64 flags, but: Code (][tristan@babylon HYPHY_Source):
Something interesting is that with MP, with the flag CPU=1, one cpu will be used at 100%, while with CPU>1, a single cpu is still used but this time at 120% (which speed up the computation: 31 -> 22s). By the way, regarding MPI, why the 4 cpus are used at 100% with speedtest since only one is necessary? I'am afraid I'm lost... thanks Sergei and sorry for all these questions. My aim is to convert a pipeline that test recombination and positive selection at the genome scale to hyphy. Today the pipeline use many different programs (phyml, phypack, paml,...). It seems that with hyphy, most of the pipeline might be summarized in a single batch file and would furthermore be deployed easily on a cluster. Tristan |
Title: Re: MPI compilation Post by tlefebure on Aug 25th, 2006 at 2:28pm
Ouh, I found at least one answer few second before I give up.
On Xeon 64bit (= Xeon EM64T = nocona cpu), you should compile with the following flags: [code] COMPILER_FLAGS=" -w -c -O2 -march=nocona -pipe -fsigned-char -fpermissive -I`pwd`/Source -I`pwd`/Source/SQLite "; [/code] now it takes 11s to perform speedtest.bf with SP. (that does not fixed the MP problem) Tristan |
Title: Re: MPI compilation Post by Sergei on Aug 25th, 2006 at 2:33pm
Dear Tristan,
Thanks so much for the tip! I'll put that into the build.sh file for the next update. Does the MP build (with the new flags) take the same amount of time as the single build? Cheers, Sergei |
Title: Re: MPI compilation Post by Sergei on Aug 25th, 2006 at 3:53pm
Dear Tristan,
Quote:
I'd like to try the Xeon - this odd behavior is a bit troubling. Cheers, Sergei |
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