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Subject: Re: [OMPI users] A Problem with RAxML
From: Gokhan Kir (gkir_at_[hidden])
Date: 2010-08-16 19:01:57


Thanks Richard,
Actually I am not sure how to try the way you told in RAxML. I don't have
too much experience with these programs.

Thanks again.

On Mon, Aug 16, 2010 at 5:40 PM, Richard Walsh
<Richard.Walsh_at_[hidden]>wrote:

>
> Hey Gokhan,
>
> The following worked for me with OpenMPI 1.4.1 with the latest Intel
> compiler
> (May release) although there have been reports that with full vectorization
> there
> are some unexplained inflight failures:
>
> #
> # Parallel Version
> #
> service0:/share/apps/raxml/7.0.4/build # make -f Makefile.MPI
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o axml.o
> axml.c
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o
> raxmlParsimony.o raxmlParsimony.c
> mpicc -c -o rev_functions.o rev_functions.c
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o
> optimizeModel.o optimizeModel.c
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o multiple.o
> multiple.c
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o
> searchAlgo.o searchAlgo.c
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o
> topologies.o topologies.c
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o
> parsePartitions.o parsePartitions.c
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o treeIO.o
> treeIO.c
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o models.o
> models.c
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o
> bipartitionList.o bipartitionList.c
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o
> rapidBootstrap.o rapidBootstrap.c
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o
> evaluatePartialGeneric.o evaluatePartialGeneric.c
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o
> evaluateGeneric.o evaluateGeneric.c
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o
> newviewGeneric.o newviewGeneric.c
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o
> makenewzGeneric.o makenewzGeneric.c
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o
> evaluateGenericVector.o evaluateGenericVector.c
> mpicc -O3 -DPARALLEL -fomit-frame-pointer -funroll-loops -c -o
> categorizeGeneric.o categorizeGeneric.c
> mpicc -o raxmlHPC-MPI axml.o raxmlParsimony.o rev_functions.o
> optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o
> treeIO.o models.o bipartitionList.o rapidBootstrap.o
> evaluatePartialGeneric.o evaluateGeneric.o newviewGeneric.o
> makenewzGeneric.o evaluateGenericVector.o categorizeGeneric.o -lm
>
> The lastest PGI-built OpenMPI 1.4.1 release is said to behave correctly
> with the following
> flags regardless of the level of optimization. I have both versions
> installed. Both compile
> and link without error for me. This is with and IB built OpenMPI.
>
> CC = /share/apps/openmpi-pgi/default/bin/mpicc
> CFLAGS = -O3 -DPARALLEL -Mnoframe -Munroll
>
> Hope this is useful ...
>
> rbw
>
> Richard Walsh
> Parallel Applications and Systems Manager
> CUNY HPC Center, Staten Island, NY
> 718-982-3319
> 612-382-4620
>
> Reason does give the heart pause;
> As the heart gives reason fits.
>
> Yet, to live where reason always rules;
> Is to kill one's heart with wits.
> ________________________________________
> From: users-bounces_at_[hidden] [users-bounces_at_[hidden]] On Behalf Of
> Gokhan Kir [gkir_at_[hidden]]
> Sent: Monday, August 16, 2010 5:43 PM
> To: users_at_[hidden]
> Subject: [OMPI users] A Problem with RAxML
>
> Hi,
> I am currently using RAxML 7.0, and recently I got a problem. Even though I
> Googled it, I couldn't find a satisfying answer.
> I got this message from BATCH_ERRORs file " raxmlHPC-MPI: topologies.c:179:
> restoreTL: Assertion `n >= 0 && n < rl->max' failed. "
>
> Any help is appreciated,
>
> Thanks,
>
> --
> Gokhan
>
> Think green before you print this email.
>
> _______________________________________________
> users mailing list
> users_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>

-- 
Gokhan Kir
Graduate Student
Program of Interdepartmental Genetics
Department of Genetics,Development and Cell Biology
2188 Molecular Biology Building