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.wa...@csi.cuny.edu>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-boun...@open-mpi.org [users-boun...@open-mpi.org] On Behalf Of > Gokhan Kir [g...@iastate.edu] > Sent: Monday, August 16, 2010 5:43 PM > To: us...@open-mpi.org > 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 > us...@open-mpi.org > 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
