Re: [OMPI users] A Problem with RAxML
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
Re: [OMPI users] A Problem with RAxML
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.
Re: [OMPI users] A Problem with RAxML
You might want to start by contacting someone from that software package - this is the Open MPI mailing list. On Aug 16, 2010, at 3:43 PM, Gokhan Kir wrote: > 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 > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
[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
