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.
