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Subject: Re: [OMPI users] A Problem with RAxML
From: Richard Walsh (Richard.Walsh_at_[hidden])
Date: 2010-08-16 18:40:16


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.