I believe that this problem is about mpi installation. What mpi version was installed ? Lampi or openmpi.
There is a good tutorial about that in http://www.gromacs.org/WIKI-import/Quick_and_Dirty_Installation Best regards, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 On Thu, Aug 27, 2009 at 7:14 AM, Silvia Giuliani <[email protected]>wrote: > Dear All > > Has anybody tried version 4.0.5 on an IBM Power6 (4.7Ghz) cluster? > We have installed the program with the following configure options (using > fftw we installed separately): > > ./configure --with-fft=fftw2 --enable-mpi --enable-float CC=mpcc_r > F77=mpxlf_r CXX=mpCC_r CFLAGS="-O3 -qarch=pwr6 -qtune=pwr6 -qcpluscmt" > > It compiles and works but the performance is poor compared to our Opteron > Cluster (2.6Ghz) > For example with 8 procs for a small protein in water we get 5.8ns/+day > compared to 9.6 ns/day on the Linux cluster, which is a bit disappointing. > Since there alot of compiler options to play with we would be grateful if > somebody who has already found a good set would share them with us. > > best wishes > Silvia Giuliani > > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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