Additionally, if you care about a few percent extra performance, you should use gcc 4.5 or 4.6 for compiling Gromacs as well as FFTW (unless you have a bleeding-edge OS which was built with any of these latest gcc versions). While you might not see a lot of improvement in mdrun performance (wrt gcc >v4.5), as far as I remember, FFTW gets slightly more boost form the new gcc versions.
I can't comment on other compilers, I haven't tried to run binaries compiled with Intel Compiler on AMD lately. -- Szilárd On Wed, Jul 6, 2011 at 3:08 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 6/07/2011 1:36 AM, Anthony Cruz Balberdi wrote: > > Thank you very much Mark. Another question, will be better if I compile FFTW > than use the one included in my linux distro? > > Per the GROMACS installation instructions, you want the precision of FFTW to > match the precision of GROMACS. You'll have to find out what precision of > FFTW is available for your distro and then decide. Note that > single-precision will often be labelled fftwf or fftws, and double-precision > fftw or fftwd. > > Mark > > Anthony > > On Tue, Jul 5, 2011 at 11:08 AM, Mark Abraham <mark.abra...@anu.edu.au> > wrote: >> >> On 6/07/2011 12:28 AM, Matthew Zwier wrote: >>> >>> Sorry about that. >>> >>> The default options are nearly optimal, and the difference between a >>> modern (4.4 or 4.5) series GCC and the Intel compilers are only a >>> couple of percent. Just be sure to have FFTW available. >> >> ... if planning to use PME. Also, Intel MKL is only a percent or two >> faster than FFTW3, last I tested, but much more fiddly to link. >> >> Mark >> >>> On Tue, Jul 5, 2011 at 10:26 AM, Matthew Zwier<mczw...@gmail.com> wrote: >>>> >>>> Hi Anthony, >>>> >>>> The default options are nearly optimal, and the difference between a >>>> modern (4.4 or 4.5) GCC >>>> >>>> On Tue, Jul 5, 2011 at 10:01 AM, Anthony Cruz Balberdi >>>> <anthony.cr...@upr.edu> wrote: >>>>> >>>>> Dear Users: >>>>> >>>>> We recently received our new computer. This computer have 4 multicore >>>>> Opteron AMD cpus and I am planning to install GROMAS. Which options I >>>>> will >>>>> need to use in order to achieve the best possible performance? >>>>> Which compiler GNU or Intel? >>>>> >>>>> Thank you for all you help. >>>>> >>>>> Anthony >>>>> >>>>> -- >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at >>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>>> Please don't post (un)subscribe requests to the list. Use the >>>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
