Hi, David, One question. I know that fftw3 can not be enabled with mpi, while fftw2 can. Your email implies that fftw3 without mpi can be used with gromacs that is mpi enabled. I guess my question is. Can you use fftw3 without mpi with mpi enabled gromacs? I appreciate your help.
Best wishes, Art --- David van der Spoel <[EMAIL PROTECTED]> wrote: > Arthur Roberts wrote: > > To Whom It May Concern: > > > > I have checked the archives, but I have not found > a > > good solution for the following problem: > > > > When I try to compile Gromacs 3.3.1, I get > complaints > > from the compiler that I have undefined symbols. > The > > symbols are present in the libraries, so I don't > know > > why ld can not seem to find them. I checked the > > libraries with the following command. > > > > nm library.a | grep undefined_symbol > > > the missing symbols are from FFTW2. > > First you'll get slightly better performance from > FFTW3 > Second it may be necessary to link in the mpi > version of the FFTW libs > as well, check which libs are in the fftw/lib > directory > Third, with FFTW3 you only have one library to link > to, which may make > it slightly simpler > Fourth, it seems that configure for gromacs doesn't > add a -lfftw to the > link command line, but instead puts the library > itself on the command > line, which is strange. > > > > > > Perhaps, there is a flag that I need to see on the > LD > > command or something. There is a detailed > description > > of the problem at: > > > > > http://cetus.mchem.washington.edu/pub/supercomputer/Gromacs-compiling-problems.html > > > > I appreciate input that any you could give. > Perhaps, > > you know someone that has installed Gromacs on a > > computer system that runs AIX 5.2. > > > > Appreciate your help... > > > > Best wishes, > > Art Roberts > > Department of Medicinal Chemistry > > University of Washington > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > 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 > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular > Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala > University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] > http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
