<br> Thank you very much for help me.<br> I have try to install gromacs 3.3.3 on rhel 4.0.<br> I try to configure gromacs single with the command <span style="font-family: monospace;">"</span>./configure --enable-mpi --program-suffix=_mpi--prefix=/usr/local/gromacs332", but when I try to install, I have this error:<br> usr/bin/install: cannot create regular file `/usr/local/gromacs/bin/grompp_mpi_d--prefix=/usr/local/gromacs333': No such file or directory<br> make[3]: *** [install-binPROGRAMS] Error 1<br> make[3]: Leaving directory `/home/mario/gromacs-3.3.3/src/kernel'<br> make[2]: *** [install-am] Error 2<br> make[2]: Leaving directory `/home/mario/gromacs-3.3.3/src/kernel'<br> make[1]: *** [install-recursive] Error 1<br> make[1]: Leaving directory `/home/mario/gromacs-3.3.3/src'<br> make: *** [install-recursive] Error 1<br> I have try to edit the end of the configure command "/usr/local/gromacs332" with"/usr/local/gromacs333" and "/usr/local/gromacs" but
I have anlogue errors. Can you help me?<br> <br> Thanks in advance.<br> <br> Mario<br><b><i>Diego Enry <diego.enry@gmail.com></i></b> ha scritto:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> You should check the user guide.<br>http://www.mcs.anl.gov/research/projects/mpich2/documentation/index.php?s=docs<br><br>In a nutshell:<br>1) You need is to install mpich in all machines. Actually you can sync<br>the mpich install directory (also gromacs).<br>2) You also need to have the same /etc/hosts on every machine. rsync that.<br>3) You need to grant ssh access without password by creating a rsa-key<br>for every user<br><br>Fell free to private message if you need any additional help.<br><br>Ciao.<br><br>On Tue, Mar 4, 2008 at 6:04 AM, mario ciappy <mariociap @yahoo.it=""> wrote:<br>> Thank's Diego,<br>> I'm grateful to you. I have only one question. How can I configure mpi/lam<br>> for
relaize the comunication between nodes?<br>> I have created an hostsfile with my ip addresses.<br>> Thank's a lot in advance.<br>><br>> Mario<br>><br>> Diego Enry <diego.enry @gmail.com=""> ha scritto:<br>><br>> Since you didn't show us the problems you met.. try following this:<br>><br>> #1) Download essential packages<br>> #1.1) mpich<br>> wget<br>> http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/mpich2-1.0.6p1.tar.gz<br>><br>> #1.2) fftw<br>> wget ftp://ftp.fftw.org/pub/fftw/fftw-3.1.2.tar.gz<br>><br>> #1.3) gromacs<br>> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz<br>><br>><br>> #2) compile packages:<br>><br>> #2.1) mpich<br>> tar xvfz mpich2-1.0.6p1.tar.gz<br>> cd mpich2-1.0.6p1<br>> make distclean<br>> ./configure --with-device=ch3:nemesis --enable-fast --disable-cxx<br>> --enable-error-checking=no CFLAGS=-O3 FFLAGS=-O3<br>> make<br>> make
install<br>> make distclean<br>> cd ..<br>><br>> #2.2) fftw single<br>> tar xvfz fftw-3.1.2.tar.gz<br>> cd fftw-3.1.2<br>> make distclean<br>> ./configure --enable-float --enable-sse --enable-threads<br>> make<br>> make install<br>> make distclean<br>> cd ..<br>><br>> #2.3) gromacs single<br>> tar xvfz gromacs-3.3.2.tar.gz<br>> cd gromacs-3.3.2<br>> ./configure --enable-mpi --program-suffix=_mpi<br>> --prefix=/usr/local/gromacs332<br>> make<br>> make install<br>> make links<br>> make distclean<br>> cd ..<br>><br>> #2.4) fftw double<br>> cd fftw-3.1.2<br>> ./configure --enable-sse2 --enable-threads<br>> make<br>> make install<br>> make distclean<br>> cd ..<br>><br>> #2.2) gromacs double<br>> cd gromacs-3.3.2<br>> ./configure --enable-mpi --program-suffix=_mpi_d<br>> --prefix=/usr/local/gromacs332 --enable-double<br>> make<br>> make install<br>> make
links<br>> make distclean<br>> cd ..<br>><br>><br>><br>><br>> On Mon, Mar 3, 2008 at 3:09 PM, mario ciappy wrote:<br>> > Dear all,<br>> > I'm tried to configure gromacs in parallel but I have meet some problems.<br>> > I don't understand if the problems are relative to mpi or gromacs<br>> > configuration. For this reason I'd be grateful if you explained a detailed<br>> > installation procedure of all that require to run gromacs in parallel,<br>> > started by mpi/lam configuration. I now that is an hard and demanding<br>> > request, but it is a big help for me because you are only resource.<br>> ><br>> > Thank's in advance<br>> ><br>> > Mario<br>> ><br>> ><br>> > ________________________________<br>> > ________________________________<br>> ><br>> > L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail<br>> >
_______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>><br>><br>><br>> --<br>> Diego Enry B. Gomes<br>> Laboratório de Modelagem e Dinamica Molecular<br>> Universidade Federal do Rio de Janeiro - Brasil.<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use
the<br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>><br>><br>><br>><br>> ________________________________<br>> ________________________________<br>> L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>><br><br><br><br>-- <br>Diego Enry B. Gomes<br>Laboratório de Modelagem e Dinamica Molecular<br>Universidade Federal do Rio de Janeiro -
Brasil.<br>_______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br></diego.enry></mariociap></blockquote><br><p> 
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