Did start from scratch, and things were normal this time. thank you ! On Fri, Dec 28, 2012 at 2:22 PM, maria goranovic <[email protected]>wrote:
> thank you, Mark. I will try to restart from scratch > > > On Fri, Dec 28, 2012 at 1:10 AM, Mark Abraham <[email protected]>wrote: > >> Standard procedure is to do >> >> ./configure >> make >> sudo make install >> >> or >> >> ./configure --prefix=/somewhere/you/can/write/to >> make >> make install >> >> I suggest you use sudo to get rid of your progress to date and start >> again. >> Using sudo anywhere else is a recipe for trouble. >> >> Mark >> >> On Thu, Dec 27, 2012 at 3:41 PM, maria goranovic >> <[email protected]>wrote: >> >> > I will try to fix this. Thank you. >> > >> > Now, the problem I have is that the executables all belong to root, and >> as >> > a user, I am unable to execute them. How to fix this little one? >> > >> > Maria >> > >> > On Thu, Dec 27, 2012 at 3:36 PM, Mark Abraham <[email protected] >> > >wrote: >> > >> > > sudo should not be necessary for looking in those directories. Whoever >> > set >> > > them up has not set up the permissions on them properly. Fix the >> problem, >> > > not the symptoms - you do not want to have to configure software as >> root, >> > > or you are trusting every author of that software not to trash your >> > system >> > > accidentally. >> > > >> > > On Thu, Dec 27, 2012 at 3:31 PM, maria goranovic >> > > <[email protected]>wrote: >> > > >> > > > turned out to be a sudo problem. without sudo, the compiler could >> not >> > > look >> > > > into the root directories. sorry for spamming :( >> > > > >> > > > On Thu, Dec 27, 2012 at 2:25 PM, maria goranovic >> > > > <[email protected]>wrote: >> > > > >> > > > > Yes, I can see them in printenv >> > > > > >> > > > > does this have anything to do with single or double precision? >> > > > > >> > > > > >> > > > > On Thu, Dec 27, 2012 at 1:38 PM, Mark Abraham < >> > > [email protected] >> > > > >wrote: >> > > > > >> > > > >> Are those variables actully showing up in your environment? >> > > > >> >> > > > >> On Thu, Dec 27, 2012 at 11:31 AM, maria goranovic >> > > > >> <[email protected]>wrote: >> > > > >> >> > > > >> > Dear All >> > > > >> > >> > > > >> > I am trying to install 4.5.5 on my mac. I have installed fftw3 >> > with >> > > > >> > --enable-float, and have used the CPPFLAGS and LDFLAGS options >> in >> > my >> > > > >> > .bashrc file. GROMACS still complains that "configure: error: >> > Cannot >> > > > >> find >> > > > >> > fftw3f library". >> > > > >> > >> > > > >> > Why is it not able to find the libraries? >> > > > >> > >> > > > >> > Here are the specific details: >> > > > >> > >> > > > >> > content of .bashrc: >> > > > >> > >> > > > >> > export CPPFLAGS="-I/usr/local/include" >> > > > >> > export LDFLAGS="-L/usr/local/lib" >> > > > >> > >> > > > >> > % ls /usr/local/lib/*fft* >> > > > >> > /usr/local/lib/libfftw3f.a /usr/local/lib/libfftw3f.la >> > > > >> > >> > > > >> > % ls /usr/local/include/*fft* >> > > > >> > /usr/local/include/fftw3.f /usr/local/include/fftw3.f03 >> > > > >> > /usr/local/include/fftw3.h /usr/local/include/fftw3l.f03 >> > > > >> > /usr/local/include/fftw3q.f03 >> > > > >> > >> > > > >> > Any ideas what might be going wrong? >> > > > >> > >> > > > >> > Thank you >> > > > >> > >> > > > >> > >> > > > >> > -- >> > > > >> > Maria G. >> > > > >> > Technical University of Denmark >> > > > >> > Copenhagen >> > > > >> > -- >> > > > >> > gmx-users mailing list [email protected] >> > > > >> > 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 [email protected]. >> > > > >> > * Can't post? Read >> http://www.gromacs.org/Support/Mailing_Lists >> > > > >> > >> > > > >> -- >> > > > >> gmx-users mailing list [email protected] >> > > > >> 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 [email protected]. >> > > > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > >> >> > > > > >> > > > > >> > > > > >> > > > > -- >> > > > > Maria G. >> > > > > Technical University of Denmark >> > > > > Copenhagen >> > > > > >> > > > >> > > > >> > > > >> > > > -- >> > > > Maria G. >> > > > Technical University of Denmark >> > > > Copenhagen >> > > > -- >> > > > gmx-users mailing list [email protected] >> > > > 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 [email protected]. >> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > >> > > -- >> > > gmx-users mailing list [email protected] >> > > 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 [email protected]. >> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > >> > >> > >> > >> > -- >> > Maria G. >> > Technical University of Denmark >> > Copenhagen >> > -- >> > gmx-users mailing list [email protected] >> > 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 [email protected]. >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Maria G. > Technical University of Denmark > Copenhagen > -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
