For future reference, I was able to install gromacs and this is what finally worked - installing gromacs in a folder different than the untared. It somehow helped to not create the folder but just directly using the name in the prefix
301 cd gromacs 302 ls 303 export CPPFLAGS="-I/fs/home/sm868/fftw-3.2.2/include" 304 export LDFLAGS="-L/fs/home/sm868/fftw-3.2.2/lib" 305 clear 306 ls 307 ./configure --help 308 ./configure --prefix=/fs/home/sm868/gromacsnew 309 make &>log 310 ls 311 jmacs log 312 grep "error" log 313 grep "Error" log 314 make install I got the msg - GROMACS is installed under /fs/home/sm868/gromacsnew. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Thanks for the help. *One question - There is already another version of gromacs installed in the /usr/local so I used a different directory to install it. Now do I need to use "make links"?* * * Pooja On Sun, Jun 20, 2010 at 2:17 AM, Sai Pooja <[email protected]> wrote: > I redid the entire thing after that first mail in which i reported the > error related to fftw(including running the make uninstall commands and > removing the folders entirely and getting fresh ones). I apologize for not > specifying this and like I said... there seemed to be no errors this time > except when I ran make install for gromacs. The error looks like this: > make[3]: *** [install-man1] Error 1 > > make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1' > > make[2]: *** [install-am] Error 2 > > make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' > > make[1]: *** [install-recursive] Error 1 > > make[1]: Leaving directory `/fs/home/sm868/gromacs/man' > > make: *** [install-recursive] Error 1 > I didn't find any other error.. is there a way to look for them other than > looking at what is being printed while the command is running? I tried $ > grep "Error" */* in the folder but found nothing more than entries in > different scripts etc. > > > > > > > On Sun, Jun 20, 2010 at 1:27 AM, Mark Abraham <[email protected]>wrote: > >> >> >> ----- Original Message ----- >> From: Sai Pooja <[email protected]> >> Date: Sunday, June 20, 2010 15:09 >> Subject: Re: [gmx-users] Installing gromacs from git >> To: Discussion list for GROMACS users <[email protected]> >> >> > History log: >> >> > 189 ./configure --enable-threads --enable-float >> --prefix=/fs/home/sm868/fftw-3.2.2 >> > 190 make >> > 191 clear >> > 192 make install >> > 193 cd .. >> > 194 cd gromacs >> > 195 ls >> > 196 export CPPFLAGS="-I/fs/home/sm868/fftw-3.2.2/include" >> > 197 export LDFLAGS="-L/fs/home/sm868/fftw-3.2.2/lib" >> > 198 ./bootstrap >> > 199 ls >> > 200 ./configure --prefix=/fs/home/sm868/gromacs >> > 201 make >> > 202 make install >> > >> > Everything works till I get the following error with make install(after >> it runs for a while) : >> > make[3]: *** [install-man1] Error 1 >> > make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1' >> > make[2]: *** [install-am] Error 2 >> > make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' >> > make[1]: *** [install-recursive] Error 1 >> > make[1]: Leaving directory `/fs/home/sm868/gromacs/man' >> > make: *** [install-recursive] Error 1 >> >> This is just make cleaning up after recursive invocation. The actual error >> is further up. Note that if configure failed according to your previous >> email, then there's no point to using make. >> >> Mark >> >> > On Sat, Jun 19, 2010 at 7:49 PM, Mark Abraham >> > <[email protected]>wrote: >> >>> > >>> > >>> > ----- Original Message ----- >>> > From: Sai Pooja <[email protected]> >>> > Date: Sunday, June 20, 2010 9:35 >>> > Subject: Re: [gmx-users] Installing gromacs from git >>> > To: Discussion list for GROMACS users <[email protected]> >>> > >>> > > I am sorry that was a typo in the mail. It was set to lib >>> > >>> > That makes it hard for us to have confidence in the rest of your >>> command lines - copying and pasting the results of "history" is a good way >>> to avoid such problems. >>> > >>> > As such I can only suggest looking for "error" in the last 100 lines >>> of config.log and seeing what you find. That, and trying it all again :-) >>> > >>> > Mark >>> > >>> > >>> > > On Sat, Jun 19, 2010 at 7:28 PM, Justin A. Lemkul >>> > > <[email protected]>wrote: >>> >>>> > > >>>> > > >>>> > > Sai Pooja wrote: >>>> >>>>> > > Hi, >>>>> > > >>>>> > > I followed the following steps to install gromacs from the git >>>>> repository: >>>>> > > >>>>> > > 1) installed git >>>>> > > 2) got a clone of gromacs using the anonymous option >>>>> > > >>>>> > > 3) installed fftw libraries using >>>>> > > ./configure --enable-float --prefix=/fs/home/sm868 >>>>> > > make >>>>> > > make install >>>>> > > >>>>> > > 4)export CPPFLAGS=-I/fs/home/sm868/include >>>>> > > export LDFLAGS=-L/fs/home/sm868/include >>>>> > > >>>>> > > 6)ran ./bootstrap >>>>> > > 7)ran ./configure --prefix=/fs/home/sm868 >>>>> > > 8)I get the error - checking for sqrt in -lm... yes >>>>> > > checking for fftw3.h... yes >>>>> > > checking for main in -lfftw3f... no >>>>> > > configure: error: Cannot find fftw3f library >>>>> > > >>>>> > >>>> >>>> > >>>> > > You set your LDFLAGS to the /include subdirectory; you want to set >>>> it to the /lib subdirectory. >>>> > > >>>> > > -Justin >>>> >>>> > > >>>> >>>>> > > Can someone help me with this? >>>>> > > >>>>> > > >>>>> > > Pooja >>>>> > > >>>>> > > -- >>>>> > > Quaerendo Invenietis-Seek and you shall discover. >>>>> > > >>>>> > >>>> >>>> > >>>> > > -- >>>> > > ======================================== >>>> > > >>>> > > Justin A. Lemkul >>>> > > Ph.D. Candidate >>>> > > ICTAS Doctoral Scholar >>>> > > MILES-IGERT Trainee >>>> > > Department of Biochemistry >>>> > > Virginia Tech >>>> > > Blacksburg, VA >>>> > > jalemkul[at]vt.edu | (540) 231-9080 >>>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>>> > > >>>> > > ======================================== >>>> > > -- >>>> > > gmx-users mailing list [email protected] >>>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users<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 >>>> >>> > > >>> > > >>> > > >>> > > -- >>> > > Quaerendo Invenietis-Seek and you shall discover. >>> > > -- >>> > > 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 >>> > >>> > -- >>> > gmx-users mailing list [email protected] >>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<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 >>> >> > >> > >> > >> > -- >> > Quaerendo Invenietis-Seek and you shall discover. >> > -- >> > 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 >> >> -- >> >> 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 >> > > > > -- > Quaerendo Invenietis-Seek and you shall discover. > -- Quaerendo Invenietis-Seek and you shall discover.
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