Hi, I had used the following steps to install a git version of gromacs. It installed correctly and I have been using it for a while. However, even though I didnt install the parallel version, when I use mdrun it runs in parallel. Is installation in the parallel mode by default? Is there a way to use it without parallelization?
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 Pooja On Sun, Jun 20, 2010 at 2:17 PM, Justin A. Lemkul <[email protected]> wrote: > > > Sai Pooja wrote: > >> 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"?* >> > > Do you normally make links? If so, you'll be over-writing the executables > in /usr/local/bin. One other possible side effect is that if both > /usr/local/bin and /usr/local/gromacs/bin are in your $PATH, you can't > define which executable to use unambiguously without specifying the whole > path name for each executable. > > If you're using several version of Gromacs concurrently on the same > machine, it's probably best to just install them in their own locations and > source the proper GMXRC when you log in to use the version you want. > > -Justin > > * >> * >> Pooja >> >> >> >> >> >> >> On Sun, Jun 20, 2010 at 2:17 AM, Sai Pooja <[email protected] <mailto: >> [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] <mailto:[email protected]>> wrote: >> >> >> >> ----- Original Message ----- >> From: Sai Pooja <[email protected] <mailto:[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] >> <mailto:[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 <http://vt.edu> | (540) 231-9080 >> >> > > >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> > > >> > > ======================================== >> > > -- >> > > 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. >> > > -- >> > > 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. >> > -- >> > gmx-users mailing list [email protected] >> <mailto:[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] >> <mailto:[email protected]>. >> >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> -- >> >> gmx-users mailing list [email protected] >> <mailto:[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] >> <mailto:[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. >> >> > -- > ======================================== > > 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 > > ======================================== > -- > 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.
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