Hi, if you configure the git version without the "--enable-mpi" flag, it will turn on threads by default. Depending on the number of processors you have on your workstation, it will then use these many threads. You can disable that with
mdrun -nt 1 ... Carsten On Jul 10, 2010, at 1:57 AM, Sai Pooja wrote: > 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 <jalem...@vt.edu> 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 <saipo...@gmail.com > <mailto:saipo...@gmail.com>> 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 > <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote: > > > > ----- Original Message ----- > From: Sai Pooja <saipo...@gmail.com <mailto:saipo...@gmail.com>> > Date: Sunday, June 20, 2010 15:09 > Subject: Re: [gmx-users] Installing gromacs from git > To: Discussion list for GROMACS users <gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org>> > > > 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 > <mark.abra...@anu.edu.au> wrote: > > > > > > > ----- Original Message ----- > > From: Sai Pooja <saipo...@gmail.com> > > Date: Sunday, June 20, 2010 9:35 > > Subject: Re: [gmx-users] Installing gromacs from git > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > > > 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 > <jalem...@vt.edu> 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 gmx-users@gromacs.org > > > 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 > gmx-users-requ...@gromacs.org. > > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > > > > > -- > > > Quaerendo Invenietis-Seek and you shall discover. > > > -- > > > gmx-users mailing list gmx-users@gromacs.org > > > 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 gmx-users-requ...@gromacs.org. > > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > 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 gmx-users-requ...@gromacs.org. > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > -- > > Quaerendo Invenietis-Seek and you shall discover. > > -- > > gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > > > 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 gmx-users-requ...@gromacs.org > <mailto:gmx-users-requ...@gromacs.org>. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > > gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > > 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 gmx-users-requ...@gromacs.org > <mailto:gmx-users-requ...@gromacs.org>. > > 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > Quaerendo Invenietis-Seek and you shall discover. > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
