[gmx-users] Installing gromacs from git

Justin A. Lemkul jalemkul at vt.edu
Sun Jun 20 20:17:38 CEST 2010



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 <saipooja at gmail.com 
> <mailto:saipooja at 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.abraham at anu.edu.au <mailto:mark.abraham at anu.edu.au>> wrote:
> 
> 
> 
>         ----- Original Message -----
>         From: Sai Pooja <saipooja at gmail.com <mailto:saipooja at 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 at gromacs.org
>         <mailto:gmx-users at 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.abraham at anu.edu.au> wrote:
> 
>              >
>              >
>              > ----- Original Message -----
>              > From: Sai Pooja <saipooja at 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 at 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
>             <jalemkul at 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
>                  > >
>                  > > ========================================
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>              > >
>              > >
>              > >
>              > > --
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>          >
>          >
>          >
>          > --
>          > Quaerendo Invenietis-Seek and you shall discover.
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> 
> 
> 
>     -- 
>     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

========================================



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