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
> >
> > ========================================
> > --
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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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