[gmx-users] Installing gromacs from git

Sai Pooja saipooja at gmail.com
Sun Jun 20 08:17:45 CEST 2010 

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>wrote:

>
>
> ----- Original Message -----
> From: Sai Pooja <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>
>
> > 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 | (540) 231-9080
>>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> > >
>>> > > ========================================
>>> > > --
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>>>
>> > >
>> > >
>> > >
>> > > --
>> > > Quaerendo Invenietis-Seek and you shall discover.
>> > > --
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> >
> >
> >
> > --
> > Quaerendo Invenietis-Seek and you shall discover.
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-- 
Quaerendo Invenietis-Seek and you shall discover.
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