[gmx-users] Installing gromacs from git
Sai Pooja
saipooja at gmail.com
Sun Jun 20 14:07:57 CEST 2010
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"?*
*
*
Pooja
On Sun, Jun 20, 2010 at 2:17 AM, Sai Pooja <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>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>
>>>> > >
>>>> > > ========================================
>>>> > > --
>>>> > > gmx-users mailing list gmx-users at gromacs.org
>>>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users<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-request at 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 at 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-request at gromacs.org.
>>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>> >
>>> > --
>>> > gmx-users mailing list gmx-users at gromacs.org
>>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<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-request at 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 at 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-request at gromacs.org.
>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>> --
>>
>> gmx-users mailing list gmx-users at 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-request at 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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100620/0008a605/attachment.html>
More information about the gromacs.org_gmx-users
mailing list