[gmx-users] Installing gromacs from git
Sai Pooja
saipooja at gmail.com
Sat Jul 10 01:57:47 CEST 2010
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 <jalemkul at 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 <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
>> > >
>> > > ========================================
>> > > --
>> > > gmx-users mailing list gmx-users at gromacs.org
>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> > >
>> > >
>> > >
>> > > --
>> > > 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
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>> .
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>> >
>> > --
>> > gmx-users mailing list gmx-users at gromacs.org
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>> http://www.gromacs.org/search before posting!
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>> >
>> >
>> >
>> > --
>> > Quaerendo Invenietis-Seek and you shall discover.
>> > --
>> > gmx-users mailing list gmx-users at gromacs.org
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>> --
>>
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search
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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
>
> ========================================
> --
> 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.
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