<div>Hi,</div><div><br></div><div>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? </div>
<div><br></div><div> 301 cd gromacs<br> 302 ls<br> 303 export CPPFLAGS="-I/fs/home/sm868/fftw-3.2.2/include"<br> 304 export LDFLAGS="-L/fs/home/sm868/fftw-3.2.2/lib"<br> 305 clear<br> 306 ls<br> 307 ./configure --help<br>
308 ./configure --prefix=/fs/home/sm868/gromacsnew<br> 309 make &>log<br> 310 ls<br> 311 jmacs log<br> 312 grep "error" log<br> 313 grep "Error" log<br> 314 make install<br></div><div><br>
</div><div><br></div>Pooja<br><br><div class="gmail_quote">On Sun, Jun 20, 2010 at 2:17 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
<br>
Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
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<br>
<br>
301 cd gromacs<br>
302 ls<br>
303 export CPPFLAGS="-I/fs/home/sm868/fftw-3.2.2/include"<br>
304 export LDFLAGS="-L/fs/home/sm868/fftw-3.2.2/lib"<br>
305 clear<br>
306 ls<br>
307 ./configure --help<br>
308 ./configure --prefix=/fs/home/sm868/gromacsnew<br>
309 make &>log<br>
310 ls<br>
311 jmacs log<br>
312 grep "error" log<br>
313 grep "Error" log<br>
314 make install<br>
<br>
I got the msg - GROMACS is installed under /fs/home/sm868/gromacsnew.<br>
Make sure to update your PATH and MANPATH to find the<br>
programs and unix manual pages, and possibly LD_LIBRARY_PATH<br>
or /etc/ld.so.conf if you are using dynamic libraries.<br>
<br>
<br>
Thanks for the help. <br></div>
*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"?*<br>
</blockquote>
<br>
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.<br>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
*<br>
*<br>
Pooja<div class="im"><br>
<br>
<br>
<br>
<br>
<br>
On Sun, Jun 20, 2010 at 2:17 AM, Sai Pooja <<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a> <mailto:<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>>> wrote:<br>
<br>
I redid the entire thing after that first mail in which i reported<br>
the error related to fftw(including running the make uninstall<br>
commands and removing the folders entirely and getting fresh ones).<br>
I apologize for not specifying this and like I said... there seemed<br>
to be no errors this time except when I ran make install for<br>
gromacs. The error looks like this:<br>
make[3]: *** [install-man1] Error 1<br>
> make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1'<br>
> make[2]: *** [install-am] Error 2<br>
> make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1'<br>
> make[1]: *** [install-recursive] Error 1<br>
> make[1]: Leaving directory `/fs/home/sm868/gromacs/man'<br>
> make: *** [install-recursive] Error 1<br>
I didn't find any other error.. is there a way to look for them<br>
other than looking at what is being printed while the command is<br>
running? I tried $ grep "Error" */* in the folder but found nothing<br>
more than entries in different scripts etc.<br>
<br>
<br>
<br>
<br>
<br>
<br>
On Sun, Jun 20, 2010 at 1:27 AM, Mark Abraham<br></div><div class="im">
<<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a> <mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>>> wrote:<br>
<br>
<br>
<br>
----- Original Message -----<br></div><div class="im">
From: Sai Pooja <<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a> <mailto:<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>>><br>
Date: Sunday, June 20, 2010 15:09<br>
Subject: Re: [gmx-users] Installing gromacs from git<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div><div><div></div><div class="h5">
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><br>
<br>
> History log:<br>
<br>
> 189 ./configure --enable-threads --enable-float<br>
--prefix=/fs/home/sm868/fftw-3.2.2<br>
> 190 make<br>
> 191 clear<br>
> 192 make install<br>
> 193 cd ..<br>
> 194 cd gromacs<br>
> 195 ls<br>
> 196 export CPPFLAGS="-I/fs/home/sm868/fftw-3.2.2/include"<br>
> 197 export LDFLAGS="-L/fs/home/sm868/fftw-3.2.2/lib"<br>
> 198 ./bootstrap<br>
> 199 ls<br>
> 200 ./configure --prefix=/fs/home/sm868/gromacs<br>
> 201 make<br>
> 202 make install<br>
><br>
> Everything works till I get the following error with make<br>
install(after it runs for a while) :<br>
> make[3]: *** [install-man1] Error 1<br>
> make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1'<br>
> make[2]: *** [install-am] Error 2<br>
> make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1'<br>
> make[1]: *** [install-recursive] Error 1<br>
> make[1]: Leaving directory `/fs/home/sm868/gromacs/man'<br>
> make: *** [install-recursive] Error 1<br>
<br>
This is just make cleaning up after recursive invocation. The<br>
actual error is further up. Note that if configure failed<br>
according to your previous email, then there's no point to using<br>
make.<br>
<br>
Mark<br>
<br>
> On Sat, Jun 19, 2010 at 7:49 PM, Mark Abraham<br>
<<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>> wrote:<br>
<br>
><br>
><br>
> ----- Original Message -----<br>
> From: Sai Pooja <<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>><br>
> Date: Sunday, June 20, 2010 9:35<br>
> Subject: Re: [gmx-users] Installing gromacs from git<br>
> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
><br>
> > I am sorry that was a typo in the mail. It was set to lib<br>
><br>
> That makes it hard for us to have confidence in the rest<br>
of your command lines - copying and pasting the results of<br>
"history" is a good way to avoid such problems.<br>
><br>
> As such I can only suggest looking for "error" in the<br>
last 100 lines of config.log and seeing what you find. That,<br>
and trying it all again :-)<br>
><br>
> Mark<br>
><br>
><br>
> > On Sat, Jun 19, 2010 at 7:28 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>> wrote:<br>
<br>
> ><br>
> ><br>
> > Sai Pooja wrote:<br>
<br>
> > Hi,<br>
> ><br>
> > I followed the following steps to install<br>
gromacs from the git repository:<br>
> ><br>
> > 1) installed git<br>
> > 2) got a clone of gromacs using the anonymous<br>
option<br>
> ><br>
> > 3) installed fftw libraries using<br>
> > ./configure --enable-float --prefix=/fs/home/sm868<br>
> > make<br>
> > make install<br>
> ><br>
> > 4)export CPPFLAGS=-I/fs/home/sm868/include<br>
> > export LDFLAGS=-L/fs/home/sm868/include<br>
> ><br>
> > 6)ran ./bootstrap<br>
> > 7)ran ./configure --prefix=/fs/home/sm868<br>
> > 8)I get the error - checking for sqrt in -lm... yes<br>
> > checking for fftw3.h... yes<br>
> > checking for main in -lfftw3f... no<br>
> > configure: error: Cannot find fftw3f library<br>
> ><br>
> <br>
><br>
> > You set your LDFLAGS to the /include subdirectory;<br>
you want to set it to the /lib subdirectory.<br>
> ><br>
> > -Justin<br>
<br>
> ><br>
<br>
> > Can someone help me with this?<br>
> ><br>
> ><br>
> > Pooja<br>
> ><br>
> > --<br>
> > Quaerendo Invenietis-Seek and you shall discover.<br>
> ><br>
> <br>
><br>
> > --<br>
> > ========================================<br>
> ><br>
> > Justin A. Lemkul<br>
> > Ph.D. Candidate<br>
> > ICTAS Doctoral Scholar<br>
> > MILES-IGERT Trainee<br>
> > Department of Biochemistry<br>
> > Virginia Tech<br>
> > Blacksburg, VA<br></div></div>
> > jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div><div></div><div class="h5"><br>
> ><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
> ><br>
> > ========================================<br>
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-- Quaerendo Invenietis-Seek and you shall discover.<br>
<br>
<br>
<br>
<br>
-- <br>
Quaerendo Invenietis-Seek and you shall discover.<br>
<br>
</div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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