History log:<div><br></div><div><div>189 ./configure --enable-threads --enable-float --prefix=/fs/home/sm868/fftw-3.2.2</div><div> 190 make</div><div> 191 clear</div><div> 192 make install</div><div> 193 cd ..</div>
<div> 194 cd gromacs</div><div> 195 ls</div><div> 196 export CPPFLAGS="-I/fs/home/sm868/fftw-3.2.2/include"</div><div> 197 export LDFLAGS="-L/fs/home/sm868/fftw-3.2.2/lib"</div><div> 198 ./bootstrap</div>
<div> 199 ls</div><div> 200 ./configure --prefix=/fs/home/sm868/gromacs</div><div> 201 make</div><div> 202 make install</div></div><div><br></div><div>Everything works till I get the following error with make install(after it runs for a while) :</div>
<div><div>make[3]: *** [install-man1] Error 1</div><div>make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1'</div><div>make[2]: *** [install-am] Error 2</div><div>make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1'</div>
<div>make[1]: *** [install-recursive] Error 1</div><div>make[1]: Leaving directory `/fs/home/sm868/gromacs/man'</div><div>make: *** [install-recursive] Error 1</div></div><div><br></div><div>Pooja</div><div><br></div>
<div><br></div><div> </div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br><br><div class="gmail_quote">On Sat, Jun 19, 2010 at 7:49 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><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></div><div class="im"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font>I am sorry that was a typo in the mail. It was set to lib <br><br></div>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.<br>
<br>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 :-)<br><font color="#888888"><br>Mark</font><div><div></div><div class="h5">
<br><br><div class="gmail_quote"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font>On Sat, Jun 19, 2010 at 7:28 PM, Justin A. Lemkul <span dir="ltr"><<a>jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex"><div><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> Hi,<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> I followed the following steps to install gromacs from the git repository:<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> 1) installed git<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> 2) got a clone of gromacs using the anonymous option<br> <font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> 3) installed fftw libraries using<br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> ./configure --enable-float --prefix=/fs/home/sm868<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> make<br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> make install<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> 4)export CPPFLAGS=-I/fs/home/sm868/include<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> export LDFLAGS=-L/fs/home/sm868/include<br> <font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> 6)ran ./bootstrap<br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> 7)ran ./configure --prefix=/fs/home/sm868<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> 8)I get the error - checking for sqrt in -lm... yes<br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> checking for fftw3.h... yes<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> checking for main in -lfftw3f... no<br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> configure: error: Cannot find fftw3f library<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br> </blockquote> <font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br>
</div><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> You set your LDFLAGS to the /include subdirectory; you want to set it to the /lib subdirectory.<br> <font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> -Justin<div><br> <font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> Can someone help me with this?<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br> <font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> Pooja<br> <font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> -- <br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> Quaerendo Invenietis-Seek and you shall discover.<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br> </blockquote> <font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br>
</div><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> -- <br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> ========================================<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> Justin A. Lemkul<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> Ph.D. Candidate<br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> ICTAS Doctoral Scholar<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> MILES-IGERT Trainee<br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> Department of Biochemistry<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> Virginia Tech<br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> Blacksburg, VA<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> 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"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> ========================================<br>
<font color="#888888"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> -- <br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> gmx-users mailing list <a>gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font>http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a>gmx-users-request@gromacs.org</a>.<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</font></blockquote></div><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br clear="all">
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font>-- <br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font>Quaerendo Invenietis-Seek and you shall discover.<br> > -- <br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> <br>
> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a>
</div></div><br>--<br>
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<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>
</div>