<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div>Okay, I'll try with --enable-single. But as far as I understood, it seems like its an issue with --enable-shared. In the first attempt, I did enable-shared in fftw configuration, but didn't do it in gromacs configuration, and got this error. In the second attempt, I did enable-shared in ./configure for both fftw and gromacs, but still got the same message. In the third attempt, I didn't enable shared anywhere, and installation went well. Only issue is that when I run ngmx, it says "command not found", and I can't view .trr file, but this seems to be a different issue. But I don't know why --enable-shared isn't working.</div><div><br></div><div>About installing in home directory: actually I downloaded the source from gromacs website, and I did manage to install it in my home directory.
But some of the commands, like luck, and ngmx are missing. When I type any of luck, I get, command not found and you can install it by typing sudo apt-get install gromacs. I did try to download it using apt-get and software center in ubuntu, but it installs it in usr/share/gromacs, but I want to install it in my home directory.</div><div><br></div><div>Thanks,</div><div>Majid</div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> lina zhao <lnzhao99@gmail.com><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Mon, February 14, 2011 6:24:47 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users]
Gromacs Installation<br></font><br>
1. Seems the default fftw configuration is double, <br> when you install the fftw-3.2.2 configure with --enable single.<br><br>2. about your question:"I wanted to ask if I can download gromacs in my home directory using the ubuntu software center or synaptic manager?"<br>
<br>1] You can download in your home directory and install. <br><br><span>2] a better but a bit not so-easy way, is download the source (<a target="_blank" href="http://packages.debian.org/sid/gromacs">http://packages.debian.org/sid/gromacs</a>), built the package and add it into repository.</span><br>
<br>There maybe also some other ways.<br><br>HTH,<br><br>lina <br><br><div class="gmail_quote">On Tue, Feb 15, 2011 at 6:23 AM, majid hasan <span dir="ltr"><<a rel="nofollow" ymailto="mailto:pu_majidhasan@yahoo.com" target="_blank" href="mailto:pu_majidhasan@yahoo.com">pu_majidhasan@yahoo.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex;"><div><div style="font-family:times new roman, new york, times, serif;font-size:12pt;color:rgb(0, 0, 0);">
<div>Dear All,<br><br><span><span>I am trying to install gromacs in ubuntu. I configured both fftw and gromacs in my home folder following the instructions on <a target="_blank" href="http://www.gromacs.org/Downloads/Installation_Instructions">http://www.gromacs.org/Downloads/Installation_Instructions</a>. However, when I do "make", I get an error in the end (pasted below). I have also attached the log file of compilation with the email.</span></span><br>
<br>/usr/bin/ld: /home/majid/user/soft/fftw/lib/libfftw3f.a(mapflags.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC<br>/home/majid/user/soft/fftw/lib/libfftw3f.a: could not read symbols: Bad value<br>
collect2: ld returned 1 exit status<br>make[3]: *** [<a rel="nofollow" target="_blank" href="http://libmd.la">libmd.la</a>] Error
1<br>make[3]: Leaving directory `/home/majid/user/down/gromacs/src/mdlib'<br>make[2]: *** [all-recursive] Error 1<br>make[2]: Leaving directory `/home/majid/user/down/gromacs/src'<br>make[1]: *** [all] Error 2<br>
make[1]: Leaving directory `/home/majid/user/down/gromacs/src'<br>make: *** [all-recursive] Error 1<br><br>Moreover, I wanted to ask if I can download gromacs in my home directory using the ubuntu software center or synaptic manager?<br>
<br>Thanks,<br>Majid<br></div><div class="hm">
</div></div><div class="hm"><br>
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