<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 style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">Okay, thanks, I'll look into config.log. Can you tell me about this error: <span class="Apple-style-span" style="font-family: arial, helvetica, sans-serif; font-size: 13px; ">relocation R_X86_64_32 against `.rodata' can not be used when making</span></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><span class="Apple-style-span" style="font-family: arial, helvetica, sans-serif; font-size: 13px; ">> a shared object; recompile with -fPIC. Does it have something to do with --enable-shared during configuration of fftw, and gromacs?</span> </div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt;
"><br></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">Best Regards,</div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; ">Majid</div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br><div style="font-family:arial, helvetica, sans-serif;font-size:10pt"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><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 6:46:47 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Gromacs Installation<br></font><br>
<br><br>majid hasan wrote:<br>> 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.<br>> <br>> 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.<br>> <br><br>In the latest version of Gromacs, "luck" is named "g_luck." If ngmx was not installed, then probably the required X11 libraries were not found on your system. Check the output from configuration (i.e. config.log) for details.<br><br>-Justin<br><br>> Thanks,<br>> Majid<br>> <br>> ------------------------------------------------------------------------<br>> *From:* lina zhao <<a ymailto="mailto:lnzhao99@gmail.com" href="mailto:lnzhao99@gmail.com">lnzhao99@gmail.com</a>><br>> *To:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Mon, February 14, 2011 6:24:47 PM<br>> *Subject:* Re: [gmx-users] Gromacs
Installation<br>> <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>> On Tue, Feb 15, 2011 at 6:23 AM, majid hasan <<a ymailto="mailto:pu_majidhasan@yahoo.com" href="mailto:pu_majidhasan@yahoo.com">pu_majidhasan@yahoo.com</a> <mailto:<a
ymailto="mailto:pu_majidhasan@yahoo.com" href="mailto:pu_majidhasan@yahoo.com">pu_majidhasan@yahoo.com</a>>> wrote:<br>> <br>> Dear All,<br>> <br>> I am trying to install gromacs in ubuntu. I configured both fftw and<br>> gromacs in my home folder following the instructions on<br><span>> <a target="_blank" href="http://www.gromacs.org/Downloads/Installation_Instructions">http://www.gromacs.org/Downloads/Installation_Instructions</a>. However,</span><br>> when I do "make", I get an error in the end (pasted below). I have<br>> also attached the log file of compilation with the email.<br>> <br>> /usr/bin/ld: /home/majid/user/soft/fftw/lib/libfftw3f.a(mapflags.o):<br>> relocation R_X86_64_32 against `.rodata' can not be used when making<br>> a shared object; recompile with
-fPIC<br>> /home/majid/user/soft/fftw/lib/libfftw3f.a: could not read symbols:<br>> Bad value<br>> collect2: ld returned 1 exit status<br>> make[3]: *** [<a target="_blank" href="http://libmd.la">libmd.la</a><span> <<a target="_blank" href="http://libmd.la">http://libmd.la</a>>] Error 1</span><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<br>> directory using the ubuntu software center or synaptic
manager?<br>> <br>> Thanks,<br>> Majid<br>> <br>> ------------------------------------------------------------------------<br>> Never miss an email again!<br>> Yahoo! Toolbar<br><span>> <<a target="_blank" href="http://us.rd.yahoo.com/evt=49938/*http://tools.search.yahoo.com/toolbar/features/mail/">http://us.rd.yahoo.com/evt=49938/*http://tools.search.yahoo.com/toolbar/features/mail/</a>></span><br>> alerts you the instant new Mail arrives. Check it out.<br><span>> <<a target="_blank" href="http://us.rd.yahoo.com/evt=49937/*http://tools.search.yahoo.com/toolbar/features/mail/">http://us.rd.yahoo.com/evt=49937/*http://tools.search.yahoo.com/toolbar/features/mail/</a>></span><br>> <br>> --<br>> gmx-users mailing list <a
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target="_blank">http://us.rd.yahoo.com/evt=49981/*http://advision.webevents.yahoo.com/mailbeta/features_spam.html</a>><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>jalemkul[at]<a target="_blank" href="http://vt.edu">vt.edu</a> | (540) 231-9080<br><span><a target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">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
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