[gmx-users] Gromacs Installation

majid hasan pu_majidhasan at yahoo.com
Tue Feb 15 03:42:41 CET 2011

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 

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 


From: lina zhao <lnzhao99 at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Mon, February 14, 2011 6:24:47 PM
Subject: Re: [gmx-users] Gromacs Installation

1. Seems the default fftw configuration is double, 
    when you install the fftw-3.2.2 configure with --enable single.

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?"

1] You can download in your home directory and install. 

2] a better but a bit not so-easy way, is download the source 
(http://packages.debian.org/sid/gromacs), built the package and add it into 

There maybe also some other ways.



On Tue, Feb 15, 2011 at 6:23 AM, majid hasan <pu_majidhasan at yahoo.com> wrote:

Dear All,
>I am trying to install gromacs in ubuntu. I configured both fftw and gromacs in 
>my home folder following the instructions on 
>http://www.gromacs.org/Downloads/Installation_Instructions. 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.
>/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
>/home/majid/user/soft/fftw/lib/libfftw3f.a: could not read symbols: Bad value
>collect2: ld returned 1 exit status
>make[3]: *** [libmd.la] Error  1
>make[3]: Leaving directory `/home/majid/user/down/gromacs/src/mdlib'
>make[2]: *** [all-recursive] Error 1
>make[2]: Leaving directory `/home/majid/user/down/gromacs/src'
>make[1]: *** [all] Error 2
>make[1]: Leaving directory `/home/majid/user/down/gromacs/src'
>make: *** [all-recursive] Error 1
>Moreover, I wanted to ask if I can download gromacs in my home directory using 
>the ubuntu software center or synaptic manager?
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