[gmx-users] problem when install gromacs on a node of cluster

[Justin A. Lemkul]

Santan William wrote:
> Hey all,
>        I wanted to install gromacs on one node of a cluster.  Firstly I 
> downloaded all needed packages to /home/william/software, then unpack 
> all of them under this folder.
>        Then, I followed the " Quick and Dirty Installation" instruction 
> using following commands:
>       
> 
> export SOFT=$HOME/software
> 
> export CPPFLAGS="-I$SOFT/include"
> export LDFLAGS="-L$SOFT/lib"
> 
> export NCPU=2
> export PATH="$PATH":$SOFT/bin
> 
> cd ../fftw-3.2.2; ./configure --prefix=$SOFT --enable-float && make -j $NCPU && make install
> cd ../gsl-1.11; ./configure --prefix=$SOFT && make -j $NCPU && make install
> 
> cd ../gromacs-4.0.2; ./configure --prefix=$SOFT --enable-mpi --with-gsl && make -j $NCPU && make install
> 
> cd ../openmotif-2.3.1; ./configure --prefix=$SOFT && make -j $NCPU && make install
> cd ../grace-5.1.22; ./configure --prefix=$SOFT && make -j $NCPU && make install && ln -s $SOFT/grace/bin/xmgrace $SOFT/bin/xmgrace
> 
> . $SOFT/bin/GMXRC
> 
> 
>     The problem occurred when I configured gromacs, the error information's as follows:
> 
> 
> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when searching for -lX11
> 
> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when searching for -lX11
> /usr/bin/ld: cannot find -lX11
> 
> collect2: ld returned 1 exit status
> make[3]: *** [mdrun] Error 1
> 
> make[3]: *** Waiting for unfinished jobs....
> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when searching for -lX11
> 
> /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when searching for -lX11
> /usr/bin/ld: cannot find -lX11
> 
> collect2: ld returned 1 exit status
> make[3]: *** [grompp] Error 1
> 
> make[3]: Leaving directory `/home/xpwei/software/gromacs-4.0.2/src/kernel'
> make[2]: *** [all-recursive] Error 1
> 
> make[2]: Leaving directory `/home/xpwei/software/gromacs-4.0.2/src'
> make[1]: *** [all] Error 2
> 
> make[1]: Leaving directory `/home/xpwei/software/gromacs-4.0.2/src'
> make: *** [all-recursive] Error 1
> 
> 
> 
> 
>      I do want to install gromacs in /home/william/software, and I havn't root permission. I think the reason of failoue maybe because environment virieable setting, but I can't figure it out after some trying. Would anyone please give me some help, I really appreciate. Thanks.
> 
> 

The problem stems from a missing X library, which may or may not be present on 
your cluster.  In any case, it's probably unnecessary standard parallel 
calculations.  I believe only ngmx needs X libraries.  Several suggestions:

1. Use the latest version of Gromacs, 4.0.5, not one from several months ago.
2. Don't install grace, and perhaps not even openmotif.
3. Configure with --without-x.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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