[gmx-users] compiling problem on alpha-cluster, ld?

[Erik Lindahl]

Fan Hao wrote:
> Hi, all:
> 
>     I met problems when I tried to install gmx3.0
> 
> on our alpha cluster (MACHTYPE=alpha;  OSTYPE=linux).
> 
> At first, the installation was fine but it gave:
> 
> "error in loading shared libraries: libXext.so.6 ..."
> 
> Then I tried to recompile gmx without x support.
> 
> I guess: --without-motif-libraries could be the right choice
> 
> and I also include system libraries by adding "/etc/ld.so.conf"
> 
> into $path of my .cshrc file. What I did was :
> 
> "  ./configure --prefix=/home/gmx/home3.0 --enable-mpi
> 
>  --enable-x86-asm --without-motif-libraries
> 
>    make                                     "
> 
> It provided the following message:
> 
> "/opt/binutils-2.13/bin/ld: grompp:
> 
> Not enough room for program headers (allocated 6, need 7)
> 
> /opt/binutils-2.13/bin/ld: final link failed: Bad value "
> 
> I am not sure what it means. Should I change my enviroment
> 
> or change the Makefile? Any hints are sincerely appreciated!!!

Hi,

First you don't want ld.so.conf in your path; it is just a list of 
directories to search for libraries when linking. When you change the 
file you should run /sbin/ldconfig, but that's it.

Second, if you're running linux on an Alpha CPU, you most definitely do
not want the x86 assembly loops. I would recommend

make distclean
./configure --prefix=/home/gmx/home3.0 --without-motif-libraries
make
make install

When that works, recompile the mdrun binary with mpi support (if you
have multiple cpus on the machine, or multiple macines)

make distclean
./configure --prefix=/home/gmx/home3.0 --without-motif-libraries \ 
--enable-mpi
make mdrun
make install

(The \ sign just means that the line continues).

Cheers,

Erik