[gmx-users] compile gmx alpha-cluster

Fan Hao F.Hao at chem.rug.nl
Fri Oct 4 13:25:17 CEST 2002

> 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
> 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
Yes , this process works. Many thanks!
PS:  the linux system on alpha cluster is redhat 2.2.13-2, I am not sure

whether it is related to the previous problem. Maybe 2.4.* is the better

kernel for gmx3.0 or gmx3.1?

Best regards

Yours sincerely

Hao Fan :-)

Drs. Hao Fan                            email F.Hao at chem.rug.nl
Lab. of Biophysical Chemistry
University of Groningen
Nijenborgh 4                            9747 AG GRONINGEN
The Netherlands

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