AMBER Archive (2004)

Subject: Re: AMBER: Running on MPI

From: wish_71 (
Date: Tue Oct 05 2004 - 21:43:16 CDT

Dear Prof. Carlos L. Simmerling,

Thanks a lot for your reply!

I used Amber7 for molecular dynamics simulation of proteins in Single PC one year ago. Yes, sander does work under non-mpi. Now my system is more than 1000 residues, and the ruuning speed is very slowly to monitor results by using GB model. Thus, I want to move my present work into PC-cluster.

The basic information of our PC-cluster is as following:
nodes=16; ppn=2 (uses 32 CPUs total); OS: Red hat 9.0 (Fedora version).

We first installed Amber7 according to the Amber7 manual, and created a link to the Machine.g77 _mpich. However, source files of Amber7 could not be successfully made. Then we just changed all "L1, L2 and L3" from all different "Makefile" files into L0 without modifying contents following "setenv". It seems that we then made install successfully. And we can run "sander" by the single CPU.

This afternoon, we created a pbs-script by using more than 1 CPUs, "flag -p4pg" wrong message displayed, and the sander could not be run.

After above failure, we tested another PG compiler. Unfortunately, we could not make install of Amber7 together with following wrong messages:

new2oldparm.o(.text+Ox3ec2): In function 'MAIN_':
:undefined reference to 's_copy'
new2oldparm.o(.text+Ox3f20): In function 'MAIN_':
:undefined reference to 's_rsfe'
new2oldparm.o(.text+Ox3f4e): In function 'MAIN_':
:undefined reference to 'do_fio'

make[1]: ***[new2oldparm] Error 1
make[1]: leaving directory '/usr/local/amber7/src/lib'
make:***[install] Error 2


That's all, looking forward to your warm-hearted help!

Thank you very much invance!

Best Wishes,

Yingliang Wu

College of Life Science
Wuhan Univeristy
Wuhan, China

>it would be much easier to help if you tell us exactly what >sander does
>and if you get any error message or output file.

>does the single processor (non-mpi) sander work?




经典HP nx9040超强性能,突破万元底限! (
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to