Hi Dmitri,
What compiler are you using and what problems do you encounter? I build
Amber10 all the time with ifort and mpich2-1.07 without any problems on both
Opterons and Intel's.
The procedure I use is as follows:
1) Download mpich2-1.0.7.tar.gz
2) Untar to /usr/local/mpich2-1.0.7
3) cd /usr/local/mpich2-1.0.7
4) export CC=icc
5) export CXX=icc
6) export F90=ifort
7) export F77=ifort
8) export LDFLAGS=-static
9) export F90LAGS=-static
10)export CFLAGS=-static
11)export CXXFLAGS=-static
12)export CXXLDFLAGS=-static
13)./configure --prefix=/usr/local/mpich2-1.0.7-ifort-10.1.008
14)make
15)make install
16)make examples
17)edit ~/.bashrc and add
a. export MPI_HOME=/usr/local/mpich2-1.0.7-ifort-10.1.008
b. export PATH=$MPI_HOME/bin:$PATH
c. export MANPATH=$MPI_HOME/man:$MANPATH
d. export AMBERHOME=/usr/local/amber10
18)source ~/.bashrc
19)download ambertools 1.2 and amber10 tar gz files
20)untar both to /usr/local/amber10
21)Download bugfix.all files for both and apply
22)build ambertools as described in the manual - needed for netcdf etc.
23)cd $AMBERHOME/src
24)./configure_amber -mpich2 ifort
25)make clean
26)make parallel
27)cd $AMBERHOME/test
28)mpd &
29)export DO_PARALLEL='mpirun -np 4'
30)make test.parallel
31)make test.parallel.QMMM
32)cd $AMBERHOME/src/pmemd
33)./configure linux_em64t ifort mpich2 bintraj
34)(sometimes it is necessary to edit config.h and change all ifort to
mpif90 and clear the MPI_LIBS line.
35)make
36)make install
37)cd $AMBERHOME/test
38)make test.pmemd
This all works flawlessly on a vanilla install of RedHat Enterprise Linux AS
4.0 with ifort 10.1.018.
Good luck,
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Dmitri Nilov
Sent: Tuesday, October 21, 2008 9:32 AM
To: amber.scripps.edu
Subject: AMBER: Again: Installation problem of AMBER on cluster
Hi everybody,
I'm currently stuck with installing Amber 10 on a RHEL 4 cluster with
mpich2-1.07.
I've found this (
http://archive.ambermd.org/200805/0080.html ) in mailing
list, but it seems to me that the problem was not resolved.
Our processors are actually Opterons, and the head node is an Athlon 64.
If this is of any use, the system also has rather old glibc 2.3.4-2.13
Hope for any answer...
Dmitri Nilov
Lomonosov Moscow State University
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Received on Wed Oct 22 2008 - 05:10:47 PDT
