AMBER Archive (2008)

Subject: Re: AMBER: Again: Installation problem of AMBER on cluster

From: Dmitri Nilov (nilovdm_at_gmail.com)
Date: Sat Oct 25 2008 - 07:30:43 CDT

Thank you!! The problem has been resolved by usage of icc+ifort combination)

Dmitri Nilov

Lomonosov Moscow State University

On Tue, Oct 21, 2008 at 8:49 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> 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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Dmitri Nilov
> *Sent:* Tuesday, October 21, 2008 9:32 AM
> *To:* amber_at_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
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu