AMBER Archive (2007)

Subject: AMBER: RE: Amber9 compile problem

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Nov 27 2007 - 11:24:22 CST


Hi Norisham

Such questions should really go to the Amber mail reflector (see
http://amber.scripps.edu/ for sign up details) this way they make it into
the archive (http://amber.ch.ic.ac.uk/archive/) for others to see.

> -----Original Message-----
> From: norisham begek [mailto:begek_at_yahoo.com]
> Sent: Monday, November 26, 2007 23:57
> To: ross_at_rosswalker.co.uk
> Cc: azharudin_at_ibtech.com.my
> Subject: Amber9 compile problem
>
> Hi Ross,
>
> I really need your assistance to look at my problem.
> I'm installing amber9 on redhat enterprise 5.x. But
> failed in the compilation stage(ifort not found as
> shown below). Below are some info which i think u
> would require.
>
> Environment setting as below:-
> -----------------------------
> export PATH
> PATH=$PATH:$HOME/bin:/usr/local/mpich-1.2.7p1/bin:/tmp/mpich-1
.2.7p1/util:/usr/local/amber9/exe
> LIBRARY_PATH=/usr/local/mpich-1.2.7p1/lib
> LD_LIBRARY_PATH=/usr/local/intel/fc/10.1.008/lib/32
> export LIBRARY_PATH LD_LIBRARY_PATH
> export MPI_HOME=/usr/local/mpich-1.2.7p1/bin
> export AMBERHOME=/usr/local/amber9/src
> export MKL_HOME=/usr/local/intel/cmkl/10.0.011
>
> MPICH
> -----
> # mpiversion
> MPICH Version: 1.2.7p1
> MPICH Release date: $Date: 2005/11/04 11:54:51$
> MPICH Patches applied: none
> MPICH configure: --prefix=/usr/local/mpich-1.2.7p1
> -c++=g++ -cc=gcc -fc=ifort --with-common=shared
> --disable-devdebug --enable-f90 --with-arch=LINUX
> -rsh=ssh --enable-sharedlib
> MPICH Device: ch_p4
>
> Amber
> -----
> root_at_master:/usr/local/amber9/src
> [root_at_master src]# ./configure ifort_ia32
> AMBERHOME is set to /usr/local/amber9/src
> Setting up Amber configuration file for architecture:
> ifort_ia32
> Using parallel communications library: none
> MKL_HOME is set to /usr/local/intel/cmkl/10.0.011
> Using MKL libraries from
> /usr/local/intel/cmkl/10.0.011/lib/32
> The configuration file, config.h, was successfully
> created.
>
> root_at_master:/usr/local/amber9/src
> [root_at_master src]# make serial
> Starting installation of Amber9 (serial) at Tue Nov 27
> 12:45:09 MYT 2007.
> cd lib; make install
> make[1]: Entering directory
> `/usr/local/amber9/src/lib'
> cpp -traditional -P -DMKL new2oldparm.f >
> _new2oldparm.f
> ifort -c -w95 -mp1 -O0 -o new2oldparm.o
> _new2oldparm.f
> make[1]: ifort: Command not found
> make[1]: *** [new2oldparm.o] Error 127
> make[1]: Leaving directory `/usr/local/amber9/src/lib'
> make: *** [serial] Error 2
> root_at_master:/usr/local/amber9/src
> [root_at_master src]# Script done on Tue 27 Nov 2007
> 12:45:12 PM MYT

Do you have ifort in your path? It would appear not. You need to add:

source /opt/intel/path_to_ifort/bin/ifortvars.sh

to your .bashrc (or ifortvars.csh to your .cshrc if you use tcsh).

Then logout, log back in and verify that ifort is in your path with "which
ifort".

Note pasting the error message into the Google search box on the archive
site yields a number of useful hits:

http://www.google.com/custom?domains=amber.ch.ic.ac.uk&q=ifort%3A+Command+no
t+found&sa=Search&sitesearch=amber.ch.ic.ac.uk&client=pub-9700140137778662&f
orid=1&channel=0921873412&ie=ISO-8859-1&oe=ISO-8859-1&cof=GALT%3A%23008000%3
BGL%3A1%3BDIV%3A%23336699%3BVLC%3A663399%3BAH%3Acenter%3BBGC%3AFFFFFF%3BLBGC
%3A336699%3BALC%3A0000FF%3BLC%3A0000FF%3BT%3A000000%3BGFNT%3A0000FF%3BGIMP%3
A0000FF%3BFORID%3A1&hl=en

All the best
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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