AMBER Archive (2006)

Subject: RE: AMBER: Amber install on RedHat Linux

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu May 04 2006 - 10:31:56 CDT

Dear Annie,

> These are the files in exe directory:
> am1bcc bondtype cpinutil.pl espgen makeDIP_RST.dna
> makeSHF_RST molsurf prepgen senergy teLeap
> antechamber calcpka.pl crdgrow makeANG_RST
> makeDIP_RST.protein
> mm_pbsa.pl parmcal README sviol tleap
> atomtype CPin.pm database makeCHIR_RST
> makeDIST_RST
> mm_pbsa_statistics.pl parmchk respgen sviol2 xleap
>
> Did anything is missing?

Yes, lots it seems you got only the things that are written in c compiled.
 
> ifort -c -w95 -tpp7 -mp1 -O0 -o new2oldparm.o _new2oldparm.f
> make[1]: ifort: Command not found

This should be a fairly obvious error. As part of the Intel compiler
installation it tells you (or the system admin) to modify your login scripts
to source the intel setup files. I.e.

source /opt/intel/fc/9.0/bin/ifortvars.sh

Indeed, pasting the above error message into Google gives you many useful
hits:

http://www.google.com/search?sourceid=navclient&ie=UTF-8&rls=GGLG,GGLG:2005-
52,GGLG:en&q=make%5B1%5D%3A+ifort%3A+Command+not+found

Alternatively as I see below it is likely that you do not have the Intel
compiler suite installed.

> Since I suspect no compilation has done, I type "make -i"

So this was a bad idea. What you told make to do is to ignore errors and
continue, which is exactly what it did. It has gone through, ignored the
fact that it can't find ifort as it was not setup in your path correctly and
then just merrily compiled anything written in c with the gcc compiler that
is in your path. Hence you only got a subset of the programs compiled.

> What should I do next? Based on the inforamtion about, do I
> need to buy a
> compiler, if yes, could you mind to recommend a compiler that
> is compatible
> with amber8 and could solve the problems I raised above?

You need a Fortran 90 compiler to compile Amber 8 (Fortran 95 for Amber 9).
You can download the Intel fortran compiler for Linux from the Intel site
and it is free for personal use. Although technically for academic use one
has to pay a licence fee to Intel. Alternatively you can use the free g95
compiler which is available here: http://www.g95.org The attached config.h
file ('I believe') should work for Amber 8 with g95.

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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