AMBER Archive (2004)

Subject: Re: AMBER: Compiling Amber 8

From: Robert Duke (
Date: Mon Apr 12 2004 - 09:22:27 CDT

John -
Presumably you have installed the intel fortran compiler? When done, did
you include a line something like
"source /<fortan install dir>/bin/ifcvars.csh" in your .login file and log
out and back in? (this is for csh/tcsh; if you use bash, there is a script
ending in .sh that should be sourced in .profile). Amber 7 probably
installed "out of the box" using g77 as the compiler which is typically
installed as part of the system; here you get the intel fortran compiler,
which produces significantly faster code (also, g77 will no longer do the
job due to fortran 90 dependencies in the code). Also, note that if you
installed version 7.1 of the intel fortran compiler, you have to reference
ifc7 in the configure command. I recommend using ifc 7.1.038 because it
supports building pmemd, which is faster than sander. You have to configure
pmemd separately per the instructions under amber8/src/pmemd/README, so if
you are sufficiently traumatized by the other build issues and don't care
about performance, it does not hurt to put this off (pmemd currently won't
work with ifort 8, due to bugs in ifort 8, which will hopefully be fixed
sometime before amber 9 is released...).
Regards - Bob Duke

----- Original Message -----
From: "Beale, John" <>
To: <>
Sent: Monday, April 12, 2004 9:44 AM
Subject: AMBER: Compiling Amber 8

> I have been trying to compile Amber 8 on a Pentium 4 system with the
Redhat Linux 9 operating system. Let me begin by stating that Amber 7
compiled "out of the box" on this machine and works fine. Every time I
execute the "make serial" command in the Amber 8 installation instructions
this is what happens:
> [jbeale_at_PS3030 src]$ ./configure -p4 ifort
> AMBERHOME is set to /home/jbeale/amber8
> Setting up Amber configuration file for architecture: ifort
> Using parallel communications library: none
> The MKL_HOME environment variable is not defined.
> The MKL is recommended for optimal performance.
> The configuration file, config.h, was successfully created.
> [jbeale_at_PS3030 src]$ make serial
> Starting installation of Amber8 (serial) at Mon Apr 12 08:25:30 CDT 2004.
> mkdir ../exe
> mkdir: cannot create directory `../exe': File exists
> make: [serial] Error 1 (ignored)
> cd lib; make install
> make[1]: Entering directory `/home/jbeale/amber8/src/lib'
> cpp -traditional -P -I/home/jbeale/amber8/src/include new2oldparm.f >
> ifort -c -w95 -tpp7 -mp1 -O0 -o new2oldparm.o _new2oldparm.f
> make[1]: ifort: Command not found
> make[1]: *** [new2oldparm.o] Error 127
> make[1]: Leaving directory `/home/jbeale/amber8/src/lib'
> make: *** [serial] Error 2
> Can anyone help me understand what is going on here and suggest a fix?
> John Beale
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to