Re: [AMBER] compile Amber16 with the intel compiler

From: Vlad Cojocaru <>
Date: Tue, 18 Oct 2016 15:01:58 +0200

Below is the modufile loaded for the intel compiler ... So, it looks
like its the CPATH variable ...


#%Module -*- tcl -*-
## modulefile
proc ModulesHelp { } {

   puts stderr "\tAdds Intel compilers to your environment variables,"

module-whatis "adds Intel compilers to your environment variables"

set root

prepend-path PATH $root/mpi/intel64/bin
prepend-path PATH $root/bin/intel64

prepend-path LD_LIBRARY_PATH $root/mpi/intel64/lib
prepend-path LD_LIBRARY_PATH $root/compiler/lib/intel64

prepend-path LIBRARY_PATH $root/compiler/lib/intel64

prepend-path MIC_LD_LIBRARY_PATH $root/compiler/lib/mic

prepend-path MIC_LIBRARY_PATH $root/compiler/lib/mic

prepend-path CPATH $root/compiler/include
prepend-path CPATH $root/compiler/include/intel64

prepend-path NLSPATH $root/compiler/lib/intel64/locale/%l_%t/%N

prepend-path INTEL_LICENSE_FILE /cm/shared/licenses/intel

On 10/18/2016 02:49 PM, David A Case wrote:
> On Mon, Oct 17, 2016, Vlad Cojocaru wrote:
>> The environment for the intel compiler is loaded on top of the basis
>> which includes gcc 4.8.5 ... This means that the list of directories to
>> search for .h files (I called these "include" directories or "include
>> list") begins with those from intel ("last" loaded)... Then, the gcc
>> compiler will find the intel .h files first and will try to use those
>> ... I guess this is what is happening ....
> Understood, but where is this list stored? In some environment variable? The
> gcc invocation for FEW has no "-I" flag, so gcc should be looking in standard
> paths:
> Further, installation of the Intel compiler suite should not disable gcc.
> I suspect that there is something quite odd about your setup.
> That said, Amber should be repecting the CC variable requested at configure
> time.
> ....dac
> _______________________________________________
> AMBER mailing list

Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
AMBER mailing list
Received on Tue Oct 18 2016 - 06:30:02 PDT
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