Re: [AMBER] compile Amber16 with the intel compiler

From: Vlad Cojocaru <>
Date: Mon, 17 Oct 2016 18:22:14 +0200

Thanks Dave,

I don't have control over the environment on that machine, so I would
need to dig a little to understand it. The intel compiler is loaded
using "module load" on top of the basic layout which includes gcc 4.8.5 ...

Is it possible that gcc tries to load the last "math.h" file it finds in
the include list ? That would be the intel one ...

I will try with changing the Makefile as you suggested ... I can also
look further into the reasons for this ...


On 10/17/2016 06:12 PM, David A Case wrote:
> On Mon, Oct 17, 2016, Vlad Cojocaru wrote:
>> I am trying to compile Amber16 on a cluster with Intel compiler
>> (16.0.3). However, I get the error below. The error tells that even if I
>> specify the -intel option to configure, there is some stuff that
>> automatically compiles with gcc. And then I get the incompatibility
>> between the math.h file from intel and gnu.
>> (cd FEW && make install)
>> make[2]: Entering directory
>> `/home/mpg05/vcojoca/apps/gwdu102/amber/16_tools-16/AmberTools/src/FEW'
>> gcc miscellaneous/draw_membrane2.c -lm -o miscellaneous/draw_membrane2
>> In file included from miscellaneous/draw_membrane2.c:58:0:
>> /cm/shared/apps/intel/compilers_and_libraries/2016.3.210/compiler/include/math.h:29:3:
>> error: #error "This Intel <math.h> is for use with only the Intel
>> compilers!"
>> # error "This Intel <math.h> is for use with only the Intel compilers!"
>> ^
> This is rather odd: do you understand why gcc would be trying to include the
> math.h file from the Intel compiler? This hasn't happened on any of the
> machines we have access to, but (I'm guessing) you have some environment
> variable set that we haven't tried(?)
> Edit the Makefile in the AmberTools/src/FEW directory, and replace "gcc" with
> "$(CC)".
> [Or, edit AmberTools/src/Makefile to skip compiling FEW.}
> Thanks for the report....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]
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Received on Mon Oct 17 2016 - 09:30:04 PDT
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