Re: [AMBER] Unable to compile cuda version of amber14

From: Jason Swails <>
Date: Tue, 22 Jul 2014 12:57:56 -0700

On Tue, Jul 22, 2014 at 12:45 PM, Manikanthan Bhavaraju <> wrote:

> Hi All,
> I am trying to install and compile Amber14 and AmberTools14 on a
> supercomputing cluster. So far, I have successfully compiled serial and
> parallel versions of amber14. I am having issues in compiling cuda
> version. Attached is the log file. Some of the important errors are:
> -- Cleaning the src directories. This may take a few moments.
> Configure complete.
> cd AmberTools/src && make install
> make[1]: Entering directory `/home/mhb75/amber14/AmberTools/src'
> AmberTools14 has no CUDA-enabled components
> In file included from /usr/local/cuda/include/math_functions.h:7559,
> from /usr/local/cuda/include/common_functions.h:167,
> from /usr/local/cuda/include/cuda_runtime.h:76,
> from <command-line>:0:
> /opt/intel/composer_xe_2011_sp1.6.233/compiler/include/math.h:27:3: error:
> #error "This Intel <math.h> is for use with only the Intel compilers!"
> make[4]: *** [kForcesUpdate.o] Error 1
> make[4]: Leaving directory `/home/mhb75/amber14/src/pmemd/src/cuda'
> make[3]: *** [cuda/cuda.a] Error 2
> make[3]: Leaving directory `/home/mhb75/amber14/src/pmemd/src'
> make[2]: *** [cuda] Error 2
> make[2]: Leaving directory `/home/mhb75/amber14/src/pmemd'
> make[1]: *** [cuda] Error 2
> :
> I am not quite sure how to resolve this problem.

It looks like your environment is set up to use the Intel compilers but you
are trying to compile with the GNU compilers.

This error message suggests to me that you are using the GNU compilers
​(but you never said that), but your environment is set up for the Intel

Some solutions are to use the Intel compilers instead (./configure -cuda
intel) or to modify your environment to use the GNU compilers. On a cray
machine, it's often something like "module swap PrgEnv-intel PrgEnv-gnu" or
something. See the documentation for the cluster you're trying to use
where they describe how to compile your own code.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Jul 22 2014 - 13:00:03 PDT
Custom Search