Re: [AMBER] Compilation of Amber on Cray

From: Suman Chakrabarty <>
Date: Sun, 29 Sep 2019 13:37:32 +0530

On Fri, Sep 27, 2019 at 1:11 AM David Case <> wrote:

> On Thu, Sep 26, 2019, Suman Chakrabarty wrote:
> >
> >In both cases I encounter the error associated with the configure script
> >trying to run the command "cc -V" to determine the compiler version. This
> >seems to be an unrecognised option for gcc : "gcc: error: unrecognized
> >command line option '-V'
> Try changing the "-V" to "--version" in
> AMBERHOME/AmberTools/src/configure2. But I'm guessing that there will
> be other errors. I suspect that what is called "cray" in the Amber
> configure scripts doesn't match the environment you are working with:
> what is the machine and OS that you are using?

Sorry about the delayed response. I have been trying to gather more
information. Here they are:

1. I am using a Cray XC50 system with Cray OS. It allows us to choose
different compiler suites by loading appropriate modules, e.g. PrgEnv-cray
(for Cray compiler), PrgEnv-gnu, PrgEnv-intel etc. If I use the Cray
compiler, the "cc -V" works fine:

sc1.SNB-XC50-login1:~> cc -V

Cray C : Version 8.7.1 Sun Sep 29, 2019 13:14:30

Whereas, loading the PrgEnv-gnu module leads to the error associated with
unrecognised option "-V" as reported earlier. So it seems Amber configure
script only specifically caters to Cray compilers when the "./configure
cray" option is chosen. Since the cray compiler comes with the limitation
of not being able to use fftw3 etc, and also using external netcdf (which
somehow did not work for me), I decided to go the GNU way with problems
described below.

2. I load the "PrgEnv-gnu" and use "./configure -crayxt5 gnu" (-crayxt5
option is used to set the Cray environment variables: CC=cc, CXX=CC, and
FC=ftn directly). Now the compiler version checks work fine, except for a
warning about "Hugepage" library:

Testing the cc compiler:

     cc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c

libhugetlbfs [SNB-XC50-login1:792]: WARNING: No mount point found for
default huge page size. Using first available mount point.

libhugetlbfs [SNB-XC50-login1:792]: WARNING: Hugepage size 2097152

But the fatal error comes at the cpptraj compilation stage:

Configuring CPPTRAJ...

CPPTRAJ configure failed. Check
'/lustrefs0/sc/sc1/soft/amber18/AmberTools/src/cpptraj_config.log' for

Configure failed due to the errors above!

cpptraj_config.log says:

Error: gnu compilers specified but need cray based on CXX = CC

I am lost at this point and cannot convince the Amber configure script to
use GNU compilers. The compilation should just work as long as the CC=cc,
CXX=CC, and FC=ftn environment variables are correctly set and they seem to
work fine. Where do I turn off this "special" checking for Cray systems?

Thanks and regards,
AMBER mailing list
Received on Sun Sep 29 2019 - 01:30:03 PDT
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