Re: [AMBER] AMBER 14 installation in cray machine : Problem related to parallel building

From: Himanshu Joshi <>
Date: Mon, 19 Jan 2015 15:33:42 +0530

Thanks a lot Jason,
I could install it in parallel with
nofftw3 flag. but there is an issue related to FFTW while
compiling ./configure -crayxt5 -mpi intel

It gives the following error while configuring FFTW,

Configuring fftw-3.3 for mdgx (may be time-consuming)...
    Error: FFTW configure returned 1
    FFTW configure failed!

The later lines of fftw3_config.log files are as following

checking for C compiler vendor... intel
checking for cc option to accept ISO C99... -std=gnu99
checking for cc -std=gnu99 option to accept ISO Standard C... (cached)
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by cc -std=gnu99... no
configure: error: no acceptable ld found in $PATH

Though I followed the cluster manual and loaded all
required module up to my knowledge but couldn't trace this error.

Can you make a comment.
Thanks a lot in advance.

On Sat, Jan 17, 2015 at 11:43 PM, Jason Swails <>

> On Sat, Jan 17, 2015 at 12:53 PM, Himanshu Joshi <>
> wrote:
> > Dear all,
> >
> > I am trying to set up amber14 in a newly arrived cray machine.
> > I don't know how to build the parallel version using the default
> > mpi of cray (cc/ftn),
> > i.e. how to* ./confiure -mpi intel * // if I have mpi but here no mpi
> > So I installed mpich (with intel) in my local account and installed amber
> >
> ​Do not do this on a cray machine.
> Cray machines have their own MPI optimized for their hardware built into
> their own compiler wrappers (NOT mpif90 or mpicc). Note that there is a
> "-crayxt5" flag that should tell Amber to use the cray compiler wrappers
> for the MPI build (ftn, cc, and CC). So try the following:
> ./configure -crayxt5 -mpi intel
> You should also make sure your environment is set up correctly (your cray
> cluster should have documentation that can help more than we can).
> Good luck,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

*With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense Matter
TheoryDepartment of Physics IISc.,Bangalore India 560012*
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Received on Mon Jan 19 2015 - 02:30:02 PST
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