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

From: Jason Swails <>
Date: Mon, 19 Jan 2015 08:32:04 -0500

On Mon, Jan 19, 2015 at 5:03 AM, Himanshu Joshi <>

> 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)
> -std=gnu99
> 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.

‚ÄčThe only things that FFTW is used for are 3D-RISM and the mdgx program.
If you don't need either of those on the cray system, just use the -nofftw

If you *do* need one of those two things, you will need to experiment to
find out how to get fftw-3 to build (or how to modify the 3D-RISM or MDGX
makefiles to have it link to an existing system FFTW3 rather than trying to
build its own).

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jan 19 2015 - 06:00:04 PST
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