Re: [AMBER] Compilation of Amber on Cray

From: Suman Chakrabarty <>
Date: Mon, 30 Sep 2019 23:12:13 +0530

On Mon, Sep 30, 2019 at 5:18 PM Daniel Roe <> wrote:

> I'll try to work on a patch for cpptraj today (the GitHub version
> shouldn't have this issue). In the meantime, your best bet is to
> probably disable the cpptraj build. Change the following lines (around
> line 483) in $AMBERHOME/AmberTools/src/Makefile from:
> # Rule for building cpptraj.
> build_cpptraj: $(FFTW3)
> (cd cpptraj && $(MAKE) install)
> to:
> # Rule for building cpptraj.
> build_cpptraj: $(FFTW3)
> .echo Skip cpptraj build
> # (cd cpptraj && $(MAKE) install)
> **Make sure you use a tab to indent the 'echo' line**.
> -Dan

Thanks, Dan! This would block the build step, but I had to block the
configure step of cpptraj as well, and I could comment out the relevant
lines of the configure2 script. Now the configure completed smoothly
(using ./configure -noX11 -nofftw3 -static gnu). Please note that I used
the "-nofftw3" option trying to avoid the following fftw related error
message at the build stage. But even with that option I am now getting the
following error:

[SANDER] FC qm_mm.F90

[SANDER] CC fftw3_dummy.c

[SANDER] FC /lustrefs0/sc/sc1/soft/amber18/lib/

/lustrefs0/sc/sc1/soft/amber18/lib/libfftw3.a(apiplan.o): In function

apiplan.c:(.text+0x3f0): multiple definition of `fftw_destroy_plan'

fftw3_dummy.o:fftw3_dummy.c:(.text+0xe): first defined here

collect2: error: ld returned 1 exit status

Makefile:439: recipe for target
'/lustrefs0/sc/sc1/soft/amber18/lib/' failed

Any idea what is going wrong?

Thanks and regards,
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Received on Mon Sep 30 2019 - 11:00:02 PDT
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