Thanks David, this solved the issue.
On Wed, May 12, 2021 at 5:51 AM David A Case <david.case.rutgers.edu> wrote:
> On Tue, May 11, 2021, Min Chiang Gary Ong wrote:
> >
> >I am trying to install Amber2020 on my group's cluster which is running on
> >Ubuntu 18.04.
> >
> >[ 36%] Linking Fortran shared library libsander.so
> >/usr/bin/ld: /usr/local/lib/libfftw3.a(assert.o): relocation R_X86_64_PC32
> >against symbol `stdout..GLIBC_2.2.5' can not be used when making a shared
> >object; recompile with -fPIC
>
> Please edit your run_cmake script, and add the following flag:
>
> -DFORCE_INTERNAL_LIBS="fftw"
>
> Then re-run "run_cmake" and "make install".
>
> Longish explanation: Amber is looking in /usr/local/lib to try to get
> libfftw3, but doesn't realize (at the cmake step) that shared libraries,
> with position-indendepent code (PIC) are not avaialble.
>
> There is a long-standing struggle amongst Amber developers. One side wants
> to try hard to include third-party libraries that might already be on a
> user's computer, and add checks as needed to weed out libraries that have
> the right name but content that we can't use.
>
> The other side side argues that we will never know all the possible things
> that might be in /usr/local/lib, and that we are better off just compiling
> libfftw from source, so the know the right options will get chosen.
>
> There are some good arguments on both sides of this issue.
>
> ...good luck...dac
>
>
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Received on Wed May 12 2021 - 08:30:02 PDT
