Re: [AMBER] Error Installing Amber20 on group's cluster

From: David A Case <>
Date: Wed, 12 May 2021 08:50:35 -0400

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
>/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:


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 - 06:00:04 PDT
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