Re: [AMBER] upgrading to AT15 (from AT14)

From: Jason Swails <>
Date: Tue, 18 Aug 2015 13:25:55 -0400

On Tue, Aug 18, 2015 at 12:47 PM, Massimiliano Porrini <> wrote:

> Hi all,
> I am trying to upgrade AT from 14 to 15 on our servers with
> CentOS 6.6 .
> These are the commands I executed (as root) within $AMBERHOME
> (that is /usr/local/amber14):

​I strongly discourage you from installing as root. If you change
ownership of /usr/local/amber14 to your own user and build without
superuser privileges, and a mistake happens -- either one that we've made
in our configure/build/upgrade scripts or one that you've made -- there is
no way it can damage critical components of your system. For example,
consider the following command:

/bin/rm -fr $AMBERHOME/lib

which is a reasonable thing to do when uninstalling Amber. If something
happens and $AMBERHOME is undefined, this command is instead rendered as:

/bin/rm -fr /lib

And you get to spend the next couple hours (or days) reinstalling your
operating system :). While any (respectable) software developer will do
their best to avoid these types of oopses, it's happened before:

> */usr/bin/ld: /usr/local/amber14/lib/libnetcdff.a(fort-attio.o): relocation
> R_X86_64_PC32 against undefined symbol `strlen@@GLIBC_2.2.5' can not be
> used when making a shared object; recompile with -fPIC/usr/bin/ld: final
> link failed: Bad valuecollect2: ld returned 1 exit statusmake[2]: ***
> [/usr/local/amber14/lib/] Error 1make[2]: Leaving directory
> `/usr/local/amber14/AmberTools/src/sander'make[1]: *** [serial] Error
> 2make[1]: Leaving directory `/usr/local/amber14/AmberTools/src'make: ***
> [install] Error 2*
> ​Should I probably completely remove AT14 and install AT15 from ​scratch
> (as I have never had installation/compilation problems over the last 2
> years
> on the same servers)?

​That shouldn't be necessary.​ This is caused by leftover library files in
$AMBERHOME/lib that need to be deleted and recompiled. Try removing the
$AMBERHOME/lib file, reconfiguring, and recompiling.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Aug 18 2015 - 10:30:02 PDT
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