Thanks, Jason, that worked.All the best,Kris
From: Jason Swails <jason.swails.gmail.com>
To: Kris Feher <kris.feher.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, April 6, 2016 4:42 PM
Subject: Re: [AMBER] Amber14/AmberTools15 compliation error
On Wed, Apr 6, 2016 at 10:34 AM, Kris Feher <kris.feher.yahoo.com> wrote:
> Dear All,
> I tried to install Amber14/AmberTools15 on Ubuntu 14.04 LTS and got an
> error at compliation stage:
> /usr/bin/ld: /home/kris/bin/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 value
> collect2: error: ld returned 1 exit status
> make[2]: *** [/home/kris/bin/amber14/lib/libsander.so] Error 1
> make[2]: Leaving directory `/home/kris/bin/amber14/AmberTools/src/sander'
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory `/home/kris/bin/amber14/AmberTools/src'
> make: *** [install] Error 2
>
Run the command
make distclean
Then try again. It looks like there's a leftover libnetcdf that was built
without PIC (which is what was done by default in AmberTools 14). When
upgrading to AmberTools 15, this library cannot be reused in the shared
libraries it is bundled in (libsander.so in this case).
HTH,
Jason
--
Jason M. Swails
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Received on Tue Apr 12 2016 - 01:30:04 PDT
