(Changing the subject since we've gotten a bit off the original topic).
Strange - the problem area is this:
ld: warning: libfftw3.so.3, needed by
/home/krieg/source/amber_git/amber/lib/libsander.so, not found (try
using -rpath or -rpath-link)
/home/krieg/source/amber_git/amber/lib/libsander.so: undefined
reference to `fftw_alloc_complex'
...
etc. So it seems like libsander was somehow built linking to fftw3,
which i believe shouldn't happen. Try deleting libsander.so and
libsanderles.so from your $AMBERHOME/lib directory, the sander_api.mod
and sanderles_api.mod files from your $AMBERHOME/include directory,
and re-configure before rebuilding - see if that helps.
-Dan
On Fri, Feb 26, 2016 at 9:51 AM, Brent Krueger <kruegerb.hope.edu> wrote:
> Sure Dan -- thank you.
>
> Attached are stdout and stderr from running make install a second time
> right after the first failure. Let me know if it would be more informative
> to do a make clean and repeat from scratch.
>
>
> Thanks,
> Brent
>
>
>
> On Fri, Feb 26, 2016 at 11:24 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>>
>>
>> > On Feb 26, 2016, at 11:12 AM, Brent Krueger <kruegerb.hope.edu> wrote:
>> >
>> > As someone who is responsible for a multi-user facility that currently
>> > operates CentOS 5.6 and uses version 12.0 of the Intel compilers, I'd
>> like
>> > to second Ross's notes about working to support older (AND STABLE)
>> > systems. If I'm the only one running something this old, then I will
>> admit
>> > that the problem is mine and we will work to upgrade, but I suspect that
>> is
>> > not the case.
>>
>> There's a difference between what we support and what we can set up to
>> test through CI. As long as a CentOS 5 box has the necessary software, it
>> will work. You'll just need to not use GCC 4.1.2 anymore :).
>>
>> CI setups have to be balanced against hardware availability constraints
>> and what allocation of resources will best help limit bugs and detect
>> problems early. The right balance is likely to be something we have to try
>> multiple things to find the best solution.
>>
>>
>> >
>> >
>> > Also, it is probably relevant for me to note that somewhere between Jan
>> 14
>> > and today things have stopped building nicely for me. It appears that my
>> > libfftw is out of date, which seems strange to me since this is something
>> > that I believe configure checks. I wonder if the code requirements
>> > increased without someone updating configure accordingly? Anyway, the
>> most
>> > obvious error I am seeing is that I do not have libfftw3.so.3 This
>> > happens at the point when the build is working on cpptraj.
>> >
>> > I'm attaching my build output for anyone who wishes to wade through it.
>> >
>> >
>> > Cheers,
>> > Brent
>> >
>> >
>> >
>> >> On Fri, Feb 26, 2016 at 10:44 AM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>> >>
>> >> On Fri, Feb 26, 2016 at 8:37 AM, Ross Walker <ross.rosswalker.co.uk>
>> >> wrote:
>> >>> Recent means CentOS 7? Or also CentOS 6? - We should at least be
>> testing
>> >> on all OS versions that still under official support. I think this also
>> >> means CentOS 5 although I don't see many systems running this anymore.
>> But
>> >> 6 is very ubiquitous. A lot of people still install 6 on new machines
>> given
>> >> how much they screwed things up in 7.
>> >>>
>> >>> We should probably add Suse to that list as well.
>> >>>
>> >>> Do github offer CI hardware that includes various GPUs? (and KNC Xeon
>> >> Phi would be useful too).
>> >>
>> >> I don't think they do (although someone correct me if I'm wrong here).
>> >> I think we would have to set up our own test server for things like
>> >> that, but GitHub (and probably similar things like GitLab) have hooks
>> >> you can set up to do this automatically (see e.g.
>> >> https://developer.github.com/guides/building-a-ci-server/).
>> >>
>> >> Having our own servers might actually be the best way to go in the
>> >> long run since we should certainly cover as many of the common
>> >> environments as we possibly can, which may be a bit too much for
>> >> Travis, especially considering the size of the test cases for e.g.
>> >> sander. Speaking of that - after this release it may be worth seeing
>> >> if we can streamline the test cases somewhat...
>> >>
>> >> -Dan
>> >>
>> >>>
>> >>> All the best
>> >>> Ross
>> >>> _______________________________________________
>> >>> AMBER-Developers mailing list
>> >>> AMBER-Developers.ambermd.org
>> >>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>> >>
>> >>
>> >>
>> >> --
>> >> -------------------------
>> >> Daniel R. Roe, PhD
>> >> Department of Medicinal Chemistry
>> >> University of Utah
>> >> 30 South 2000 East, Room 307
>> >> Salt Lake City, UT 84112-5820
>> >> http://home.chpc.utah.edu/~cheatham/
>> >> (801) 587-9652
>> >> (801) 585-6208 (Fax)
>> >>
>> >> _______________________________________________
>> >> AMBER-Developers mailing list
>> >> AMBER-Developers.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber-developers
>> >
>> >
>> >
>> > --
>> > _______________________________________________
>> > Brent P. Krueger.....................phone: 616 395 7629
>> > Professor.................................fax: 616 395 7118
>> > Hope College..........................Schaap Hall 2120
>> > Department of Chemistry
>> > Holland, MI 49423
>> > <amber16_install_2016-02-26-0811.gz>
>> > _______________________________________________
>> > AMBER-Developers mailing list
>> > AMBER-Developers.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
>
>
> --
> _______________________________________________
> Brent P. Krueger.....................phone: 616 395 7629
> Professor.................................fax: 616 395 7118
> Hope College..........................Schaap Hall 2120
> Department of Chemistry
> Holland, MI 49423
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Fri Feb 26 2016 - 09:30:03 PST
