Re: [AMBER-Developers] 31 March release candidates for Amber

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 1 Apr 2010 12:43:09 -0400

Hello,

I figured I'd report this here, since it's an issue with compilation...

Linux x86_64; ifort/icc 10.1.015; MKL 10.0.2.018

Compilation error with AmberTools (fails in fftw-2)

if [ "/scratch/crn/aer/swails/newamber/04.01.10/amber11/lib/libfftw2xf_intel.a"
= '/scratch/crn/aer/swails/newamber/04.01.10/amber11/lib/libfftw2xf_intel.a'
]; then\
                cd /opt/intel/mkl/10.0.2.018/interfaces/fftw2xf && make libem64t \
                compiler=intel PRECISION=MKL_DOUBLE \
                INSTALL_DIR=/scratch/crn/aer/swails/newamber/04.01.10/amber11/lib; \
        else \
                cd ../fftw-2.1.5 && make install; \
        fi
make[2]: Entering directory `/opt/intel/mkl/10.0.2.018/interfaces/fftw2xf'
make clean ../../lib/em64t/libfftw2xf_intel.a _IA=em64t
make[3]: Entering directory `/opt/intel/mkl/10.0.2.018/interfaces/fftw2xf'
rm -f ../../lib/em64t/libfftw2xf_intel.a *.o
rm: cannot remove `../../lib/em64t/libfftw2xf_intel.a': Permission denied
make[3]: *** [clean] Error 1
make[3]: Leaving directory `/opt/intel/mkl/10.0.2.018/interfaces/fftw2xf'
make[2]: *** [libem64t] Error 2
make[2]: Leaving directory `/opt/intel/mkl/10.0.2.018/interfaces/fftw2xf'
make[1]: *** [/scratch/crn/aer/swails/newamber/04.01.10/amber11/lib/libfftw2xf_intel.a]
Error 2
make[1]: Leaving directory
`/scratch/crn/aer/swails/newamber/04.01.10/amber11/AmberTools/src/nab'
make: *** [serial] Error 2

Any ideas?

unset MKL_HOME; ./configure intel; make serial

the above appears to work.

Thanks!
Jason

On Thu, Apr 1, 2010 at 8:34 AM, case <case.biomaps.rutgers.edu> wrote:
> Latest RC is here:
>
>   http://ambermd.org/downloads/AmberTools.31mar10.tar.bz2
>   http://ambermd.org/downloads/Amber11.31mar10.tar.bz2
>
> Notes:
>
> 1. EVB tests are still broken, but I think that Dan and/or Mark are working
>   on that.
>
> 2. Does anyone use ti-decomp?  Do we have an example (preferably small)
>   that is known to work?  Do we know that Amber10 was working correctly?
>
> 3. This RC contains the cuda test cases (but not the 2_million_atom one).
>   But I haven't tested the CUDA stuff myself.
>
> 4. Please report most things to the wiki:
>      http://ambermd.org/pmwiki/pmwiki.php/Main/Amber11test
>
>   I've updated a couple of platforms for this RC.  If something becomes
>   obsolete, (e.g. gets fixed!) please remove it from the wiki, so that
>   we can keep that as clean as possible.  (I reserve the right to edit or
>   remove things that get out of date.)
>
> Thanks to everyone who worked hard on running the test cases over the last
> few days!  There was a gigantic change of directory structure, which led to
> glitches...I hope we are getting down more to "real" errors now.
>
> ....dac
>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>



-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Thu Apr 01 2010 - 10:00:02 PDT
Custom Search