On Thu, Apr 1, 2010 at 1:46 PM, Tyler Luchko <tluchko.rci.rutgers.edu> wrote:
> Did you have this issue with the previous release candidate?
>
> It looks like it is failing because it can't remove an old file. However, this is in Intel's makefile and not one of ours.
I didn't try on this machine with the last RC. This is not a machine
that I have any kind of privileges on, so anything outside of
AMBERHOME I can't touch. I just unset MKL_HOME and proceeded.
An unrelated note, my parallel tests in Linux with GCC/4.4.1 are
stalling on rism in MPI (it takes ~20-30 minutes for a test to fail
with "program error") in both nab and sander. Since it takes so long
to reproduce and it doesn't throw out any output outside of the
headers of the files, I've just proceeded without -rismmpi in the
configure call. If this issue is duplicated by somebody (or there's a
general request for it), I'll try to reproduce the errors and give
more details.
All the best,
Jason
>
> Tyler
>
> On 2010-04-01, at 12:43 PM, Jason Swails wrote:
>
>> 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
>
>
> _______________________________________________
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> 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
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Received on Thu Apr 01 2010 - 11:00:04 PDT
