On 11/02/2011 04:12 PM, Jason Swails wrote:
> On Wed, Nov 2, 2011 at 11:07 AM, Jan-Philip Gehrcke<jgehrcke.googlemail.com
>> wrote:
>
>> I was finally able to build AmberTools 1.5 and then Amber using the
>> built-in libnetcdf source. Then, I successfully built pmemd.cuda. This
>> is what I did:
>>
>> 1) AmberTools 1.5 setup
>> =======================
>> - extract, set AMBERHOME, bugfix
>> - ./configure intel
>> - make serial
>>
>> 2) Amber 11 SERIAL setup
>> ========================
>> - extracted to the same directory tree as AmberTools 1.5 from above
>> - bugfix
>> - AT15_Amber.py
>> - cd $AMBERHOME/src
>> - make serial
>> - cd $AMBERHOME/test; make test
>>
>> -> all relevant tests passed (cf.
>> http://archive.ambermd.org/201107/0510.html)
>>
>> 3) Amber 11 PARALLEL setup
>> ==========================
>> - cd $AMBERHOME/AmberTools/src
>> -wget
>> http://www.open-mpi.org/software/ompi/v1.5/downloads/openmpi-1.5.4.tar.gz
>> - setup of openmpi 1.5.4 using AmberTools/src/configure_openmpi
>> (modified version check from 1.5.2 to 1.5.4)
>> - export PATH=$AMBERHOME/bin:$PATH
>> - export LD_LIBRARY_PATH=$AMBERHOME/lib:$LD_LIBRARY_PATH
>> - cd $AMBERHOME/AmberTools/src
>> - ./configure -mpi intel
>> - AT15_Amber.py
>> - cd $AMBERHOME/src
>> - make clean
>> - make parallel
>> - cd $AMBERHOME/test; export DO_PARALLEL='mpirun -np 4'
>> - make test.parallel
>>
>> -> 297 tests passed / 1 failed (due to too many processes)
>>
>> 4) Amber 11 CUDA setup
>> ======================
>> - cd $AMBERHOME/AmberTools/src
>> - make clean
>> - ./configure -cuda intel
>> - AT15_Amber11.py
>> - cd $AMBERHOME/src
>> - make clean
>> - make cuda
>> - cd $AMBERHOME/test; ./test_amber_cuda.sh -1 SPDP
>>
>> 54 file comparisons passed
>> 3 file comparisons failed:
>> - possible FAILURE: check mdout.tip4pew_oct_nvt.dif
>> - possible FAILURE: check mdout.tip4pew_box_npt.dif
>> - possible FAILURE: check mdout.dhfr.ntb2.dif
>>
>> Is that fine?
>>
>
> Are they relatively small errors? As far as I know, different cards may
> give slightly different numerical results, so this shouldn't be too
> surprising.
Yes, the deviations are in the least significant digit in the output.
Thanks!
>
> HTH,
> Jason
>
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Received on Wed Nov 02 2011 - 08:30:06 PDT
