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.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Nov 02 2011 - 08:30:05 PDT
