Hi Ross,
I just checked the diff logs that Shawn posted at his link (we are in the
process of getting Amber installed on a new cluster at TCNJ) and some of
the differences we are seeing are a bit bigger. For example below are the
observed differences large enough to be concerning? Thanks, Joe
possible FAILURE: check mdout.vrand.dif
/opt/tcnjhpc/amberdev/amber16/test/cuda/4096wat
< NSTEP = 20 TIME(PS) = 1.020 TEMP(K) = 298.31 PRESS = 0.
> NSTEP = 20 TIME(PS) = 1.020 TEMP(K) = 296.70 PRESS = 0.
212c212
< Etot = -32126.2133 EKtot = 7283.3078 EPtot =
-39409.5211
> Etot = -32067.4187 EKtot = 7244.0343 EPtot = -39311.4530
214c214
< 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6013.9630
> 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 6025.7161
215c215
< EELEC = -45423.4842 EHBOND = 0. RESTRAINT = 0.
> EELEC = -45337.1691 EHBOND = 0. RESTRAINT = 0.
------
Joseph Baker, PhD
Assistant Professor
Department of Chemistry
C101 Science Complex
The College of New Jersey
Ewing, NJ 08628
Phone: (609) 771-3173
Web: http://bakerj.pages.tcnj.edu/
On Thu, Aug 25, 2016 at 7:30 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Shawn,
>
> Assuming the differences are all similar to the cellulose example you show
> below where they differ only on a few lines and only by a very small amount
> it is innocuous and you can ignore it. I've never tested on a Quadro NVS
> 510 GPU but I'd expect it to work fine - although it is possible some tests
> may fail due to being out of memory - it depends on how much is on the card.
>
> Other than that though the minor differences can be ignored.
>
> All the best
> Ross
>
> > On Aug 24, 2016, at 14:47, Sivy, Shawn <ssivy.tcnj.edu> wrote:
> >
> > Hello,
> >
> > I’m hoping someone could help me with compiling the Amber software on our
> > systems. I have an older model Intel Xeon 5500 server with an NVIDIA
> > Quadro NVS 510 (GK107) GPU card in it. I’ve successfully compiled the
> > serial and parallel versions of Amber using gcc 4.8.5. I’m trying to
> > compile the serial CUDA version now. The “make install” builds without
> > errors, but the “make test” gets “possible failures” on 9 comparisons.
> > I’ve tried building with CUDA 7.5 and CUDA 8.0 resulting in the same
> > failures. Does anyone have a suggestion on what to try next? I’m
> assuming
> > “make test” needs to run without any errors. I suspect maybe the GPU I’m
> > using doesn’t have the precision that a Tesla or recent GTX card has.
> >
> >
> > Below is some sample output from the “make install” and the resulting log
> > and diff files. The complete contents of the log and diff files can be
> > found at https://www.tcnj.edu/~ssivy/amberlogs/
> >
> > Thanks in advance for any assistance.
> >
> > ...
> >
> > make[2]: Leaving directory `/opt/tcnjhpc/amberdev/amber16/test'
> > 130 file comparisons passed
> > 9 file comparisons failed
> > 0 tests experienced errors
> > Test log file saved as /opt/tcnjhpc/amberdev/amber16/
> > logs/test_amber_cuda/2016-08-24_11-35-41.log
> > Test diffs file saved as /opt/tcnjhpc/amberdev/amber16/
> > logs/test_amber_cuda/2016-08-24_11-35-41.diff
> > make[1]: Leaving directory `/opt/tcnjhpc/amberdev/amber16/test'
> >
> >
> > Example from log file:
> >
> > ==============================================================
> > cd cellulose/ && ./Run.cellulose_nvt DPFP /opt/tcnjhpc/amberdev/amber16/
> > include/netcdf.mod
> > diffing mdout.cellulose_nvt.GPU_DPFP with mdout.cellulose_nvt
> > possible FAILURE: check mdout.cellulose_nvt.dif
> > ==============================================================
> >
> > Example from diff file:
> >
> > possible FAILURE: check mdout.cellulose_nvt.dif
> >
> > /opt/tcnjhpc/amberdev/amber16/test/cuda/cellulose
> >
> > 212c212
> >
> > < Etot = 5.8651 EKtot = 273.2191 EPtot =
> > 276.4278
> >
> >> Etot = 5.8650 EKtot = 273.2191 EPtot =
> > 276.4278
> >
> > ### Maximum absolute error in matching lines = 1.00e-04 at line 212
> field 3
> >
> > ### Maximum relative error in matching lines = 1.71e-05 at line 212
> field 3
> >
> > ---------------------------------------
> >
> >
> > ------------------------------
> > [image: The College of New Jersey] <http://tcnj.pages.tcnj.edu/> Shawn
> Sivy
> > HPC System Administrator
> > School of Science
> > PO Box 7718 Ewing, NJ 08628-0718
> > 609-771-3475
> > ssivy.tcnj.edu <email.tcnj.edu>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Sat Aug 27 2016 - 13:30:02 PDT
