Hi,
On Tue, Apr 25, 2017 at 3:32 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> But of course the problem is with netcdf since it doesn't seem to get cleaned properly. Does anyone know a simple way to make this work?
The built-in NetCDF should reconfigure and rebuild if you switch to a
compiler that won't work with the current NetCDF libraries. You should
see something like:
```
Checking NetCDF...
Using bundled NetCDF library.
NetCDF must be rebuilt.
Configuring NetCDF C interface (may be time-consuming)...
```
Is this not the case?
-Dan
>
> All the best
> Ross
>
>> On Apr 25, 2017, at 1:27 PM, David Case <david.case.rutgers.edu> wrote:
>>
>> On Tue, Apr 25, 2017, Scott Brozell wrote:
>>>
>>> On 1.:
>>> Perhaps it was not clear, but i showed both the small and large
>>> test results. In other words, intel gives 4 energies for small
>>> and 2 energies for large; gnu gives 1 energy for small and
>>> 1 energy for large.
>>>
>>> There have also been multiple experiments over the whole cluster
>>> yielding the same exact energies.
>>>
>>> This certainly seems like good gpu's and some issue with intel
>>> compilers. Perhaps it is time to contact our intel colleagues
>>> if we have no explanation.
>>
>> Agreed...but it may also be time to stop trying to support intel compilers for
>> pmemd.cuda. People will try that (to no benefit) simply because it is an
>> avialable option and because they think the Intel compilers are "better".
>>
>> (There are a very small number of people who somehow have Intel compilers
>> but not gnu compilers available, and for some reason cannot install the
>> latter. On the other side of the equation, 99+% of the real-world testing
>> of pmemd.cuda is done using the gnu compilers, and Intel keeps putting in
>> new bugs in their compiler every year, so it's a big headache to support
>> this combination.)
>>
>> Have you tried putting the Intel compilers into debug mode (-O0), to see
>> what happens?
>>
>> ....dac
>>
>>>
>>> On Tue, Apr 25, 2017 at 09:09:14AM -0400, Daniel Roe wrote:
>>>>
>>>> My experience with the GPU validation test is that with Intel
>>>> compilers I usually end up with final energies flipping between two
>>>> different values. With GNU compilers and the same GPUs I only get one
>>>> energy each time. This is why I only use GNU compilers for the CUDA
>>>> stuff. If there is more variation than that (i.e. 2 values for Intel,
>>>> 1 for GNU) that indicates a "bad" GPU.
>>>>
>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Apr 25 2017 - 13:30:02 PDT
