Re: [AMBER-Developers] CUDA build fails for PBSA

From: Ray Luo <rluo.uci.edu>
Date: Mon, 13 Mar 2017 14:38:03 -0700

Thanks!

Ray
--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical Physics, Biomedical Engineering, and Chemical Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Mon, Mar 13, 2017 at 12:03 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> I will test for cray.
>
> -Dan
>
> On Mon, Mar 13, 2017 at 2:46 PM, Ray Luo <rluo.uci.edu> wrote:
>> Cool! Ruxi is testing it ... I think we can at least make sure it
>> works under gfortran, clang, and intel compilers before release.  We
>> don't have access to cray machines so can't test it.
>>
>> Ray
>> --
>> Ray Luo, Ph.D.
>> Professor of Structural Biology/Biochemistry/Biophysics,
>> Chemical Physics, Biomedical Engineering, and Chemical Engineering
>> Department of Molecular Biology and Biochemistry
>> University of California, Irvine, CA 92697-3900
>>
>>
>> On Mon, Mar 13, 2017 at 6:16 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>> I just pushed a potential fix. Seems to work well for me. Let me know
>>> if anyone sees something break.
>>>
>>> -Dan
>>>
>>> On Sat, Mar 11, 2017 at 4:03 PM, Ruxi Qi <ruxiq.uci.edu> wrote:
>>>> Hi Jason,
>>>>
>>>> I'll test pmemd CUDA flags with PBSA.
>>>>
>>>> Best,
>>>>
>>>> Ruxi
>>>>
>>>>
>>>> On 3/11/17 12:49, Jason Swails wrote:
>>>>> I saw the same thing as Dan.  I needed to add -lstdc++ to the linker line
>>>>> to resolve this.
>>>>>
>>>>> It seems either your gfortran build links the C++ libraries on its own or
>>>>> it doesn't.  If it does, then everything will work.  If it doesn't, you get
>>>>> the error unless you explicitly link libstdc++.  We saw exactly the same
>>>>> problem with pmemd.cuda in the early days and spent a fair bit of effort
>>>>> iterating over the available compilers and options and such before we
>>>>> finally got something that works.  Look at line 1406 of configure2 and
>>>>> you'll see fc_cxx_link_flag being added to the CUDA library.  Note that not
>>>>> all compilers use libstdc++, though (which is why fc_cxx_link_flag exists
>>>>> and changes based on your compiler choice).
>>>>>
>>>>> I *highly* recommend specifying flags in configure rather than hardcoding
>>>>> them in the Makefile.  In fact, I would recommend just trying the pmemd
>>>>> CUDA flags and see if that works.  If not, you may need to add another
>>>>> variable for PBSA's CUDA libraries.
>>>>>
>>>>> All the best,
>>>>> Jason
>>>>>
>>>>> On Sat, Mar 11, 2017 at 3:20 PM, Ray Luo <rluo.uci.edu> wrote:
>>>>>
>>>>>>     From Ruxi ...
>>>>>>     It's strange our gnu 4.8.2 with cuda-7.5 on gpu-1-1 passed the tests,
>>>>>> even I
>>>>>>     didn't use -lstdc++.
>>>>>>     Best,
>>>>>>     Ruxi
>>>>>>
>>>>>>     On Mar 11, 2017 11:59 AM, Ray Luo <rluo.uci.edu> wrote:
>>>>>>
>>>>>>     Thanks for spotting this! Will fix it soon.
>>>>>>     Ray
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>>>>>>
>>>>>
>>>>>
>>>>
>>>>
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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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>>
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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
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
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Received on Mon Mar 13 2017 - 15:00:02 PDT
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