PBSA in general still doesn't build with the cray compilers, so I'll
disable pbsa for the CUDA build with cray compilers. Working on it
now.
-Dan
On Mon, Mar 13, 2017 at 5:38 PM, Ray Luo <rluo.uci.edu> wrote:
> 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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>>
>>
>> --
>> -------------------------
>> 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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--
-------------------------
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 Mon Mar 13 2017 - 15:00:03 PDT
