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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>>
>> --
>> -------------------------
>> 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
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Received on Mon Mar 13 2017 - 12:30:02 PDT
