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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Received on Mon Mar 13 2017 - 06:30:03 PDT
