Hi Brent,
Sorry for my jumping to the conclusion. I just realized it's impossible
to fully remove <cuda_runtime.h>. As we used other libraries cublas and
cusparse which also include that header file. I am afraid this option
doesn't work, and we have to go back tweaking the configure to fix this
issue.
Right now If you want, you can comment out the #error line in you
cuda/include/host_config.h to see whether it gets fixed. Thanks!
Best,
Ruxi
On 04/07/2017 05:32 AM, Brent Krueger wrote:
> Thank you Ruxi for identifying the source of this issue.
>
> I've commented out the cuda_rutime.h line from the file cuda_cg_wrapper.cu
> in AmberTools/src/pbsa, did a make clean, reran configure -cuda intel and
> that build also seemed to fail in the same spot. I've done a make
> uninstall and am now building again.
>
> I'm afraid I've got to run to a meeting now and I've got meetings/class
> pretty much all day so I'm not sure when I'll be able to get to testing,
> but I should at least be able to verify whether this build worked for me or
> not in a couple hours...
>
>
> Cheers,
> Brent
>
>
> On Fri, Apr 7, 2017 at 2:42 AM, Ruxi Qi <ruxiq.uci.edu> wrote:
>
>> Just found a similar story with GCC in pmemd.cuda of Amber12. See
>> http://archive.ambermd.org/201307/0456.html
>>
>> Best,
>>
>> Ruxi
>>
>> On 04/06/2017 11:38 PM, Ruxi Qi wrote:
>>> Hi All,
>>>
>>> I found the real cause. It is the <cuda_runtime.h> included in our
>>> cuda wrapper code (not cusp) that triggered the ICC version checking
>>> in host_config.h. In contrast, pmemd.cuda doesn't use this header,
>>> thus won't trigger the runtime compiler checking. A quick "fix" is
>>> just removing the <cuda_runtime.h> inclusion in our code as long as we
>>> use nvcc to compile.
>>>
>>> Two concerns:
>>>
>>> 1) As shown by those OS/Compiler/CUDA compatibility matrices from
>>> Nvidia, allowing the use of the compiler not officially supported
>>> (tested) by CUDA is of risk. I don't know to what extent this effect
>>> will be, maybe not a big deal?
>>>
>>> 2) For now, we can fix this compiler error either through a) Add a
>>> logic checking on the icc version to configure as suggested
>>> previously, or b) I remove the <cuda_rutime.h> inclusion in our code -
>>> this will need another round combination tests. Also just mention
>>> again, user manually commenting out the #error line in host_config.h
>>> will also be a workaround (not recommended?).
>>>
>>> Thanks!
>>>
>>> Ruxi
>>>
>>>
>>>
>>> On 04/06/2017 07:55 PM, Daniel Roe wrote:
>>>> Hi,
>>>>
>>>> On Thu, Apr 6, 2017 at 6:59 PM, Ruxi Qi <ruxiq.uci.edu> wrote:
>>>>> 1. I once encountered the same error. Indeed, this error is not because
>>>>> of linking CUSP library. It's nvcc that complains the outdated ICC
>>>>> version. Per the Nvidia official documents, CUDA 7.5 only supports ICC
>>>>> 15.0.0, as shown bellow:
>>>> This is not really the case, at least for Intel compilers version 14.
>>>> I was just able to compile pmemd.cuda from Amber 16 and
>>>> cpptraj/pmemd.cuda from amber17-with-patches with Intel V 14 compilers
>>>> and CUDA 7.5. I think this issue is really CUSP-related since as Brent
>>>> stated he was previously able to compile pmemd.cuda from Amber 16 with
>>>> Intel V12 compilers and CUDA 7.5.
>>>>
>>>>> 3. Adding a --no-pbsa.cuda option is good for safety's sake in this
>>>>> release. I agree with Hai that we may put it built as default, since it
>>>>> generally follows the Nvidia CUDA installation rule.
>>>> Probably the best solution would be to add logic to 'configure' that
>>>> will disable pbsa.cuda if the Intel compiler version is not high
>>>> enough. May need to do the same thing for GNU compilers if there is a
>>>> similar issue.
>>>>
>>>> -Dan
>>>>
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
>
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Fri Apr 07 2017 - 11:00:02 PDT
