[NLPL Task Force (A)] NLPL modules python issue

[Andrei Kutuzov]

Hi,

This story will never end :)

Even without the dependency on GCC 8.3, the new Saga modules
cuDNN/7.6.4.38-CUDA-10.1.243 and CUDA/10.1.243 conflict with
nlpl-tensorflow/1.15.0/3.7
The reason seems to be that the TF module is compiled using CUDA
10.0.130, not CUDA 10.1.243. Thus, nlpl-tensorflow/1.15.0/3.7 and
CUDA/10.1.243 cannot be loaded together.

27.01.2020 11:04, Andrei Kutuzov wrote:
> Hi Stephan,
> 
> The correct version of CuDNN is now installed on Saga, and I can load
> it, but there is another problem. It seems that all these three modules
> are dependent on GCCcore/8.2.0:
> nlpl-python-candy/201912/3.7 nlpl-scipy/201910/3.7
> nlpl-tensorflow/1.15.0/3.7
> 
> As far as I can tell, this makes them incompatible with the new CUDA
> modules, which use GCCcore/8.3.0.
> 
> Is it possible to re-compile the NLPL modules with GCC 8.3?
> 
> 23.01.2020 18:10, Andrei Kutuzov wrote:
>> Hi Stephan,
>>
>> In the end, it was too early to celebrate. Indeed, I can run python3
>> from the nlpl-tensorflow/1.15.0/3.7 module now.
>>
>> But it seems that TF in this module was compiled a different CuDNN
>> version than the one used currently on the Saga GPU nodes.
>>
>> The result is that it is impossible to run GPU jobs with this module. TF
>> first produces the following warnings:
>>
>> 2020-01-23 17:55:36.543187: E
>> tensorflow/stream_executor/cuda/cuda_dnn.cc:319] Loaded runtime CuDNN
>> library: 7.4.2 but source was compiled with: 7.6.0.  CuDNN library major
>> and minor version needs to match or have higher minor version in case of
>> CuDNN 7.0 or later version. If using a binary install, upgrade your
>> CuDNN library.  If building from sources, make sure the library loaded
>> at runtime is compatible with the version specified during compile
>> configuration.
>>
>> ...and then it fails like this:
>>
>> tensorflow.python.framework.errors_impl.UnknownError: 2 root error(s) found.
>>   (0) Unknown: Failed to get convolution algorithm. This is probably
>> because cuDNN failed to initialize, so try looking to see if a warning
>> log message was printed above.
>>
>>
>> I guess, TF should be compiled with CuDNN 7.4.2 in order to work
>> properly on Saga.
>>
>>
>> On 1/13/20 10:10 AM, Sara Stymne wrote:
>>> Hi Stephan,
>>>
>>> Yes, it seems to work fine for me as well. I can load and run nlpl-uuparser/2.3.1, which also loads many of the other modules, and python seems to work fine.
>>>
>>> Thanks for resolving this so quickly!
>>>
>>> Best,
>>> Sara
>>>
>>>
>>> 12 jan 2020 kl. 20:34 skrev Andrei Kutuzov <andreku at ifi.uio.no>
>>> :
>>>
>>>> Hi Stephan,
>>>>
>>>> Yes, I can confirm that at least for me this works. I can now run
>>>> python3 from the nlpl-tensorflow/1.15.0/3.7 module.
>>>>
>>>> Thanks for resolving this!
>>>>
>>>> 12.01.2020 4:26, Stephan Oepen wrote:
>>>>> hi again, sara, andrey, all,
>>>>>
>>>>> i believe i managed to track down this problem and was relieved to see
>>>>> it is a recently introduced issue: the NLPL binaries for these Python
>>>>> add-on modules had inadvertently had their set-group-id bit ('g+s')
>>>>> set, which i am pretty sure was the result of a major recursive
>>>>> adjustment of file permissions right before the holidays.  this bit
>>>>> (probably) should be set on directories, where it will cause the group
>>>>> owner to be inherited onto new sub-directories or files; but on
>>>>> executable files (run by anyone but me or root), it actually caused a
>>>>> loss of privileges that prevented the search for the base shared
>>>>> libraries.  note to self: this was tedious to debug, because the
>>>>> problem goes away when running in the scope of strace(1); it turns
>>>>> out, strace(1) prevents setuid(2) and setgid(2) execution ...
>>>>>
>>>>> sara and andrey, please try again.  i hope the NLPL add-on modules are
>>>>> back to normal now?
>>>>>
>>>>> all best, oe
>>>>>
>>>>> On Fri, Jan 10, 2020 at 11:52 AM Sara Stymne <sara.stymne at lingfil.uu.se> wrote:
>>>>>>
>>>>>> No, neither of us had tried it before. I think it might have worked for Ali, but I'm not sure.
>>>>>>
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Sara
>>>>>>
>>>>>>
>>>>>> ________________________________
>>>>>> Från: Stephan Oepen <oe at ifi.uio.no>
>>>>>> Skickat: den 10 januari 2020 11:50:14
>>>>>> Till: Sara Stymne
>>>>>> Kopia: Martin Matthiesen; Ali Basirat; infrastructure
>>>>>> Ämne: Re: [NLPL Task Force (A)] NLPL modules python issue
>>>>>>
>>>>>>> We tried it on both my and Artur's accounts here, and had the same issue.
>>>>>>
>>>>>>>> python: error while loading shared libraries: libpython3.7m.so.1.0: cannot open shared object file: No such file or directory
>>>>>>
>>>>>> had either of you tried before (in other words, is this a recent
>>>>>> problem)?  i installed most of these modules last november, but cannot
>>>>>> know how many people have tried using them (i believe i know for sure
>>>>>> several of them work for vinit and yves) ...
>>>>>>
>>>>>> oe
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
>>>>>>
>>>>>> E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
>>>>
>>>>
>>>> -- 
>>>> Andrei
>>>> PhD Candidate at Language Technology Group (LTG)
>>>> University of Oslo
>>>
>>
>>
> 
> 


-- 
Andrei
PhD Candidate at Language Technology Group (LTG)
University of Oslo