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

Fri Jan 31 18:00:41 UTC 2020

...and here is the updated wiki page:

http://wiki.nlpl.eu/index.php/Vectors/elmo/tutorial

On 1/30/20 8:03 PM, Andrei Kutuzov wrote:
> Yeah, it works finally :)
> 
> Thanks! Will update the wiki page today or tomorrow.
> 
> On 1/30/20 7:28 PM, Stephan Oepen wrote:
>> okay, please try again:
>>
>> module purge; module load nlpl-tensorflow/1.15.2/3.7
>>
>> oe
>>
>>
>>
>> On Tue, Jan 28, 2020 at 11:00 AM Stephan Oepen <oe at ifi.uio.no> wrote:
>>>
>>> do you have a minimum test case that i could use to validate a new
>>> (forthcoming) TF installation?  i use the script in
>>> $NLPLROOT/operation/python/test/tensorflow.py, which confirms basic
>>> CUDA functionality but apparently does not validate the parts that
>>> depend on cuDNN ... something involving convolutions, i suspect?
>>>
>>> i expect we will see cuDNN 7.6 and CUDA 10.1 decoupled during the day
>>> today, so then i should be able to produce a fresh install of TF
>>> 1.15.2.
>>>
>>> oe
>>>
>>>
>>> On Mon, Jan 27, 2020 at 4:05 PM Andrei Kutuzov <andreku at ifi.uio.no> wrote:
>>>>
>>>> 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/
>>>>>>>>>>
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>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Andrei
>>>>>>>> PhD Candidate at Language Technology Group (LTG)
>>>>>>>> University of Oslo
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Andrei
>>>> PhD Candidate at Language Technology Group (LTG)
>>>> University of Oslo
> 
> 


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