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

Thu Jan 30 19:03:18 UTC 2020

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/
>>>>>>>>>
>>>>>>>>> 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

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