[Darshan-users] h5py python application error : Darshan failed to map symbol: H5get_libversion

[Shane Snyder]

Do you know how many files this application is creating?

By default, Darshan should stop tracking new file records on a specific 
process after either tracking more than 1,024 files for a given module 
or if it has exhausted all of its allocated memory. This is to keep its 
memory footprint bounded. The warning message you get from 
darshan-job-summary seems to imply this is what's going on, but if your 
application isn't opening that many files, maybe something else is wrong?

Thanks,
--Shane

On 04/09/2017 10:49 AM, pramod kumbhar wrote:
> It seems like hdf5 library is not loaded into memory and hence dlsym() 
> is failing ?
> I tried LD_PRELOAD-ing both darshan as well as hdf5 library and the 
> above example is working fine.
>
> darshan-parser --file-list show the hdf5 file and then I use 
> darshan-convert --file to get profile of specific hdf5 that I am 
> interested in.
>
> But, while profiling actual application, I have another issue. In the 
> profile of large application, darshan-parser --file-list doesn't show 
> the hdf5 created by application. What could be wrong?
>
> The application is using scipy, numpy, Image etc. Initially I thought 
> importing scipy modules somehow causing the issue but I am not able to 
> reproduce it with small isolated test.
>
> Could someone provide any hints? (note that the job_name.darshan log 
> file is generated but pdf from darshan-job-summary.pl 
> <http://darshan-job-summary.pl> says "This Darshan log contains 
> incomplete data which...").
>
> Thanks in advance!
>
> -Pramod
>
> On Sun, Apr 9, 2017 at 1:02 PM, pramod kumbhar 
> <pramod.s.kumbhar at gmail.com <mailto:pramod.s.kumbhar at gmail.com>> wrote:
>
>     Hello All,
>
>     I have used darshan for parallel c/c++ application without issue
>     but trying to analyse python(3) application first time. This
>     application uses h5py.
>
>     I compiled darshan with --enable-HDF5-pre-1.10
>     (or --enable-HDF5-post-1.10).
>
>     When I now run simple h5py test serially I get :
>
>     $ python3 test.py
>     Darshan failed to map symbol: H5get_libversion
>
>     If I don't enable hdf5 during configure then I see profiles being
>     generated.
>     What am I missing here? Do I need parallel h5py application? Any
>     hints will be helpful!
>
>     Regards,
>     Pramod
>
>     p.s. h5py test program
>
>     import h5py
>     a = [1,2,3,4,5]
>     h5f = h5py.File('data.h5', 'w')
>     h5f.create_dataset('dataset_1', data=a)
>     h5f.close()
>
>
>
>
> _______________________________________________
> Darshan-users mailing list
> Darshan-users at lists.mcs.anl.gov
> https://lists.mcs.anl.gov/mailman/listinfo/darshan-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/darshan-users/attachments/20170413/dadd62fc/attachment.html>