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

[pramod kumbhar]

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 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>
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()
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/darshan-users/attachments/20170409/c55655c8/attachment.html>