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

[Wadud Miah]

Hi Pramod,


I generally use the LD_LIBRARY_PATH variable as there is no need to use LD_PRELOAD. I would also check the PYTHONPATH variable too to ensure Python knows how to load HDF5 and this is probably what is causing your issue.


Regards,

Wadud.

________________________________
From: darshan-users-bounces at lists.mcs.anl.gov <darshan-users-bounces at lists.mcs.anl.gov> on behalf of pramod kumbhar <pramod.s.kumbhar at gmail.com>
Sent: 09 April 2017 16:49:24
To: darshan-users at lists.mcs.anl.gov
Subject: Re: [Darshan-users] h5py python application error : Darshan failed to map symbol: H5get_libversion

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()


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