libhdf5.so.7: cannot open shared object file

Hdf-forum archives
1

I recently deleted my libhdf5 files from the lib/ folder and reinstalled hdf5 (a newer version). Now when I run a python application, it crashes. I checked my lib/ folder, it only contains libhdf5.so.8 file.

Traceback (most recent call last):
   File "NSfracStep.py", line 154, in <module>
     from common import *
   File "/uio/hume/student-u29/imranal/Work/Oasis/common/__init__.py", line 1, in <module>
     from io import *
   File "/uio/hume/student-u29/imranal/Work/Oasis/common/io.py", line 8, in <module>
     from dolfin import MPI, Function, XDMFFile, HDF5File, info_red, VectorFunctionSpace
   File "/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/dolfin/__init__.py", line 16, in <module>
     import cpp
   File "/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/dolfin/cpp/__init__.py", line 42, in <module>
     exec("import %s" % module_name)
   File "<string>", line 1, in <module>
   File "/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/dolfin/cpp/common.py", line 28, in <module>
     _common = swig_import_helper()
   File "/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/dolfin/cpp/common.py", line 24, in swig_import_helper
     _mod = imp.load_module('_common', fp, pathname, description)
ImportError: libhdf5.so.7: cannot open shared object file: No such file or directory

Imran

2

Try reinstalling dolfin -- it looks as if it has been linked against the older version of libhdf5.

Dave

···

On 8/05/14 12:40 pm, Imran Ali wrote:

I recently deleted my libhdf5 files from the lib/ folder and reinstalled hdf5 (a newer version). Now when I run a python application, it crashes. I checked my lib/ folder, it only contains libhdf5.so.8 file.

Traceback (most recent call last):
  File "NSfracStep.py", line 154, in <module>
    from common import *
  File "/uio/hume/student-u29/imranal/Work/Oasis/common/__init__.py", line 1, in <module>
    from io import *
  File "/uio/hume/student-u29/imranal/Work/Oasis/common/io.py", line 8, in <module>
    from dolfin import MPI, Function, XDMFFile, HDF5File, info_red, VectorFunctionSpace
  File "/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/dolfin/__init__.py", line 16, in <module>
    import cpp
  File "/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/dolfin/cpp/__init__.py", line 42, in <module>
    exec("import %s" % module_name)
  File "<string>", line 1, in <module>
  File "/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/dolfin/cpp/common.py", line 28, in <module>
    _common = swig_import_helper()
  File "/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/dolfin/cpp/common.py", line 24, in swig_import_helper
    _mod = imp.load_module('_common', fp, pathname, description)
ImportError: libhdf5.so.7: cannot open shared object file: No such file or directory

Imran

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Hdf-forum@lists.hdfgroup.org
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3

Try reinstalling dolfin -- it looks as if it has been linked against
the older version of libhdf5.

Thanks Dave :slight_smile: Will let you know if this fixed the problem.

···

On 2014-05-08 03:13, David Brooks wrote:

Dave

On 8/05/14 12:40 pm, Imran Ali wrote:

I recently deleted my libhdf5 files from the lib/ folder and reinstalled hdf5 (a newer version). Now when I run a python application, it crashes. I checked my lib/ folder, it only contains libhdf5.so.8 file.

Traceback (most recent call last):
  File "NSfracStep.py", line 154, in <module>
    from common import *
  File "/uio/hume/student-u29/imranal/Work/Oasis/common/__init__.py", line 1, in <module>
    from io import *
  File "/uio/hume/student-u29/imranal/Work/Oasis/common/io.py", line 8, in <module>
    from dolfin import MPI, Function, XDMFFile, HDF5File, info_red, VectorFunctionSpace
  File "/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/dolfin/__init__.py", line 16, in <module>
    import cpp
  File "/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/dolfin/cpp/__init__.py", line 42, in <module>
    exec("import %s" % module_name)
  File "<string>", line 1, in <module>
  File "/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/dolfin/cpp/common.py", line 28, in <module>
    _common = swig_import_helper()
  File "/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/dolfin/cpp/common.py", line 24, in swig_import_helper
    _mod = imp.load_module('_common', fp, pathname, description)
ImportError: libhdf5.so.7: cannot open shared object file: No such file or directory

Imran

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org