OSError when `import openmc.lib` or `import openmc.deplete`

[jimin ma]

I have installed openMC on Ubuntu16lts-x86_64 system by cmake after I installed mpich, libmpich-dev, openmpi, libopenmpi-dev, libhdf5-dev and hdf5. The python API has been installed by `python3 steup.py install`. Everything seems fine when I tested examples.

However, when I tested `import openmc.lib` or `import openmc.deplete`, error happened as following:

import openmc.lib

 

 >>>

  ---------------------------------------------------------------------------

  OSError                                   Traceback (most recent call last)

   in ()

  9 print(os.environ.get('READTHEDOCS', None))

     10 

  ---> 11 import openmc.lib

   12 

~/anaconda3/lib/python3.6/site-packages/openmc-0.12.0.dev0-py3.6-linux-x86_64.egg/openmc/lib/__init__.py in ()

     30     _filename = pkg_resources.resource_filename(

     31         __name__, 'libopenmc.{}'.format(_suffix))

---> 32     _dll = CDLL(_filename)

     33 else:

     34     # For documentation builds, we don't actually have the shared library

~/anaconda3/lib/python3.6/ctypes/__init__.py in __init__(self, name, mode, handle, use_errno, use_last_error)

    346 

    347         if handle is None:

--> 348             self._handle = _dlopen(self._name, mode)

    349         else:

    350             self._handle = handle

  OSError: /home/ma/anaconda3/lib/python3.6/site-packages/openmc-0.12.0.dev0-py3.6-linux-x86_64.egg/openmc/lib/libopenmc.so: undefined symbol: H5Tget_native_type

  

I checked the libopenmc.so in terminal which showed:

  $ ldd -r /usr/local/lib/libopenmc.so

linux-vdso.so.1 =>  (0x00007fffd9da5000)

libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f1b8d04a000)

libmpi.so.12 => /home/ma/RMC/lib/libmpi.so.12 (0x00007f1b8cbc0000)

libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f1b8c83e000)

libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f1b8c535000)

libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f1b8c313000)

libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f1b8c0fd000)

libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f1b8bee0000)

libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f1b8bb17000)

/lib64/ld-linux-x86-64.so.2 (0x00007f1b8d9b1000)

librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f1b8b90f000)

undefined symbol: H5Tget_native_type (/usr/local/lib/libopenmc.so)

undefined symbol: H5Tget_tag (/usr/local/lib/libopenmc.so)

undefined symbol: H5Tset_tag (/usr/local/lib/libopenmc.so)

undefined symbol: H5Tget_cset (/usr/local/lib/libopenmc.so)

undefined symbol: H5Tget_member_value (/usr/local/lib/libopenmc.so)

undefined symbol: H5Tset_cset (/usr/local/lib/libopenmc.so)

undefined symbol: H5Tenum_insert (/usr/local/lib/libopenmc.so)

undefined symbol: H5Tenum_create (/usr/local/lib/libopenmc.so)

I searched the Internet. Someone advised to install the HDF5. However, after I downloaded hdf5-1.10.5.tar.gz and manually installed it, the error still exist.

Thanks!

[Andrew Johnson]

Ma,

Interesting. Can you provide more information on your build steps? How did you install the dependencies, specifically HDF5? It looks like OpenMC isn't linked against your HDF5 library. What command did you use to build OpenMC?

Thanks,

Andrew

[ma]

Andrew,

    Thanks for your attention. The problem has been solved. There were several 'libhdf5.so' on the location of PATH in my system. When I installed OpenMC by source, it caused chaos. After I specified only one right `libhdf5.so` file, the compilation was right.

  Thanks!

Ma

在 2020年1月5日星期日 UTC+8上午1:20:06，Andrew Johnson写道：