RUNPATH seemingly ignored by Python 3 on RHEL 7.4












0














I built TensorFlow 1.12 from source using Bazel 15.0, Python 3.6.5, and GCC 7.3.0. It seems to work properly, but that when I import pandas before importing tensorflow it uses /lib64/libstdc++.so.6, rather than the one associated with GCC 7.3.0:



$ python3 -c "import tensorflow, pandas" # no error
$ python3 -c "import pandas, tensorflow"
Traceback (most recent call last):
File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
from tensorflow.python.pywrap_tensorflow_internal import *
File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
_pywrap_tensorflow_internal = swig_import_helper()
File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
_mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
File "/apps/python/3.6.5/gcc-7.3.0/lib/python3.6/imp.py", line 243, in load_module
return load_dynamic(name, filename, file)
File "/apps/python/3.6.5/gcc-7.3.0/lib/python3.6/imp.py", line 343, in load_dynamic
return _load(spec)
ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/__init__.py", line 24, in <module>
from tensorflow.python import pywrap_tensorflow # pylint: disable=unused-import
File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 49, in <module>
from tensorflow.python import pywrap_tensorflow
File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 74, in <module>
raise ImportError(msg)
ImportError: Traceback (most recent call last):
File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
from tensorflow.python.pywrap_tensorflow_internal import *
File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
_pywrap_tensorflow_internal = swig_import_helper()
File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
_mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
File "/apps/python/3.6.5/gcc-7.3.0/lib/python3.6/imp.py", line 243, in load_module
return load_dynamic(name, filename, file)
File "/apps/python/3.6.5/gcc-7.3.0/lib/python3.6/imp.py", line 343, in load_dynamic
return _load(spec)
ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so)


Failed to load the native TensorFlow runtime.

See https://www.tensorflow.org/install/errors

for some common reasons and solutions. Include the entire stack trace
above this error message when asking for help.


I made sure when building to use -Wl,--enable-new-dtags,-rpath,/apps/gcc/7.3.0/lib64, and have confirmed that the RUNPATH is actually set:



$ readelf -d /apps/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so | grep RUNPATH
0x000000000000001d (RUNPATH) Library runpath: [$ORIGIN/../../_solib_k8/_U_S_Stensorflow_Spython_C_Upywrap_Utensorflow_Uinternal.so___Utensorflow:$ORIGIN/../../_solib_k8/_U@mkl_Ulinux_S_S_Cmkl_Ulibs_Ulinux___Uexternal_Smkl_Ulinux_Slib:$ORIGIN/:$ORIGIN/..:/apps/gcc/7.3.0/lib64]
$ ldd /apps/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so | grep libstdc++
libstdc++.so.6 => /apps/gcc/7.3.0/lib64/libstdc++.so.6 (0x00007f82c9711000)


It seems odd that despite the fact that ldd finds the right libstdc++.so.6 (so probably not a duplicate of this issue), the wrong one is used under this circumstance. LD_LIBRARY_PATH and LD_PRELOAD aren't set, and the ld.so man page shows that RUNPATH should thus have precedence. It could be that I'm misunderstanding what should be happening--it's my impression that, absent LD_LIBRARY_PATH and LD_PRELOAD, an ELF's RUNPATH is the supreme authority on where libraries should be searched, and that whatever ldd sees should be exactly what is used at runtime. Am I misunderstanding? Is there a real way (i.e. NOT just sloppily using LD_LIBRARY_PATH) to fix this?



There's a little more background at this GitHub issue, although I don't know how much of it will be helpful.










share|improve this question



























    0














    I built TensorFlow 1.12 from source using Bazel 15.0, Python 3.6.5, and GCC 7.3.0. It seems to work properly, but that when I import pandas before importing tensorflow it uses /lib64/libstdc++.so.6, rather than the one associated with GCC 7.3.0:



    $ python3 -c "import tensorflow, pandas" # no error
    $ python3 -c "import pandas, tensorflow"
    Traceback (most recent call last):
    File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
    from tensorflow.python.pywrap_tensorflow_internal import *
    File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
    _pywrap_tensorflow_internal = swig_import_helper()
    File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
    _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
    File "/apps/python/3.6.5/gcc-7.3.0/lib/python3.6/imp.py", line 243, in load_module
    return load_dynamic(name, filename, file)
    File "/apps/python/3.6.5/gcc-7.3.0/lib/python3.6/imp.py", line 343, in load_dynamic
    return _load(spec)
    ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so)

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/__init__.py", line 24, in <module>
    from tensorflow.python import pywrap_tensorflow # pylint: disable=unused-import
    File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 49, in <module>
    from tensorflow.python import pywrap_tensorflow
    File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 74, in <module>
    raise ImportError(msg)
    ImportError: Traceback (most recent call last):
    File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
    from tensorflow.python.pywrap_tensorflow_internal import *
    File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
    _pywrap_tensorflow_internal = swig_import_helper()
    File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
    _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
    File "/apps/python/3.6.5/gcc-7.3.0/lib/python3.6/imp.py", line 243, in load_module
    return load_dynamic(name, filename, file)
    File "/apps/python/3.6.5/gcc-7.3.0/lib/python3.6/imp.py", line 343, in load_dynamic
    return _load(spec)
    ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so)


    Failed to load the native TensorFlow runtime.

    See https://www.tensorflow.org/install/errors

    for some common reasons and solutions. Include the entire stack trace
    above this error message when asking for help.


    I made sure when building to use -Wl,--enable-new-dtags,-rpath,/apps/gcc/7.3.0/lib64, and have confirmed that the RUNPATH is actually set:



    $ readelf -d /apps/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so | grep RUNPATH
    0x000000000000001d (RUNPATH) Library runpath: [$ORIGIN/../../_solib_k8/_U_S_Stensorflow_Spython_C_Upywrap_Utensorflow_Uinternal.so___Utensorflow:$ORIGIN/../../_solib_k8/_U@mkl_Ulinux_S_S_Cmkl_Ulibs_Ulinux___Uexternal_Smkl_Ulinux_Slib:$ORIGIN/:$ORIGIN/..:/apps/gcc/7.3.0/lib64]
    $ ldd /apps/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so | grep libstdc++
    libstdc++.so.6 => /apps/gcc/7.3.0/lib64/libstdc++.so.6 (0x00007f82c9711000)


    It seems odd that despite the fact that ldd finds the right libstdc++.so.6 (so probably not a duplicate of this issue), the wrong one is used under this circumstance. LD_LIBRARY_PATH and LD_PRELOAD aren't set, and the ld.so man page shows that RUNPATH should thus have precedence. It could be that I'm misunderstanding what should be happening--it's my impression that, absent LD_LIBRARY_PATH and LD_PRELOAD, an ELF's RUNPATH is the supreme authority on where libraries should be searched, and that whatever ldd sees should be exactly what is used at runtime. Am I misunderstanding? Is there a real way (i.e. NOT just sloppily using LD_LIBRARY_PATH) to fix this?



    There's a little more background at this GitHub issue, although I don't know how much of it will be helpful.










    share|improve this question

























      0












      0








      0







      I built TensorFlow 1.12 from source using Bazel 15.0, Python 3.6.5, and GCC 7.3.0. It seems to work properly, but that when I import pandas before importing tensorflow it uses /lib64/libstdc++.so.6, rather than the one associated with GCC 7.3.0:



      $ python3 -c "import tensorflow, pandas" # no error
      $ python3 -c "import pandas, tensorflow"
      Traceback (most recent call last):
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
      from tensorflow.python.pywrap_tensorflow_internal import *
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
      _pywrap_tensorflow_internal = swig_import_helper()
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
      _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
      File "/apps/python/3.6.5/gcc-7.3.0/lib/python3.6/imp.py", line 243, in load_module
      return load_dynamic(name, filename, file)
      File "/apps/python/3.6.5/gcc-7.3.0/lib/python3.6/imp.py", line 343, in load_dynamic
      return _load(spec)
      ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so)

      During handling of the above exception, another exception occurred:

      Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/__init__.py", line 24, in <module>
      from tensorflow.python import pywrap_tensorflow # pylint: disable=unused-import
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 49, in <module>
      from tensorflow.python import pywrap_tensorflow
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 74, in <module>
      raise ImportError(msg)
      ImportError: Traceback (most recent call last):
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
      from tensorflow.python.pywrap_tensorflow_internal import *
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
      _pywrap_tensorflow_internal = swig_import_helper()
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
      _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
      File "/apps/python/3.6.5/gcc-7.3.0/lib/python3.6/imp.py", line 243, in load_module
      return load_dynamic(name, filename, file)
      File "/apps/python/3.6.5/gcc-7.3.0/lib/python3.6/imp.py", line 343, in load_dynamic
      return _load(spec)
      ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so)


      Failed to load the native TensorFlow runtime.

      See https://www.tensorflow.org/install/errors

      for some common reasons and solutions. Include the entire stack trace
      above this error message when asking for help.


      I made sure when building to use -Wl,--enable-new-dtags,-rpath,/apps/gcc/7.3.0/lib64, and have confirmed that the RUNPATH is actually set:



      $ readelf -d /apps/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so | grep RUNPATH
      0x000000000000001d (RUNPATH) Library runpath: [$ORIGIN/../../_solib_k8/_U_S_Stensorflow_Spython_C_Upywrap_Utensorflow_Uinternal.so___Utensorflow:$ORIGIN/../../_solib_k8/_U@mkl_Ulinux_S_S_Cmkl_Ulibs_Ulinux___Uexternal_Smkl_Ulinux_Slib:$ORIGIN/:$ORIGIN/..:/apps/gcc/7.3.0/lib64]
      $ ldd /apps/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so | grep libstdc++
      libstdc++.so.6 => /apps/gcc/7.3.0/lib64/libstdc++.so.6 (0x00007f82c9711000)


      It seems odd that despite the fact that ldd finds the right libstdc++.so.6 (so probably not a duplicate of this issue), the wrong one is used under this circumstance. LD_LIBRARY_PATH and LD_PRELOAD aren't set, and the ld.so man page shows that RUNPATH should thus have precedence. It could be that I'm misunderstanding what should be happening--it's my impression that, absent LD_LIBRARY_PATH and LD_PRELOAD, an ELF's RUNPATH is the supreme authority on where libraries should be searched, and that whatever ldd sees should be exactly what is used at runtime. Am I misunderstanding? Is there a real way (i.e. NOT just sloppily using LD_LIBRARY_PATH) to fix this?



      There's a little more background at this GitHub issue, although I don't know how much of it will be helpful.










      share|improve this question













      I built TensorFlow 1.12 from source using Bazel 15.0, Python 3.6.5, and GCC 7.3.0. It seems to work properly, but that when I import pandas before importing tensorflow it uses /lib64/libstdc++.so.6, rather than the one associated with GCC 7.3.0:



      $ python3 -c "import tensorflow, pandas" # no error
      $ python3 -c "import pandas, tensorflow"
      Traceback (most recent call last):
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
      from tensorflow.python.pywrap_tensorflow_internal import *
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
      _pywrap_tensorflow_internal = swig_import_helper()
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
      _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
      File "/apps/python/3.6.5/gcc-7.3.0/lib/python3.6/imp.py", line 243, in load_module
      return load_dynamic(name, filename, file)
      File "/apps/python/3.6.5/gcc-7.3.0/lib/python3.6/imp.py", line 343, in load_dynamic
      return _load(spec)
      ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so)

      During handling of the above exception, another exception occurred:

      Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/__init__.py", line 24, in <module>
      from tensorflow.python import pywrap_tensorflow # pylint: disable=unused-import
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 49, in <module>
      from tensorflow.python import pywrap_tensorflow
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 74, in <module>
      raise ImportError(msg)
      ImportError: Traceback (most recent call last):
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
      from tensorflow.python.pywrap_tensorflow_internal import *
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
      _pywrap_tensorflow_internal = swig_import_helper()
      File "/zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
      _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
      File "/apps/python/3.6.5/gcc-7.3.0/lib/python3.6/imp.py", line 243, in load_module
      return load_dynamic(name, filename, file)
      File "/apps/python/3.6.5/gcc-7.3.0/lib/python3.6/imp.py", line 343, in load_dynamic
      return _load(spec)
      ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /zapps7/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so)


      Failed to load the native TensorFlow runtime.

      See https://www.tensorflow.org/install/errors

      for some common reasons and solutions. Include the entire stack trace
      above this error message when asking for help.


      I made sure when building to use -Wl,--enable-new-dtags,-rpath,/apps/gcc/7.3.0/lib64, and have confirmed that the RUNPATH is actually set:



      $ readelf -d /apps/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so | grep RUNPATH
      0x000000000000001d (RUNPATH) Library runpath: [$ORIGIN/../../_solib_k8/_U_S_Stensorflow_Spython_C_Upywrap_Utensorflow_Uinternal.so___Utensorflow:$ORIGIN/../../_solib_k8/_U@mkl_Ulinux_S_S_Cmkl_Ulibs_Ulinux___Uexternal_Smkl_Ulinux_Slib:$ORIGIN/:$ORIGIN/..:/apps/gcc/7.3.0/lib64]
      $ ldd /apps/python-3.6.5-tensorflow/1.12.0/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so | grep libstdc++
      libstdc++.so.6 => /apps/gcc/7.3.0/lib64/libstdc++.so.6 (0x00007f82c9711000)


      It seems odd that despite the fact that ldd finds the right libstdc++.so.6 (so probably not a duplicate of this issue), the wrong one is used under this circumstance. LD_LIBRARY_PATH and LD_PRELOAD aren't set, and the ld.so man page shows that RUNPATH should thus have precedence. It could be that I'm misunderstanding what should be happening--it's my impression that, absent LD_LIBRARY_PATH and LD_PRELOAD, an ELF's RUNPATH is the supreme authority on where libraries should be searched, and that whatever ldd sees should be exactly what is used at runtime. Am I misunderstanding? Is there a real way (i.e. NOT just sloppily using LD_LIBRARY_PATH) to fix this?



      There's a little more background at this GitHub issue, although I don't know how much of it will be helpful.







      linux python redhat-enterprise-linux pip






      share|improve this question













      share|improve this question











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      share|improve this question










      asked 2 days ago









      Michael Greenburg

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