RUNPATH seemingly ignored by Python 3 on RHEL 7.4
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
add a comment |
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
add a comment |
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
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
linux python redhat-enterprise-linux pip
asked 2 days ago
Michael Greenburg
112
112
add a comment |
add a comment |
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