翻译I have a question regarding GOMP, that I figured is related to gcc.
I am using this image as a base for some experiments. It seems that I am using an alright version (4.9.2) based on this unmodified image, but I get some strange behaviour with a number of Cython related packages.
Example 1
When running this on the unmodified jupyter/all-spark-notebook docker image, when attempting to run Python I get the following issue,
import lightfm Traceback (most recent call last): File "", line 1, in File "/opt/conda/lib/python3.4/site-packages/lightfm/init.py", line 1, in from .lightfm import LightFM File "/opt/conda/lib/python3.4/site-packages/lightfm/lightfm.py", line 7, in from .lightfm_fast import (CSRMatrix, FastLightFM, ImportError: /opt/conda/lib/python3.4/site-packages/lightfm/lightfm_fast.cpython-34m.so: undefined symbol: GOMP_parallelThings I have tried:
Going to the file lightfm.py and moving all of the dependencies onto one line like so:
from .lightfm_fast import (CSRMatrix, FastLightFM, fit_logistic, predict_lightfm, fit_warp, fit_bpr, fit_warp_kos)
to
from .lightfm_fast import (CSRMatrix, FastLightFM, fit_logistic, predict_lightfm, fit_warp, fit_bpr, fit_warp_kos).Same error.
Also tried ".lightfm" to "lightfm" to change from relative import. Same error.
Checking gcc and kernel versions: gcc 4.9.2 Ubuntu 14.04 Linux 00846c176840 3.13.0-67-generic #110-Ubuntu SMP Fri Oct 23 13:24:41 UTC 2015 x86_64 GNU/LinuxBut I think if you just pull the docker image and do a pip install lightfm it should replicate the error precisely.
Example 2
When running pip install xgboost, the installation succeeds, but when in notebook I attempt to do:
--------------------------------------------------------------------------- OSError Traceback (most recent call last) <ipython-input-2-afdaff4619ce> in <module>() ----> 1 import xgboost /home/jovyan/.local/lib/python3.5/site-packages/xgboost-0.4-py3.5.egg/xgboost/__init__.py in <module>() 9 import os 10 ---> 11 from .core import DMatrix, Booster 12 from .training import train, cv 13 from . import rabit /home/jovyan/.local/lib/python3.5/site-packages/xgboost-0.4-py3.5.egg/xgboost/core.py in <module>() 81 82 # load the XGBoost library globally ---> 83 _LIB = _load_lib() 84 85 def _check_call(ret): /home/jovyan/.local/lib/python3.5/site-packages/xgboost-0.4-py3.5.egg/xgboost/core.py in _load_lib() 75 if len(lib_path) == 0: 76 return None ---> 77 lib = ctypes.cdll.LoadLibrary(lib_path[0]) 78 lib.XGBGetLastError.restype = ctypes.c_char_p 79 return lib /opt/conda/lib/python3.5/ctypes/__init__.py in LoadLibrary(self, name) 423 424 def LoadLibrary(self, name): --> 425 return self._dlltype(name) 426 427 cdll = LibraryLoader(CDLL) /opt/conda/lib/python3.5/ctypes/__init__.py in __init__(self, name, mode, handle, use_errno, use_last_error) 345 346 if handle is None: --> 347 self._handle = _dlopen(self._name, mode) 348 else: 349 self._handle = handle OSError: /opt/conda/bin/../lib/libgomp.so.1: version `GOMP_4.0' not found (required by /home/jovyan/.local/lib/python3.5/site-packages/xgboost-0.4-py3.5.egg/xgboost/libxgboost.so)I have just noticed that this is a recurring pattern and at times can be quite limiting, but I don't understand compilers that well to know if this actually a problem with the image or if that's not really an 'issue', but rather a design decision. Any ideas?
Much appreciated!
Things I have tried:
I tried
conda install -c https://conda.anaconda.org/anaconda gccin the terminal but to no avail.Also when I tried to do
install.packages('xgboost')(equivalent) in R, I got this error:Error : .onLoad failed in loadNamespace() for 'xgboost', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/usr/local/spark-1.6.0-bin-hadoop2.6/R/lib/xgboost/libs/xgboost.so': /usr/local/spark-1.6.0-bin-hadoop2.6/R/lib/xgboost/libs/xgboost.so: undefined symbol: GOMP_parallel
sudo apt-get install libgomp1 also did not help me as it was already installed.
- Upon suggestion of someone from project Jupyter I ran
conda listand found this line:libgcc 4.8.5 1 r
But no gcc I also have glib. But in terminal:
jovyan@aaaaaaa:~/work$ gcc --version gcc (Debian 4.9.2-10) 4.9.2 Copyright (C) 2014 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR UPDATE: I now think that the detected compiler is actually an earlier version, so perhaps that is the source of the problem, because upon running
%install_ext https://raw.githubusercontent.com/rasbt/watermark/master/watermark.py %load_ext watermark # show a watermark for this environment %watermark -d -m -v -p numpy,matplotlib -gI get the following response:
CPython 2.7.11 IPython 4.1.2 numpy 1.10.4 matplotlib 1.5.1 compiler : GCC 4.4.7 20120313 (Red Hat 4.4.7-1) system : Linux release : 4.4.5-15.26.amzn1.x86_64 machine : x86_64 processor : CPU cores : 4 interpreter: 64bit Git hash : Any other thoughts?