我会尽量做到非常具体和翔实。为了地理空间/地理科学社区的利益,我想创建一个包含地球科学中使用的所有包的 Dockerfile。Dockerfile 建立在scipy-notebook docker- stack 之上。
问题:
我正在尝试构建 HPGL(地统计学的 Python 包)。
对于依赖项:我使用下载的 .deb 包构建了一些包apt-get
,对于那些我无法安装的包。apt
下面的 Dockerfile 显示了构建所有 HPGL 依赖项的步骤:
FROM jupyter/scipy-notebook
###
### HPGL - High Performance Geostatistics Library
###
USER root
RUN apt-get update && \
apt-get install -y \
gcc \
g++ \
libboost-all-dev
RUN apt-get update && \
apt-get install -y \
liblapack-dev \
libblas-dev \
liblapacke-dev
RUN apt-get update && \
apt-get install -y \
scons
RUN wget http://ftp.us.debian.org/debian/pool/main/libf/libf2c2/libf2c2_20090411-2_amd64.deb && \
dpkg -i libf2c2_20090411-2_amd64.deb
RUN wget http://ftp.us.debian.org/debian/pool/main/libf/libf2c2/libf2c2-dev_20090411-2_amd64.deb && \
dpkg -i libf2c2-dev_20090411-2_amd64.deb
RUN wget http://mirrors.kernel.org/ubuntu/pool/universe/c/clapack/libcblas3_3.2.1+dfsg-1_amd64.deb && \
dpkg -i libcblas3_3.2.1+dfsg-1_amd64.deb
RUN wget http://mirrors.kernel.org/ubuntu/pool/universe/c/clapack/libcblas-dev_3.2.1+dfsg-1_amd64.deb && \
dpkg -i libcblas-dev_3.2.1+dfsg-1_amd64.deb
RUN wget http://ftp.us.debian.org/debian/pool/main/c/clapack/libclapack3_3.2.1+dfsg-1_amd64.deb && \
dpkg -i libclapack3_3.2.1+dfsg-1_amd64.deb
RUN wget http://ftp.us.debian.org/debian/pool/main/c/clapack/libclapack-dev_3.2.1+dfsg-1_amd64.deb && \
dpkg -i libclapack-dev_3.2.1+dfsg-1_amd64.deb
RUN wget https://mirror.kku.ac.th/ubuntu/ubuntu/pool/main/l/lapack/libtmglib3_3.7.1-1_amd64.deb && \
dpkg -i libtmglib3_3.7.1-1_amd64.deb
RUN wget http://ftp.us.debian.org/debian/pool/main/l/lapack/libtmglib-dev_3.7.1-1_amd64.deb && \
dpkg -i libtmglib-dev_3.7.1-1_amd64.deb
RUN git clone https://github.com/hpgl/hpgl.git
RUN cd hpgl/src/ && \
bash -c "source activate python2 && scons -j 2"
RUN cd hpgl/src/ && \
bash -c "source activate python2 && python2 setup.py install"
RUN rm -rf hpgl \
scons-2.5.0* \
libf2c2_20090411-2_amd64.deb \
libf2c2-dev_20090411-2_amd64.deb \
libtmglib3_3.7.1-1_amd64.deb \
libtmglib-dev_3.7.1-1_amd64.deb \
libcblas3_3.2.1+dfsg-1_amd64.deb \
libcblas-dev_3.2.1+dfsg-1_amd64.deb \
libclapack3_3.2.1+dfsg-1_amd64.deb \
libclapack-dev_3.2.1+dfsg-1_amd64.deb
USER $NB_USER
这运行顺利,我可以运行 Docker 容器并启动笔记本,但是当我在 Python 中导入 HPGL 时,我收到这个错误,我不知道发生了什么或如何解决这个问题:
---------------------------------------------------------------------------
OSError Traceback (most recent call last)
<ipython-input-1-604a7d0744ab> in <module>()
----> 1 import geo_bsd
/opt/conda/envs/python2/lib/python2.7/site-packages/HPGL_BSD-0.9.9-py2.7.egg/geo_bsd/__init__.py in <module>()
2
3
----> 4 from geo import *
5 from sgs import sgs_simulation
6 from sis import sis_simulation
/opt/conda/envs/python2/lib/python2.7/site-packages/HPGL_BSD-0.9.9-py2.7.egg/geo_bsd/geo.py in <module>()
3 import ctypes as C
4
----> 5 from hpgl_wrap import _HPGL_SHAPE, _HPGL_CONT_MASKED_ARRAY, _HPGL_IND_MASKED_ARRAY, _HPGL_UBYTE_ARRAY, _HPGL_FLOAT_ARRAY, _HPGL_OK_PARAMS, _HPGL_SK_PARAMS, _HPGL_IK_PARAMS, _HPGL_MEDIAN_IK_PARAMS, __hpgl_cov_params_t, __hpgl_cockriging_m1_params_t, __hpgl_cockriging_m2_params_t, _hpgl_so
6 from hpgl_wrap import hpgl_output_handler, hpgl_progress_handler
7
/opt/conda/envs/python2/lib/python2.7/site-packages/HPGL_BSD-0.9.9-py2.7.egg/geo_bsd/hpgl_wrap.py in <module>()
144 _hpgl_so = NC.load_library('hpgl_d', __file__)
145 else:
--> 146 _hpgl_so = NC.load_library('hpgl', __file__)
147
148 _hpgl_so.hpgl_set_output_handler.restype = None
/opt/conda/envs/python2/lib/python2.7/site-packages/numpy/ctypeslib.pyc in load_library(libname, loader_path)
148 if os.path.exists(libpath):
149 try:
--> 150 return ctypes.cdll[libpath]
151 except OSError:
152 ## defective lib file
/opt/conda/envs/python2/lib/python2.7/ctypes/__init__.pyc in __getitem__(self, name)
435
436 def __getitem__(self, name):
--> 437 return getattr(self, name)
438
439 def LoadLibrary(self, name):
/opt/conda/envs/python2/lib/python2.7/ctypes/__init__.pyc in __getattr__(self, name)
430 if name[0] == '_':
431 raise AttributeError(name)
--> 432 dll = self._dlltype(name)
433 setattr(self, name, dll)
434 return dll
/opt/conda/envs/python2/lib/python2.7/ctypes/__init__.pyc in __init__(self, name, mode, handle, use_errno, use_last_error)
360
361 if handle is None:
--> 362 self._handle = _dlopen(self._name, mode)
363 else:
364 self._handle = handle
OSError: /usr/lib/libf2c.so.2: undefined symbol: MAIN__
编辑1:
所以显然@Jean-François Fabre Here 指出了这个非常相似的问题!. 在那里,问题与文件有关,libf2c.so
并按如下方式解决:
rm /usr/lib/libf2c.so && ln -s /usr/lib/libf2c.a /usr/lib/libf2c.so
@p929 在同一线程中解释了此解决方案:
它所做的实际上是删除动态库并为静态库创建别名。
现在,我知道我有同样的问题,但文件不同(/usr/lib/libf2c.so.2
)。解决方案是“删除动态库并创建静态库的别名”。我用相同的静态库尝试过,/usr/lib/libf2c.a
但没有成功。