pyflow
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Published
20 hours ago •
pathak22
pathak22
/cs/software/anaconda3/compiler_compat/ld: cannot find -lm
Can you please have a look and suggest fixes?
[jalal@goku HW4]$ git clone https://github.com/pathak22/pyflow.git
Cloning into 'pyflow'...
remote: Counting objects: 96, done.
remote: Total 96 (delta 0), reused 0 (delta 0), pack-reused 96
Unpacking objects: 100% (96/96), done.
[jalal@goku HW4]$ ls
pyflow
[jalal@goku HW4]$ cd pyflow/
[jalal@goku pyflow]$ ls
LICENSE README.md demo.py examples pyflow.pyx setup.py src
[jalal@goku pyflow]$ python demo.py
Traceback (most recent call last):
File "demo.py", line 11, in <module>
import pyflow
ImportError: No module named 'pyflow'
[jalal@goku pyflow]$ python setup.py build_ext -i
Compiling pyflow.pyx because it changed.
[1/1] Cythonizing pyflow.pyx
running build_ext
building 'pyflow' extension
creating build
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/src
gcc -pthread -B /cs/software/anaconda3/compiler_compat -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/local/anaconda3/lib/python3.5/site-packages/numpy/core/include -I/usr/local/anaconda3/lib/python3.5/site-packages/numpy/core/include -I/usr/local/anaconda3/include/python3.5m -c pyflow.cpp -o build/temp.linux-x86_64-3.5/pyflow.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
In file included from /usr/local/anaconda3/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
from /usr/local/anaconda3/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /usr/local/anaconda3/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from pyflow.cpp:564:
/usr/local/anaconda3/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
gcc -pthread -B /cs/software/anaconda3/compiler_compat -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/local/anaconda3/lib/python3.5/site-packages/numpy/core/include -I/usr/local/anaconda3/lib/python3.5/site-packages/numpy/core/include -I/usr/local/anaconda3/include/python3.5m -c src/Coarse2FineFlowWrapper.cpp -o build/temp.linux-x86_64-3.5/src/Coarse2FineFlowWrapper.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
gcc -pthread -B /cs/software/anaconda3/compiler_compat -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/local/anaconda3/lib/python3.5/site-packages/numpy/core/include -I/usr/local/anaconda3/lib/python3.5/site-packages/numpy/core/include -I/usr/local/anaconda3/include/python3.5m -c src/GaussianPyramid.cpp -o build/temp.linux-x86_64-3.5/src/GaussianPyramid.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
In file included from src/Image.h:9:0,
from src/GaussianPyramid.h:7,
from src/GaussianPyramid.cpp:4:
src/ImageProcessing.h: In instantiation of ‘static void ImageProcessing::vfiltering(const T1*, T2*, int, int, int, const double*, int) [with T1 = double; T2 = double]’:
src/Image.h:1331:96: required from ‘void Image<T>::imfilter_hv(Image<T1>&, const double*, int, const double*, int) const [with T1 = double; T = double]’
src/Image.h:1199:47: required from ‘void Image<T>::GaussianSmoothing(Image<T1>&, double, int) const [with T1 = double; T = double]’
src/GaussianPyramid.cpp:67:45: required from here
src/ImageProcessing.h:344:14: warning: unused variable ‘offset’ [-Wunused-variable]
int i,j,l,k,offset,ii;
^
gcc -pthread -B /cs/software/anaconda3/compiler_compat -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/local/anaconda3/lib/python3.5/site-packages/numpy/core/include -I/usr/local/anaconda3/lib/python3.5/site-packages/numpy/core/include -I/usr/local/anaconda3/include/python3.5m -c src/OpticalFlow.cpp -o build/temp.linux-x86_64-3.5/src/OpticalFlow.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
src/OpticalFlow.cpp: In static member function ‘static void OpticalFlow::SmoothFlowSOR(const DImage&, const DImage&, DImage&, DImage&, DImage&, double, int, int, int)’:
src/OpticalFlow.cpp:267:11: warning: unused variable ‘power_alpha’ [-Wunused-variable]
double power_alpha = 0.5;
^
src/OpticalFlow.cpp:287:11: warning: unused variable ‘_a’ [-Wunused-variable]
double _a = 10000, _b = 0.1;
^
src/OpticalFlow.cpp:287:24: warning: unused variable ‘_b’ [-Wunused-variable]
double _a = 10000, _b = 0.1;
^
src/OpticalFlow.cpp: In static member function ‘static void OpticalFlow::SmoothFlowPDE(const DImage&, const DImage&, DImage&, DImage&, DImage&, double, int, int, int)’:
src/OpticalFlow.cpp:545:11: warning: unused variable ‘power_alpha’ [-Wunused-variable]
double power_alpha = 0.5;
^
src/OpticalFlow.cpp:565:11: warning: unused variable ‘_a’ [-Wunused-variable]
double _a = 10000, _b = 0.1;
^
src/OpticalFlow.cpp:565:24: warning: unused variable ‘_b’ [-Wunused-variable]
double _a = 10000, _b = 0.1;
^
In file included from src/Image.h:9:0,
from src/OpticalFlow.h:6,
from src/OpticalFlow.cpp:4:
src/ImageProcessing.h: In instantiation of ‘static void ImageProcessing::vfiltering(const T1*, T2*, int, int, int, const double*, int) [with T1 = double; T2 = double]’:
src/Image.h:1331:96: required from ‘void Image<T>::imfilter_hv(Image<T1>&, const double*, int, const double*, int) const [with T1 = double; T = double]’
src/OpticalFlow.cpp:52:42: required from here
src/ImageProcessing.h:344:14: warning: unused variable ‘offset’ [-Wunused-variable]
int i,j,l,k,offset,ii;
^
In file included from src/OpticalFlow.h:6:0,
from src/OpticalFlow.cpp:4:
src/Image.h: In instantiation of ‘void Image<T>::warpImageBicubicRef(const Image<T>&, Image<T>&, const Image<T1>&, const Image<T1>&, const Image<T1>&, const Image<T2>&, const Image<T2>&) const [with T1 = double; T2 = double; T = double]’:
src/Image.h:2482:55: required from ‘void Image<T>::warpImageBicubicRef(const Image<T>&, Image<T>&, const Image<T1>&, const Image<T1>&) const [with T1 = double; T = double]’
src/OpticalFlow.cpp:437:43: required from here
src/Image.h:2525:4: warning: variable ‘ImgMax’ set but not used [-Wunused-but-set-variable]
T ImgMax;
^
gcc -pthread -B /cs/software/anaconda3/compiler_compat -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/local/anaconda3/lib/python3.5/site-packages/numpy/core/include -I/usr/local/anaconda3/lib/python3.5/site-packages/numpy/core/include -I/usr/local/anaconda3/include/python3.5m -c src/Stochastic.cpp -o build/temp.linux-x86_64-3.5/src/Stochastic.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
g++ -pthread -shared -L/cs/software/anaconda3/lib -B /cs/software/anaconda3/compiler_compat -Wl,-rpath=/cs/software/anaconda3/lib,--no-as-needed build/temp.linux-x86_64-3.5/pyflow.o build/temp.linux-x86_64-3.5/src/Coarse2FineFlowWrapper.o build/temp.linux-x86_64-3.5/src/GaussianPyramid.o build/temp.linux-x86_64-3.5/src/OpticalFlow.o build/temp.linux-x86_64-3.5/src/Stochastic.o -L/cs/software/anaconda3/lib -lpython3.5m -o /home/grad3/jalal/CS585/HW4/pyflow/pyflow.cpython-35m-x86_64-linux-gnu.so
/cs/software/anaconda3/compiler_compat/ld: cannot find -lm
/cs/software/anaconda3/compiler_compat/ld: cannot find -lpthread
/cs/software/anaconda3/compiler_compat/ld: cannot find -lc
collect2: error: ld returned 1 exit status
error: command 'g++' failed with exit status 1
[jalal@goku pyflow]$ uname -a
Linux goku.bu.edu 3.10.0-693.5.2.el7.x86_64 #1 SMP Fri Oct 20 20:32:50 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
[jalal@goku pyflow]$ lsb_release -a
LSB Version: :core-4.1-amd64:core-4.1-noarch
Distributor ID: CentOS
Description: CentOS Linux release 7.4.1708 (Core)
Release: 7.4.1708
Codename: Core
Just in case its not anaconda path issue, can you try without anaconda once?
Why shouldn't work with Anaconda though because Anaconda is pretty much standard nowadays in the community.
/* though my system might have library problems */
It should work with anaconda.
Removing anaconda is just to check if system vs. anaconda library paths are not entangled i.e. incorrectly specified.