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installation for scikit-learn-0.15.2 failing #3728

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cosmos2006 opened this issue Oct 1, 2014 · 9 comments
Closed

installation for scikit-learn-0.15.2 failing #3728

cosmos2006 opened this issue Oct 1, 2014 · 9 comments
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Bug Build / CI
Milestone
0.16

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@cosmos2006
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while installation, I get the following error during

python setup.py build

Error is:

/usr/bin/gfortran -Wall -g -L/usr/local/lib -L/sw/lib build/temp.linux-x86_64-2.7/sklearn/cluster/_k_means.o -L/usr/lib64 -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.7 -lcblas -lm -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/sklearn/cluster/_k_means.so
/usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: error: ld returned 1 exit status
/usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: error: ld returned 1 exit status
error: Command "/usr/bin/gfortran -Wall -g -L/usr/local/lib -L/sw/lib build/temp.linux-x86_64-2.7/sklearn/cluster/_k_means.o -L/usr/lib64 -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.7 -lcblas -lm -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/sklearn/cluster/_k_means.so" failed with exit status 1

May I know what is the problem and how to sort it out?

Thanks
Mradul
@larsmans
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larsmans commented Oct 7, 2014

Can you run env | egrep '(CC|CXX)(FLAGS)?' and post the output?

@cosmos2006
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No output is returned with the above command.

Thanks
Mradul

@cosmos2006
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here is the log of "python setup.py build"

blas_opt_info:
blas_mkl_info:
  libraries mkl,vml,guide not found in ['/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
  NOT AVAILABLE

openblas_info:
  libraries openblas not found in ['/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib64', '/usr/local/lib', '/usr/lib64/atlas', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib/sse2', '/usr/lib']
  NOT AVAILABLE

atlas_blas_info:
  libraries f77blas,cblas,atlas not found in ['/usr/local/lib64', '/usr/local/lib', '/usr/lib64/atlas', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib/sse2', '/usr/lib']
  NOT AVAILABLE

blas_info:
  FOUND:
    libraries = ['blas']
    library_dirs = ['/usr/lib64']
    language = f77

  FOUND:
    libraries = ['blas']
    library_dirs = ['/usr/lib64']
    define_macros = [('NO_ATLAS_INFO', 1)]
    language = f77

running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building library "libsvm-skl" sources
building library "cblas" sources
building extension "sklearn.__check_build._check_build" sources
building extension "sklearn.svm.libsvm" sources
building extension "sklearn.svm.liblinear" sources
building extension "sklearn.svm.libsvm_sparse" sources
building extension "sklearn.datasets._svmlight_format" sources
building extension "sklearn.feature_extraction._hashing" sources
building extension "sklearn.cluster._hierarchical" sources
building extension "sklearn.cluster._k_means" sources
building extension "sklearn.ensemble._gradient_boosting" sources
building extension "sklearn.utils.sparsetools._min_spanning_tree" sources
building extension "sklearn.utils.sparsetools._traversal" sources
building extension "sklearn.utils.sparsetools._graph_tools" sources
building extension "sklearn.utils.sparsefuncs_fast" sources
building extension "sklearn.utils.arrayfuncs" sources
building extension "sklearn.utils.murmurhash" sources
building extension "sklearn.utils.lgamma" sources
building extension "sklearn.utils.graph_shortest_path" sources
building extension "sklearn.utils.fast_dict" sources
building extension "sklearn.utils.seq_dataset" sources
building extension "sklearn.utils.weight_vector" sources
building extension "sklearn.utils._random" sources
building extension "sklearn.utils._logistic_sigmoid" sources
building extension "sklearn.neighbors.ball_tree" sources
building extension "sklearn.neighbors.kd_tree" sources
building extension "sklearn.neighbors.dist_metrics" sources
building extension "sklearn.neighbors.typedefs" sources
building extension "sklearn.manifold._utils" sources
building extension "sklearn.metrics.pairwise_fast" sources
building extension "sklearn.tree._tree" sources
building extension "sklearn.tree._utils" sources
building extension "sklearn.metrics/cluster.expected_mutual_info_fast" sources
building extension "sklearn._hmmc" sources
building extension "sklearn._isotonic" sources
building extension "sklearn.linear_model.cd_fast" sources
building extension "sklearn.linear_model.sgd_fast" sources
building extension "sklearn.utils.sparsetools._min_spanning_tree" sources
building extension "sklearn.utils.sparsetools._traversal" sources
building extension "sklearn.utils.sparsetools._graph_tools" sources
building extension "sklearn.utils.sparsefuncs_fast" sources
building extension "sklearn.utils.arrayfuncs" sources
building extension "sklearn.utils.murmurhash" sources
building extension "sklearn.utils.lgamma" sources
building extension "sklearn.utils.graph_shortest_path" sources
building extension "sklearn.utils.fast_dict" sources
building extension "sklearn.utils.seq_dataset" sources
building extension "sklearn.utils.weight_vector" sources
building extension "sklearn.utils._random" sources
building extension "sklearn.utils._logistic_sigmoid" sources
building data_files sources
build_src: building npy-pkg config files
running build_py
running build_clib
customize UnixCCompiler
customize UnixCCompiler using build_clib
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
resetting extension 'sklearn.svm.liblinear' language from 'f77' to 'c++'.
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'sklearn.cluster._k_means' extension
compiling C sources
C compiler: gcc -pthread -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -I/usr/local/include -I/sw/include -fPIC

compile options: '-DNO_ATLAS_INFO=1 -Isklearn/src/cblas -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c'
gcc: sklearn/cluster/_k_means.c
In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                 from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from sklearn/cluster/_k_means.c:347:
/usr/lib64/python2.7/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]
In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:317:0,
                 from sklearn/cluster/_k_means.c:348:
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
/usr/bin/gfortran -Wall -g -L/usr/local/lib -L/sw/lib build/temp.linux-x86_64-2.7/sklearn/cluster/_k_means.o -L/usr/lib64 -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.7 -lcblas -lm -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/sklearn/cluster/_k_means.so
/usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: error: ld returned 1 exit status
/usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: error: ld returned 1 exit status

@larsmans
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larsmans commented Oct 8, 2014

This is strange. Does the error go away if you install ATLAS? yum install atlas-devel, I believe.

@cosmos2006
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yes, the error disappeared after installing ATLAS.

Attached is the log file "python setup.py build"

blas_opt_info:
blas_mkl_info:
libraries mkl,vml,guide not found in ['/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
NOT AVAILABLE

openblas_info:
libraries openblas not found in ['/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using config
compiling '_configtest.c':

/* This file is generated from numpy/distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
ATL_buildinfo();
return 0;
}

C compiler: gcc -pthread -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -I/usr/local/include -I/sw/include -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/usr/lib64/atlas -lptf77blas -lptcblas -latlas -o configtest
ATLAS version 3.8.4 built by mockbuild on Fri Sep 2 01:16:43 UTC 2011:
UNAME : Linux x86-04.phx2.fedoraproject.org 2.6.32-131.2.1.el6.x86_64 #1 SMP Wed May 18 07:07:37 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux
INSTFLG : -1 0 -a 1
ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_Core2 -DATL_CPUMHZ=2333 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664
F2CDEFS : -DAdd -DF77_INTEGER=int -DStringSunStyle
CACHEEDGE: 98304
F77 : gfortran, version GNU Fortran (GCC) 4.6.1 20110804 (Red Hat 4.6.1-7)
F77FLAGS : -O -g -Wa,--noexecstack -fPIC -m64
SMC : gcc, version gcc (GCC) 4.6.1 20110804 (Red Hat 4.6.1-7)
SMCFLAGS : -fomit-frame-pointer -mfpmath=sse -msse2 -O2 -g -Wa,--noexecstack -fPIC -m64
SKC : gcc, version gcc (GCC) 4.6.1 20110804 (Red Hat 4.6.1-7)
SKCFLAGS : -fomit-frame-pointer -mfpmath=sse -msse2 -O2 -g -Wa,--noexecstack -fPIC -m64
success!
removing: _configtest.c _configtest.o _configtest
Setting PTATLAS=ATLAS
FOUND:
libraries = ['ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/usr/lib64/atlas']
language = c
define_macros = [('ATLAS_INFO', '""3.8.4""')]
include_dirs = ['/usr/include']

FOUND:
libraries = ['ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/usr/lib64/atlas']
language = c
define_macros = [('ATLAS_INFO', '""3.8.4""')]
include_dirs = ['/usr/include']

running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building library "libsvm-skl" sources
building extension "sklearn.__check_build._check_build" sources
building extension "sklearn.svm.libsvm" sources
building extension "sklearn.svm.liblinear" sources
building extension "sklearn.svm.libsvm_sparse" sources
building extension "sklearn.datasets._svmlight_format" sources
building extension "sklearn.feature_extraction._hashing" sources
building extension "sklearn.cluster._hierarchical" sources
building extension "sklearn.cluster._k_means" sources
building extension "sklearn.ensemble._gradient_boosting" sources
building extension "sklearn.utils.sparsetools._min_spanning_tree" sources
building extension "sklearn.utils.sparsetools._traversal" sources
building extension "sklearn.utils.sparsetools._graph_tools" sources
building extension "sklearn.utils.sparsefuncs_fast" sources
building extension "sklearn.utils.arrayfuncs" sources
building extension "sklearn.utils.murmurhash" sources
building extension "sklearn.utils.lgamma" sources
building extension "sklearn.utils.graph_shortest_path" sources
building extension "sklearn.utils.fast_dict" sources
building extension "sklearn.utils.seq_dataset" sources
building extension "sklearn.utils.weight_vector" sources
building extension "sklearn.utils._random" sources
building extension "sklearn.utils._logistic_sigmoid" sources
building extension "sklearn.neighbors.ball_tree" sources
building extension "sklearn.neighbors.kd_tree" sources
building extension "sklearn.neighbors.dist_metrics" sources
building extension "sklearn.neighbors.typedefs" sources
building extension "sklearn.manifold._utils" sources
building extension "sklearn.metrics.pairwise_fast" sources
building extension "sklearn.tree._tree" sources
building extension "sklearn.tree._utils" sources
building extension "sklearn.metrics/cluster.expected_mutual_info_fast" sources
building extension "sklearn._hmmc" sources
building extension "sklearn._isotonic" sources
building extension "sklearn.linear_model.cd_fast" sources
building extension "sklearn.linear_model.sgd_fast" sources
building extension "sklearn.utils.sparsetools._min_spanning_tree" sources
building extension "sklearn.utils.sparsetools._traversal" sources
building extension "sklearn.utils.sparsetools._graph_tools" sources
building extension "sklearn.utils.sparsefuncs_fast" sources
building extension "sklearn.utils.arrayfuncs" sources
building extension "sklearn.utils.murmurhash" sources
building extension "sklearn.utils.lgamma" sources
building extension "sklearn.utils.graph_shortest_path" sources
building extension "sklearn.utils.fast_dict" sources
building extension "sklearn.utils.seq_dataset" sources
building extension "sklearn.utils.weight_vector" sources
building extension "sklearn.utils._random" sources
building extension "sklearn.utils._logistic_sigmoid" sources
building data_files sources
build_src: building npy-pkg config files
running build_py
running build_clib
customize UnixCCompiler
customize UnixCCompiler using build_clib
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
resetting extension 'sklearn.svm.liblinear' language from 'c' to 'c++'.
customize UnixCCompiler
customize UnixCCompiler using build_ext
running install_lib
running install_data
running install_egg_info
Removing /usr/lib64/python2.7/site-packages/scikit_learn-0.15.2-py2.7.egg-info
Writing /usr/lib64/python2.7/site-packages/scikit_learn-0.15.2-py2.7.egg-info
running install_clib

However during "nosetests -v sklearn", error appeared. Last few lines of error are:

ERROR: Test that linear regression also works with sparse data

Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/lib64/python2.7/site-packages/sklearn/linear_model/tests/test_base.py", line 78, in test_linear_regression_sparse
ols.fit(X, y.ravel())
File "/usr/lib64/python2.7/site-packages/sklearn/linear_model/base.py", line 359, in fit
out = lsqr(X, y)
File "/usr/lib64/python2.7/site-packages/scipy/sparse/linalg/isolve/lsqr.py", line 440, in lsqr
test3 = 1 / acond

ZeroDivisionError: float division by zero

Thanks
Mradul

@larsmans
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larsmans commented Oct 8, 2014

This is really strange, because it means that when CBLAS (e.g., ATLAS) is not installed, Fortran BLAS and a Fortran linker are used by the build system. This shouldn't happen.

@amueller amueller added this to the 0.16 milestone Jan 22, 2015
@amueller
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The error you currently get was fixed in newer versions of scipy.

@amueller
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@larsmans should we close this or try to reproduce ourselves?

@amueller
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amueller commented Sep 9, 2015

Closing.

@amueller amueller closed this as completed Sep 9, 2015
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