[Numpy-discussion] Instaling numpy without root access
Dear all,
I am trying to install numpy without root access. So I am building from the
source. I have installed atlas which also has lapack with it. I changed
the site.cfg file as given below
[DEFAULT]
library_dirs = /home/svu/a0095654/ATLAS/build/lib
include_dirs = /home/svu/a0095654/ATLAS/build/include
However, I am getting a segmentation fault when importing numpy.
Please advise. I also put the build log file at the end of the email if
necessary.
Thank you,
Best Regards,
Lahiru
Log starts below.
* python2.7 setup.py build --fcompiler=gnu95*
Running from numpy source directory.
/home/svu/a0095654/lib/python2.7/distutils/dist.py:267: UserWarning:
Unknown distribution option: 'test_suite'
warnings.warn(msg)
non-existing path in 'numpy/f2py': 'docs'
non-existing path in 'numpy/f2py': 'f2py.1'
F2PY Version 2
blas_opt_info:
blas_mkl_info:
libraries mkl,vml,guide not found in
['/home/svu/a0095654/ATLAS/build/lib']
NOT AVAILABLE
openblas_info:
libraries openblas not found in ['/home/svu/a0095654/ATLAS/build/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 -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv
-O3 -Wall -Wstrict-prototypes -fPIC
compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/home/svu/a0095654/ATLAS/build/install/lib
-lptf77blas -lptcblas -latlas -o _configtest
_configtest.o: In function `main':
/hpctmp/a0095654/Software/numpy-1.9.0/_configtest.c:5: undefined reference
to `ATL_buildinfo'
collect2: ld returned 1 exit status
_configtest.o: In function `main':
/hpctmp/a0095654/Software/numpy-1.9.0/_configtest.c:5: undefined reference
to `ATL_buildinfo'
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
Status: 255
Output: 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 -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv
-O3 -Wall -Wstrict-prototypes -fPIC
compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/home/svu/a0095654/ATLAS/build/install/lib
-lptf77blas -lptcblas -latlas -o _configtest
_configtest.o: In function `main':
/hpctmp/a0095654/Software/numpy-1.9.0/_configtest.c:5: undefined reference
to `ATL_buildinfo'
collect2: ld returned 1 exit status
Setting PTATLAS=ATLAS
FOUND:
libraries = ['ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/home/svu/a0095654/ATLAS/build/install/lib']
language = c
define_macros = [('ATLAS_INFO', '"\\"None\\""')]
FOUND:
libraries = ['ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/home/svu/a0095654/ATLAS/build/install/lib']
language = c
define_macros = [('ATLAS_INFO', '"\\"None\\""')]
non-existing path in 'numpy/lib': 'benchmarks'
lapack_opt_info:
openblas_lapack_info:
libraries openblas not found in ['/home/svu/a0095654/ATLAS/build/lib']
NOT AVAILABLE
lapack_mkl_info:
mkl_info:
libraries mkl,vml,guide not found in
['/home/svu/a0095654/ATLAS/build/lib']
NOT AVAILABLE
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
libraries lapack_atlas not found in
/home/svu/a0095654/ATLAS/build/install/lib
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
/hpctmp/a0095654/Software/numpy-1.9.0/numpy/distutils/system_info.py:1095:
UserWarning:
*
Lapack library (from ATLAS) is probably incomplete:
size of /home/svu/a0095654/ATLAS/build/install/lib/liblapack.so is
5.0673828125k (expected >4000k)
Follow the instructions in the KNOWN PROBLEMS section of the file
numpy/INSTALL.txt.
*
warnings.warn(message)
Setting PTATLAS=ATLAS
FOUND:
libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/home/svu/a0095654/ATLAS/build/install/lib']
language = c
define_macros = [('ATLAS_INFO', '"\\"None\\""')]
FOUND:
libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/home/svu/a0095654/ATLAS/build/install/lib']
language = c
define_macros = [('ATLAS_INFO', '"\\"None\\""')]
/home/svu/a0095654/lib/python2.7/distutils/dist.py:267: UserWarning:
Unknown distribution option: 'define_macros'
warnings.warn(msg)
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 py_modules sources
building library "npymath" sources
Re: [Numpy-discussion] Instaling numpy without root access
On 10.10.2014 18:51, Lahiru Samarakoon wrote: > Dear all, > > I am trying to install numpy without root access. So I am building from > the source. I have installed atlas which also has lapack with it. I > changed the site.cfg file as given below > > [DEFAULT] > library_dirs = /home/svu/a0095654/ATLAS/build/lib > include_dirs = /home/svu/a0095654/ATLAS/build/include > > > However, I am getting a segmentation fault when importing numpy. > > Please advise. I also put the build log file at the end of the email if > necessary. Which platform are you working on? Which compiler version? We just solved a segfault on import on red hat 5 gcc 4.1.2. Very likely caused by a compiler bug. See https://github.com/numpy/numpy/issues/5163 The build log is complaining about your atlas being to small, possibly the installation is broken? ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Instaling numpy without root access
Red Hat Enterprise Linux release 5.8 gcc (GCC) 4.1.2 I am also trying to install numpy 1.9. On Sat, Oct 11, 2014 at 12:59 AM, Julian Taylor < jtaylor.deb...@googlemail.com> wrote: > On 10.10.2014 18:51, Lahiru Samarakoon wrote: > > Dear all, > > > > I am trying to install numpy without root access. So I am building from > > the source. I have installed atlas which also has lapack with it. I > > changed the site.cfg file as given below > > > > [DEFAULT] > > library_dirs = /home/svu/a0095654/ATLAS/build/lib > > include_dirs = /home/svu/a0095654/ATLAS/build/include > > > > > > However, I am getting a segmentation fault when importing numpy. > > > > Please advise. I also put the build log file at the end of the email if > > necessary. > > > Which platform are you working on? Which compiler version? > We just solved a segfault on import on red hat 5 gcc 4.1.2. Very likely > caused by a compiler bug. See https://github.com/numpy/numpy/issues/5163 > > The build log is complaining about your atlas being to small, possibly > the installation is broken? > ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Instaling numpy without root access
On 10.10.2014 19:26, Lahiru Samarakoon wrote: > Red Hat Enterprise Linux release 5.8 > gcc (GCC) 4.1.2 > > I am also trying to install numpy 1.9. that is the broken platform, please try the master branch or the maintenance/1.9.x branch, those should work now. Are there volunteers to report this to redhat? > > On Sat, Oct 11, 2014 at 12:59 AM, Julian Taylor > mailto:jtaylor.deb...@googlemail.com>> > wrote: > > On 10.10.2014 18:51, Lahiru Samarakoon wrote: > > Dear all, > > > > I am trying to install numpy without root access. So I am building from > > the source. I have installed atlas which also has lapack with it. I > > changed the site.cfg file as given below > > > > [DEFAULT] > > library_dirs = /home/svu/a0095654/ATLAS/build/lib > > include_dirs = /home/svu/a0095654/ATLAS/build/include > > > > > > However, I am getting a segmentation fault when importing numpy. > > > > Please advise. I also put the build log file at the end of the email if > > necessary. > > > Which platform are you working on? Which compiler version? > We just solved a segfault on import on red hat 5 gcc 4.1.2. Very likely > caused by a compiler bug. See https://github.com/numpy/numpy/issues/5163 > > The build log is complaining about your atlas being to small, possibly > the installation is broken? > > ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Instaling numpy without root access
I switched to numpy-1.8.2. . Now getting following error. I am using LAPACK that comes with atlast installation. Can this be a problem? Traceback (most recent call last): File "", line 1, in File "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/__init__.py", line 170, in from . import add_newdocs File "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in from numpy.lib import add_newdoc File "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/lib/__init__.py", line 18, in from .polynomial import * File "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/lib/polynomial.py", line 19, in from numpy.linalg import eigvals, lstsq, inv File "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/linalg/__init__.py", line 51, in from .linalg import * File "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/linalg/linalg.py", line 29, in from numpy.linalg import lapack_lite, _umath_linalg ImportError: /home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so: undefined symbol: zgesdd_ On Sat, Oct 11, 2014 at 1:30 AM, Julian Taylor < jtaylor.deb...@googlemail.com> wrote: > On 10.10.2014 19:26, Lahiru Samarakoon wrote: > > Red Hat Enterprise Linux release 5.8 > > gcc (GCC) 4.1.2 > > > > I am also trying to install numpy 1.9. > > that is the broken platform, please try the master branch or the > maintenance/1.9.x branch, those should work now. > > Are there volunteers to report this to redhat? > > > > > On Sat, Oct 11, 2014 at 12:59 AM, Julian Taylor > > mailto:jtaylor.deb...@googlemail.com>> > > wrote: > > > > On 10.10.2014 18:51, Lahiru Samarakoon wrote: > > > Dear all, > > > > > > I am trying to install numpy without root access. So I am building > from > > > the source. I have installed atlas which also has lapack with > it. I > > > changed the site.cfg file as given below > > > > > > [DEFAULT] > > > library_dirs = /home/svu/a0095654/ATLAS/build/lib > > > include_dirs = /home/svu/a0095654/ATLAS/build/include > > > > > > > > > However, I am getting a segmentation fault when importing numpy. > > > > > > Please advise. I also put the build log file at the end of the > email if > > > necessary. > > > > > > Which platform are you working on? Which compiler version? > > We just solved a segfault on import on red hat 5 gcc 4.1.2. Very > likely > > caused by a compiler bug. See > https://github.com/numpy/numpy/issues/5163 > > > > The build log is complaining about your atlas being to small, > possibly > > the installation is broken? > > > > > > ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Instaling numpy without root access
Guys, any advice is highly appreciated. I am a little new to building in Linux. Thanks, Lahiru On Sat, Oct 11, 2014 at 9:43 AM, Lahiru Samarakoon wrote: > I switched to numpy-1.8.2. . Now getting following error. I am using > LAPACK that comes with atlast installation. Can this be a problem? > > Traceback (most recent call last): > File "", line 1, in > File > "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/__init__.py", > line 170, in > from . import add_newdocs > File > "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/add_newdocs.py", > line 13, in > from numpy.lib import add_newdoc > File > "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/lib/__init__.py", > line 18, in > from .polynomial import * > File > "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/lib/polynomial.py", > line 19, in > from numpy.linalg import eigvals, lstsq, inv > File > "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/linalg/__init__.py", > line 51, in > from .linalg import * > File > "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/linalg/linalg.py", > line 29, in > from numpy.linalg import lapack_lite, _umath_linalg > ImportError: > /home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so: > undefined symbol: zgesdd_ > > On Sat, Oct 11, 2014 at 1:30 AM, Julian Taylor < > jtaylor.deb...@googlemail.com> wrote: > >> On 10.10.2014 19:26, Lahiru Samarakoon wrote: >> > Red Hat Enterprise Linux release 5.8 >> > gcc (GCC) 4.1.2 >> > >> > I am also trying to install numpy 1.9. >> >> that is the broken platform, please try the master branch or the >> maintenance/1.9.x branch, those should work now. >> >> Are there volunteers to report this to redhat? >> >> > >> > On Sat, Oct 11, 2014 at 12:59 AM, Julian Taylor >> > mailto:jtaylor.deb...@googlemail.com>> >> > wrote: >> > >> > On 10.10.2014 18:51, Lahiru Samarakoon wrote: >> > > Dear all, >> > > >> > > I am trying to install numpy without root access. So I am >> building from >> > > the source. I have installed atlas which also has lapack with >> it. I >> > > changed the site.cfg file as given below >> > > >> > > [DEFAULT] >> > > library_dirs = /home/svu/a0095654/ATLAS/build/lib >> > > include_dirs = /home/svu/a0095654/ATLAS/build/include >> > > >> > > >> > > However, I am getting a segmentation fault when importing numpy. >> > > >> > > Please advise. I also put the build log file at the end of the >> email if >> > > necessary. >> > >> > >> > Which platform are you working on? Which compiler version? >> > We just solved a segfault on import on red hat 5 gcc 4.1.2. Very >> likely >> > caused by a compiler bug. See >> https://github.com/numpy/numpy/issues/5163 >> > >> > The build log is complaining about your atlas being to small, >> possibly >> > the installation is broken? >> > >> > >> >> > ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Instaling numpy without root access
Have you considered virtual environments? http://docs.python-guide.org/en/latest/dev/virtualenvs/ Inside of each environment you can build a local python version and packages with different versions through pip. Maybe not exactly what you need help with but it is a good tool to have so that you have less dependency issues. On Mon, Oct 13, 2014 at 2:52 AM, Lahiru Samarakoon wrote: > Guys, any advice is highly appreciated. I am a little new to building in > Linux. > Thanks, > Lahiru > > On Sat, Oct 11, 2014 at 9:43 AM, Lahiru Samarakoon > wrote: > >> I switched to numpy-1.8.2. . Now getting following error. I am using >> LAPACK that comes with atlast installation. Can this be a problem? >> >> Traceback (most recent call last): >> File "", line 1, in >> File >> "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/__init__.py", >> line 170, in >> from . import add_newdocs >> File >> "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/add_newdocs.py", >> line 13, in >> from numpy.lib import add_newdoc >> File >> "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/lib/__init__.py", >> line 18, in >> from .polynomial import * >> File >> "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/lib/polynomial.py", >> line 19, in >> from numpy.linalg import eigvals, lstsq, inv >> File >> "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/linalg/__init__.py", >> line 51, in >> from .linalg import * >> File >> "/home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/linalg/linalg.py", >> line 29, in >> from numpy.linalg import lapack_lite, _umath_linalg >> ImportError: >> /home/svu/a0095654/.local/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so: >> undefined symbol: zgesdd_ >> >> On Sat, Oct 11, 2014 at 1:30 AM, Julian Taylor < >> jtaylor.deb...@googlemail.com> wrote: >> >>> On 10.10.2014 19:26, Lahiru Samarakoon wrote: >>> > Red Hat Enterprise Linux release 5.8 >>> > gcc (GCC) 4.1.2 >>> > >>> > I am also trying to install numpy 1.9. >>> >>> that is the broken platform, please try the master branch or the >>> maintenance/1.9.x branch, those should work now. >>> >>> Are there volunteers to report this to redhat? >>> >>> > >>> > On Sat, Oct 11, 2014 at 12:59 AM, Julian Taylor >>> > mailto:jtaylor.deb...@googlemail.com>> >>> > wrote: >>> > >>> > On 10.10.2014 18:51, Lahiru Samarakoon wrote: >>> > > Dear all, >>> > > >>> > > I am trying to install numpy without root access. So I am >>> building from >>> > > the source. I have installed atlas which also has lapack with >>> it. I >>> > > changed the site.cfg file as given below >>> > > >>> > > [DEFAULT] >>> > > library_dirs = /home/svu/a0095654/ATLAS/build/lib >>> > > include_dirs = /home/svu/a0095654/ATLAS/build/include >>> > > >>> > > >>> > > However, I am getting a segmentation fault when importing numpy. >>> > > >>> > > Please advise. I also put the build log file at the end of the >>> email if >>> > > necessary. >>> > >>> > >>> > Which platform are you working on? Which compiler version? >>> > We just solved a segfault on import on red hat 5 gcc 4.1.2. Very >>> likely >>> > caused by a compiler bug. See >>> https://github.com/numpy/numpy/issues/5163 >>> > >>> > The build log is complaining about your atlas being to small, >>> possibly >>> > the installation is broken? >>> > >>> > >>> >>> >> > > ___ > NumPy-Discussion mailing list > NumPy-Discussion@scipy.org > http://mail.scipy.org/mailman/listinfo/numpy-discussion > > ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
