Re: Error when importing PySparse
Hi Daniel, I asked for help at my IT service and we could figure out what was not working on the cluster (mainly no blast package was installed, and the version of pysparse downloaded with pip is not the most recent version and that was causing problems). Thank you very much for your answer! Best, Clara > On 20 Jul 2017, at 11:57, Daniel Wheeler wrote: > > > Hi Clara, > > I would seriously recommend using Conda and Python 2.7 for FiPy and > installing PySparse from the "guyer" conda channel. I'm no longer sure > which versions of PySparse work or don't work with FiPy. I have used > this Dockerfile successfully to run FiPy, > https://github.com/wd15/extremefill2D-dockerize/blob/master/Dockerfile. > > Specifically, this stuff will help you get up and running in a Conda > environment: > > > wget https://repo.continuum.io/miniconda/Miniconda2-4.3.11-Linux-x86_64.sh > bash Miniconda2-4.3.11-Linux-x86_64.sh -b -p $ANACONDAPATH > conda update conda > conda install libgfortran=1.0 && conda clean --all > conda install matplotlib && conda clean --all > conda install --channel guyer scipy gmsh && conda clean --all > conda install --channel guyer pysparse openmpi mpi4py && conda clean --all > conda install --channel guyer trilinos && conda clean --all > ~~~ > > There are a lot of additional packages in the Dockerfile so you might > not want to use it as is, however, it might give you some clues about > what's necessary to get FiPy working even if you don't use Docker. > > I hope this helps. > > Cheers, > > Daniel > > On Thu, Jul 20, 2017 at 9:38 AM, Clara Maurel wrote: >> Hello, >> >> I have trouble trying to install PySparse on a Linux cluster. The pip >> command: >> >> pip install --user pysparse >> >> did not work. >> >> I found on a forum this command: >> >> pip install --user git+http://git.code.sf.net/p/pysparse/git#egg=PySparse >> >> after which it said the installation was successful. However, when I try to >> import Pysparse, I have an error message that says: >> >> Traceback (most recent call last): >> File "", line 1, in >> File >> "/home/cmaurel/.local/lib/python2.6/site-packages/pysparse/__init__.py", >> line 13, in >>from sparse import spmatrix >> File >> "/home/cmaurel/.local/lib/python2.6/site-packages/pysparse/sparse/__init__.py", >> line 6, in >>from pysparseMatrix import * >> File >> "/home/cmaurel/.local/lib/python2.6/site-packages/pysparse/sparse/pysparseMatrix.py", >> line 57, in >>from pysparse.sparse import spmatrix >> ImportError: >> /home/cmaurel/.local/lib/python2.6/site-packages/pysparse/sparse/spmatrix.so: >> undefined symbol: __intel_security_cookie >> >> >> >> I also independently tried to run: >> >> python setup.py build >> >> but this was also unsuccessful with the error: >> >> creating build/temp.linux-x86_64-2.6 >> creating build/temp.linux-x86_64-2.6/src >> compile options: '-DLENFUNC_OK=1 -DATLAS_INFO="\"3.8.4\"" -Isrc >> -I/usr/include -I/usr/lib64/python2.6/site-packages/numpy/core/include >> -I/usr/include/python2.6 -c' >> icc: src/spmatrixmodule.c >> icc: command line warning #10006: ignoring unknown option '-fwrapv' >> icc: command line warning #10006: ignoring unknown option '-fwrapv' >> icc: error #10236: File not found: 'src/spmatrixmodule.c' >> icc: command line error: no files specified; for help type "icc -help" >> icc: command line warning #10006: ignoring unknown option '-fwrapv' >> icc: command line warning #10006: ignoring unknown option '-fwrapv' >> icc: error #10236: File not found: 'src/spmatrixmodule.c' >> icc: command line error: no files specified; for help type "icc -help" >> error: Command "icc -fno-strict-aliasing -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 >> -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 -fPIC -DLENFUNC_OK=1 -DATLAS_INFO="\"3.8.4\"" >> -Isrc -I/usr/include -I/usr/lib64/python2.6/site-packages/numpy/core/include >> -I/usr/include/python2.6 -c src/spmatrixmodule.c -o >> build/temp.linux-x86_64-2.6/src/spmatrixmodule.o" failed with exit status 1 >> >> Would anyone have an idea on how to fix this? >> >> Any help would be very much appreciated! Thank you in advance! >> >> Clara >> >> >> ___ >> fipy mailing list >> fipy@nist.gov >> http://www.ctcms.nist.gov/fipy >> [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] >> > > > > -- > Daniel Wheeler > ___ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] smime.p7s Description: S/MIME cryptographic signature ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/
Re: Error when importing PySparse
Hi Clara, I would seriously recommend using Conda and Python 2.7 for FiPy and installing PySparse from the "guyer" conda channel. I'm no longer sure which versions of PySparse work or don't work with FiPy. I have used this Dockerfile successfully to run FiPy, https://github.com/wd15/extremefill2D-dockerize/blob/master/Dockerfile. Specifically, this stuff will help you get up and running in a Conda environment: wget https://repo.continuum.io/miniconda/Miniconda2-4.3.11-Linux-x86_64.sh bash Miniconda2-4.3.11-Linux-x86_64.sh -b -p $ANACONDAPATH conda update conda conda install libgfortran=1.0 && conda clean --all conda install matplotlib && conda clean --all conda install --channel guyer scipy gmsh && conda clean --all conda install --channel guyer pysparse openmpi mpi4py && conda clean --all conda install --channel guyer trilinos && conda clean --all ~~~ There are a lot of additional packages in the Dockerfile so you might not want to use it as is, however, it might give you some clues about what's necessary to get FiPy working even if you don't use Docker. I hope this helps. Cheers, Daniel On Thu, Jul 20, 2017 at 9:38 AM, Clara Maurel wrote: > Hello, > > I have trouble trying to install PySparse on a Linux cluster. The pip > command: > > pip install --user pysparse > > did not work. > > I found on a forum this command: > > pip install --user git+http://git.code.sf.net/p/pysparse/git#egg=PySparse > > after which it said the installation was successful. However, when I try to > import Pysparse, I have an error message that says: > > Traceback (most recent call last): > File "", line 1, in > File > "/home/cmaurel/.local/lib/python2.6/site-packages/pysparse/__init__.py", > line 13, in > from sparse import spmatrix > File > "/home/cmaurel/.local/lib/python2.6/site-packages/pysparse/sparse/__init__.py", > line 6, in > from pysparseMatrix import * > File > "/home/cmaurel/.local/lib/python2.6/site-packages/pysparse/sparse/pysparseMatrix.py", > line 57, in > from pysparse.sparse import spmatrix > ImportError: > /home/cmaurel/.local/lib/python2.6/site-packages/pysparse/sparse/spmatrix.so: > undefined symbol: __intel_security_cookie > > > > I also independently tried to run: > > python setup.py build > > but this was also unsuccessful with the error: > > creating build/temp.linux-x86_64-2.6 > creating build/temp.linux-x86_64-2.6/src > compile options: '-DLENFUNC_OK=1 -DATLAS_INFO="\"3.8.4\"" -Isrc > -I/usr/include -I/usr/lib64/python2.6/site-packages/numpy/core/include > -I/usr/include/python2.6 -c' > icc: src/spmatrixmodule.c > icc: command line warning #10006: ignoring unknown option '-fwrapv' > icc: command line warning #10006: ignoring unknown option '-fwrapv' > icc: error #10236: File not found: 'src/spmatrixmodule.c' > icc: command line error: no files specified; for help type "icc -help" > icc: command line warning #10006: ignoring unknown option '-fwrapv' > icc: command line warning #10006: ignoring unknown option '-fwrapv' > icc: error #10236: File not found: 'src/spmatrixmodule.c' > icc: command line error: no files specified; for help type "icc -help" > error: Command "icc -fno-strict-aliasing -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 > -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 -fPIC -DLENFUNC_OK=1 -DATLAS_INFO="\"3.8.4\"" > -Isrc -I/usr/include -I/usr/lib64/python2.6/site-packages/numpy/core/include > -I/usr/include/python2.6 -c src/spmatrixmodule.c -o > build/temp.linux-x86_64-2.6/src/spmatrixmodule.o" failed with exit status 1 > > Would anyone have an idea on how to fix this? > > Any help would be very much appreciated! Thank you in advance! > > Clara > > > ___ > fipy mailing list > fipy@nist.gov > http://www.ctcms.nist.gov/fipy > [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ] > -- Daniel Wheeler ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
Error when importing PySparse
Hello, I have trouble trying to install PySparse on a Linux cluster. The pip command: pip install --user pysparse did not work. I found on a forum this command: pip install --user git+http://git.code.sf.net/p/pysparse/git#egg=PySparse http://git.code.sf.net/p/pysparse/git#egg=PySparse> after which it said the installation was successful. However, when I try to import Pysparse, I have an error message that says: Traceback (most recent call last): File "", line 1, in File "/home/cmaurel/.local/lib/python2.6/site-packages/pysparse/__init__.py", line 13, in from sparse import spmatrix File "/home/cmaurel/.local/lib/python2.6/site-packages/pysparse/sparse/__init__.py", line 6, in from pysparseMatrix import * File "/home/cmaurel/.local/lib/python2.6/site-packages/pysparse/sparse/pysparseMatrix.py", line 57, in from pysparse.sparse import spmatrix ImportError: /home/cmaurel/.local/lib/python2.6/site-packages/pysparse/sparse/spmatrix.so: undefined symbol: __intel_security_cookie I also independently tried to run: python setup.py build but this was also unsuccessful with the error: creating build/temp.linux-x86_64-2.6 creating build/temp.linux-x86_64-2.6/src compile options: '-DLENFUNC_OK=1 -DATLAS_INFO="\"3.8.4\"" -Isrc -I/usr/include -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include/python2.6 -c' icc: src/spmatrixmodule.c icc: command line warning #10006: ignoring unknown option '-fwrapv' icc: command line warning #10006: ignoring unknown option '-fwrapv' icc: error #10236: File not found: 'src/spmatrixmodule.c' icc: command line error: no files specified; for help type "icc -help" icc: command line warning #10006: ignoring unknown option '-fwrapv' icc: command line warning #10006: ignoring unknown option '-fwrapv' icc: error #10236: File not found: 'src/spmatrixmodule.c' icc: command line error: no files specified; for help type "icc -help" error: Command "icc -fno-strict-aliasing -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 -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 -fPIC -DLENFUNC_OK=1 -DATLAS_INFO="\"3.8.4\"" -Isrc -I/usr/include -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include/python2.6 -c src/spmatrixmodule.c -o build/temp.linux-x86_64-2.6/src/spmatrixmodule.o" failed with exit status 1 Would anyone have an idea on how to fix this? Any help would be very much appreciated! Thank you in advance! Clara smime.p7s Description: S/MIME cryptographic signature ___ fipy mailing list fipy@nist.gov http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
