FEniCS on Scientific Linux

[xpqian]

I am trying to use conda to install FEniCS on Scientific Linux release 6.3.

When I tried FEniCS 1.5, it gave me error: "ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/xqian29/anaconda/envs/fenics27/lib/python2.7/site-packages/ufc/_ufc.so)".

When I tried to install FEniCS 1.4 with the command "conda install "fenics=1.4.0" mkl --channel https://conda.binstar.org/juanlu001/channel/fenics:1.4.0:centos", I got the following error: "File "/home/xqian29/anaconda/lib/python2.7/site-packages/dolfin/cpp/common.py", line 28, in swig_import_helper _mod = imp.load_module('_common', fp, pathname, description) ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/xqian29/anaconda/lib/libslepc.so)".

Any idea to fix it?

Thanks, Xiaoping.

[astrojuanlu]

Thanks for the bug report @xpqian. I will have to investigate it but this smells like a problem with the slepc package. I recall compiling it properly but I see a mismatch in the path of the library, would you please post the output of this commands?

conda info -a
source activate fenics27
conda list
source deactivate
conda list

[xpqian]

Thank you for your response. Here are the outputs of the commands.

[xqian29@aci-service-1 python]$ conda info -a Current conda install:

         platform : linux-64
    conda version : 3.10.1

conda-build version : 1.12.0 python version : 2.7.9.final.0 requests version : 2.6.0 root environment : /home/xqian29/anaconda (writable) default environment : /home/xqian29/anaconda envs directories : /home/xqian29/anaconda/envs package cache : /home/xqian29/anaconda/pkgs channel URLs : https://conda.binstar.org/juanlu001/linux-64/ https://conda.binstar.org/juanlu001/noarch/ https://repo.continuum.io/pkgs/free/linux-64/ https://repo.continuum.io/pkgs/free/noarch/ https://repo.continuum.io/pkgs/pro/linux-64/ https://repo.continuum.io/pkgs/pro/noarch/ config file : /home/xqian29/.condarc is foreign system : False

conda environments:

# fenics27 /home/xqian29/anaconda/envs/fenics27 root * /home/xqian29/anaconda

sys.version: 2.7.9 |Anaconda 2.2.0 (64-bit)| (default... sys.prefix: /home/xqian29/anaconda sys.executable: /home/xqian29/anaconda/bin/python conda location: /home/xqian29/anaconda/lib/python2.7/site-packages/conda conda-build: /home/xqian29/anaconda/bin/conda-build conda-convert: /home/xqian29/anaconda/bin/conda-convert conda-develop: /home/xqian29/anaconda/bin/conda-develop conda-env: /home/xqian29/anaconda/bin/conda-env conda-index: /home/xqian29/anaconda/bin/conda-index conda-inspect: /home/xqian29/anaconda/bin/conda-inspect conda-metapackage: /home/xqian29/anaconda/bin/conda-metapackage conda-pipbuild: /home/xqian29/anaconda/bin/conda-pipbuild conda-server: /home/xqian29/anaconda/bin/conda-server conda-skeleton: /home/xqian29/anaconda/bin/conda-skeleton user site dirs:

CIO_TEST: CONDA_DEFAULT_ENV: CONDA_ENVS_PATH: LD_LIBRARY_PATH: /home/xqian29/anaconda/lib: PATH: /home/xqian29/anaconda/bin:/usr/lib64/qt-3.3/bin:/usr/lib64/ccache:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/dell/srvadmin/bin:/home/xqian29/bin PYTHONHOME: PYTHONPATH: /home/xqian29/anaconda/lib/python2.7/site-packages:/home/xqian29/anaconda/lib/python2.7/site-packages:

License directories: /home/xqian29/.continuum /home/xqian29/anaconda/licenses License files (license*.txt): Package/feature end dates: [xqian29@aci-service-1 python]$ source activate fenics27 discarding /home/xqian29/anaconda/bin from PATH prepending /home/xqian29/anaconda/envs/fenics27/bin to PATH (fenics27)[xqian29@aci-service-1 python]$ conda list

packages in environment at /home/xqian29/anaconda/envs/fenics27:

# abstract-rendering 0.5.1 argcomplete 0.8.4 astropy 1.0.1 backports.ssl-match-hostname 3.4.0.2 bcolz 0.8.1 beautifulsoup4 4.3.2 binstar 0.10.1 bitarray 0.8.1 blaze 0.7.3 blz 0.6.2 bokeh 0.8.1 boost 1.55.0 1 boto 2.36.0 cdecimal 2.3 certifi 14.5.14 cffi 0.9.2 clyent 0.3.4 cmake 3.0.1 0 colorama 0.3.3 conda 3.10.1 conda-build 1.12.0 conda-env 2.1.4 configobj 5.0.6 cython 0.22 cytoolz 0.7.2 datashape 0.4.4 decorator 3.4.0 docutils 0.12 dolfin 1.4.0 py27_2 eigen3 3.2.1 0 enum34 1.0.4 fastcache 1.0.2 fenics 1.4.0 1 ffc 1.4.0 py27_1 fiat 1.4.0 py27_1 flask 0.10.1 fontconfig 2.11.1 3 freetype 2.5.2 0 funcsigs 0.4 futures 2.2.0 gevent 1.0.1 gevent-websocket 0.9.3 greenlet 0.4.5 grin 1.2.1 h5py 2.4.0 hashdist 0.3 instant 1.4.0 py27_1 ipython 3.0.0 itsdangerous 0.24 jdcal 1.0 jedi 0.8.1 jinja2 2.7.3 jsonschema 2.4.0 libpng 1.5.13 1 libxml2 2.9.0 0 llvmlite-0.2.2-1 gbcb15be lxml 3.4.2 markupsafe 0.23 matplotlib 1.4.3 mistune 0.5.1 mkl 11.1 np18py27_p3 mkl-rt 11.1 p0 mkl-service 1.0.0 py27_p1 mock 1.0.1 mpi4py 1.3 py27_0 mpich2 1.4.1p1 0 multipledispatch 0.4.7 networkx 1.9.1 nltk 3.0.2 nose 1.3.4 numba 0.17.0 numexpr 2.3.1 np18py27_p0 [mkl] numpy 1.8.2 py27_p0 [mkl] odo 0.3.1 openpyxl 1.8.5 openssl 1.0.1k 1 pandas 0.15.2 patsy 0.3.0 pcre 8.31 0 pep8 1.6.2 petsc 3.4.5 py27_1 petsc4py 3.4 py27_1 pillow 2.7.0 pip 6.1.1 py27_0 ply 3.4 py27_0 psutil 2.2.1 ptyprocess 0.4 py 1.4.26 pyasn1 0.1.7 pycosat 0.6.1 pycparser 2.10 pycrypto 2.6.1 pycurl 7.19.5.1 pyflakes 0.8.1 pygments 2.0.2 pyopenssl 0.14 pyparsing 2.0.3 pytest 2.6.4 python 2.7.9 2 python-dateutil 2.4.1 pytz 2015.2 pyyaml 3.11 pyzmq 14.5.0 qt 4.8.6 1 readline 6.2 2 redis 2.10.3 requests 2.6.0 rope 0.9.4 runipy 0.1.3 scientificpython 2.9.4 py27_9 scikit-image 0.11.2 scikit-learn 0.15.0b1 np18py27_p0 [mkl] scipy 0.14.0 np18py27_p0 [mkl] setuptools 15.0 py27_0 six 1.9.0 py27_0 slepc 3.4.4 py27_2 sockjs-tornado 1.0.1 sphinx 1.2.3 spyder 2.3.4 sqlalchemy 0.9.9 sqlite 3.8.4.1 1 statsmodels 0.6.1 swig 3.0.2 0 sympy 0.7.6 system 5.8 2 tables 3.1.1 terminado 0.5 theano 0.6.0 tk 8.5.18 0 toolz 0.7.1 tornado 4.1 ufl 1.4.0 py27_1 ujson 1.33 unicodecsv 0.9.4 vtk 5.10.1 py27_1 werkzeug 0.10.1 xlrd 0.9.3 xlsxwriter 0.6.7 xlwt 0.7.5 zlib 1.2.8 0 (fenics27)[xqian29@aci-service-1 python]$ source deactivate discarding /home/xqian29/anaconda/envs/fenics27/bin from PATH [xqian29@aci-service-1 python]$ conda list

packages in environment at /home/xqian29/anaconda:

# _license 1.1 py27_0 abstract-rendering 0.5.1 np19py27_0 anaconda 2.2.0 np19py27_0 argcomplete 0.8.4 py27_0 astropy 1.0.1 np19py27_0 backports.ssl-match-hostname 3.4.0.2 bcolz 0.8.1 np19py27_0 beautiful-soup 4.3.2 py27_0 beautifulsoup4 4.3.2 binstar 0.10.1 py27_3 bitarray 0.8.1 py27_0 blaze 0.7.3 blaze-core 0.7.3 np19py27_0 blz 0.6.2 np19py27_0 bokeh 0.8.1 np19py27_1 boost 1.55.0 1 boto 2.36.0 py27_0 cairo 1.12.18 1 cdecimal 2.3 py27_0 certifi 14.05.14 py27_0 cffi 0.9.2 py27_0 clyent 0.3.4 py27_0 cmake 3.0.1 0 colorama 0.3.3 py27_0 conda 3.10.1 py27_0 conda-build 1.12.0 py27_0 conda-env 2.1.4 py27_0 configobj 5.0.6 py27_0 cryptography 0.8 py27_0 curl 7.38.0 0 cython 0.22 py27_0 cytoolz 0.7.2 py27_0 datashape 0.4.4 np19py27_1 decorator 3.4.0 py27_0 docutils 0.12 py27_0 dolfin 1.4.0 py27_2 dynd-python 0.6.5 np19py27_0 eigen3 3.2.1 0 enum34 1.0.4 py27_0 fastcache 1.0.2 py27_0 fenics 1.4.0 1 ffc 1.4.0 py27_1 fiat 1.4.0 py27_1 flask 0.10.1 py27_1 fontconfig 2.11.1 3 freetype 2.5.2 0 funcsigs 0.4 py27_0 futures 2.2.0 py27_0 gevent 1.0.1 py27_0 gevent-websocket 0.9.3 py27_0 greenlet 0.4.5 py27_0 grin 1.2.1 py27_1 h5py 2.4.0 np19py27_0 hashdist 0.3 hdf5 1.8.14 0 instant 1.4.0 py27_1 ipython 3.0.0 py27_0 ipython-notebook 3.0.0 py27_1 ipython-qtconsole 3.0.0 py27_0 itsdangerous 0.24 py27_0 jdcal 1.0 py27_0 jedi 0.8.1 py27_0 jinja2 2.7.3 py27_1 jpeg 8d 0 jsonschema 2.4.0 py27_0 libdynd 0.6.5 0 libffi 3.0.13 0 libpng 1.5.13 1 libsodium 0.4.5 0 libtiff 4.0.2 1 libxml2 2.9.0 0 libxslt 1.1.28 0 llvmlite 0.2.2 py27_1 lxml 3.4.2 py27_0 markupsafe 0.23 py27_0 matplotlib 1.4.3 np19py27_1 mistune 0.5.1 py27_0 mkl 11.1 np18py27_p3 mkl-rt 11.1 p0 mkl-service 1.0.0 py27_p1 mock 1.0.1 py27_0 mpi4py 1.3 py27_0 mpich2 1.4.1p1 0 multipledispatch 0.4.7 py27_0 networkx 1.9.1 py27_0 nltk 3.0.2 np19py27_0 nose 1.3.4 py27_1 numba 0.17.0 np19py27_0 numexpr 2.3.1 np18py27_p0 [mkl] numpy 1.8.2 py27_p0 [mkl] odo 0.3.1 np19py27_0 openpyxl 1.8.5 py27_0 openssl 1.0.1k 1 pandas 0.15.2 np19py27_1 patchelf 0.6 0 patsy 0.3.0 np19py27_0 pcre 8.31 0 pep8 1.6.2 py27_0 petsc 3.4.5 py27_1 petsc4py 3.4 py27_1 pillow 2.7.0 py27_1 pip 6.1.1 py27_0 pixman 0.26.2 0 ply 3.4 py27_0 psutil 2.2.1 py27_0 ptyprocess 0.4 py27_0 py 1.4.26 py27_0 py2cairo 1.10.0 py27_2 pyasn1 0.1.7 py27_0 pycosat 0.6.1 py27_0 pycparser 2.10 py27_0 pycrypto 2.6.1 py27_0 pycurl 7.19.5.1 py27_0 pyflakes 0.8.1 py27_0 pygments 2.0.2 py27_0 pyopenssl 0.14 py27_0 pyparsing 2.0.3 py27_0 pyqt 4.11.3 py27_0 pytables 3.1.1 np19py27_2 pytest 2.6.4 py27_0 python 2.7.9 2 python-dateutil 2.4.1 py27_0 pytz 2015.2 py27_0 pyyaml 3.11 py27_0 pyzmq 14.5.0 py27_0 qt 4.8.6 1 readline 6.2 2 redis 2.6.9 0 redis-py 2.10.3 py27_0 requests 2.6.0 py27_0 rope 0.9.4 py27_1 runipy 0.1.3 py27_0 scientificpython 2.9.4 py27_9 scikit-image 0.11.2 np19py27_0 scikit-learn 0.15.0b1 np18py27_p0 [mkl] scipy 0.14.0 np18py27_p0 [mkl] setuptools 15.0 py27_0 sip 4.16.5 py27_0 six 1.9.0 py27_0 slepc 3.4.4 py27_2 sockjs-tornado 1.0.1 py27_0 sphinx 1.2.3 py27_0 spyder 2.3.4 py27_1 spyder-app 2.3.4 py27_0 sqlalchemy 0.9.9 py27_0 sqlite 3.8.4.1 1 ssl_match_hostname 3.4.0.2 py27_0 statsmodels 0.6.1 np19py27_0 swig 3.0.2 0 sympy 0.7.6 py27_0 system 5.8 2 tables 3.1.1 terminado 0.5 py27_0 theano 0.6.0 np19py27_0 tk 8.5.18 0 toolz 0.7.1 py27_0 tornado 4.1 py27_0 ufl 1.4.0 py27_1 ujson 1.33 py27_0 unicodecsv 0.9.4 py27_0 util-linux 2.21 0 vtk 5.10.1 py27_1 werkzeug 0.10.1 py27_0 xlrd 0.9.3 py27_0 xlsxwriter 0.6.7 py27_0 xlwt 0.7.5 py27_0 yaml 0.1.4 0 zeromq 4.0.4 0 zlib 1.2.8 0 [xqian29@aci-service-1 python]$

[astrojuanlu]

Hello @xpqian, I think I solve the issue with slepc. Could you please do the following steps?

$ source activate fenics27
(fenics27) $ conda install "slepc==3.4.4" --channel https://conda.binstar.org/juanlu001/channel/fenics:1.4.0:centos"
(fenics27) $ conda list slepc
slepc    3.4.4     py27_3

The last line is the important one: build 3 is the updated build I just uploaded which should fix the problem.

[astrojuanlu]

Closing this issue, feel free to reopen if it persists.