Hello again, I installed everything again locally from scratch, including anaconda. I made sure $LD_LIBRARY_PATH was empty before installing anything, as this seemed to be the culprit indeed. This time 'import dolfin' worked without problems, just as a demo I tried \o/
I have tried the (apparently outdated) dorsal script, the (not-yet-for-every-platform) new install script — compiling all packages from scratch, but now it finally works! Granted, CentOS might not be the most thankful platform to support, but I think anaconda and this FEniCS package will make life a lot easier for the not-entirely-familiar-with-linux-yet folks like me. Thanks! Maarten On 28 January 2015 at 23:12, Juan Luis Cano <[email protected]> wrote: > On 2015-01-28 14:22, Maarten wrote: > > Almost there (I hope)! I removed everything (step 7) and installed again > with "conda install "fenics=1.4.0" mkl --channel > https://conda.binstar.org/juanlu001/channel/fenics:1.4.0:centos";. Here is > the result again. > > >>> import dolfin >> Traceback (most recent call last): >> File "<stdin>", line 1, in <module> >> File >> "<INSTALL_PATH>/anaconda/lib/python2.7/site-packages/dolfin/__init__.py", >> line 16, in <module> >> import cpp >> File >> "<INSTALL_PATH>/anaconda/lib/python2.7/site-packages/dolfin/cpp/__init__.py", >> line 42, in <module> >> exec("import %s" % module_name) >> File "<string>", line 1, in <module> >> File >> "<INSTALL_PATH>/anaconda/lib/python2.7/site-packages/dolfin/cpp/common.py", >> line 32, in <module> >> _common = swig_import_helper() >> File >> "<INSTALL_PATH>/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: >> <OTHER_INSTALL_PATH>/bin/opt/intel/ifc12.1/composer_xe_2011_sp1.9.293/mkl/lib/intel64/libmkl_sequential.so: >> undefined symbol: mkl_serv_mkl_print >> > > Hoping this will be the last hurdle. > > > Hmmm... I am afraid this will be a harder one :/ > > The problem is that you already have a working MKL in your system (in > <OTHER_INSTALL_PATH>/bin/opt/intel/ifc12.1/composer_xe_2011_sp1.9.293/mkl/) > and thus dolfin is ignoring the one in <INSTALL_PATH>/anaconda/lib/. Some > version mismatch is probably causing the problem. > > I guess your output of > > $ ldd .../_common.so | grep libmkl_sequential.so > > points to <OTHER_INSTALL_PATH>. The only thing I can think of is that you > may have a non empty $LD_LIBRARY_PATH, and this is modifying the > directories where the libraries are looked up. If I am correct, stripping > the corresponding path from $LD_LIBRARY_PATH and repeating the ldd step > should yield the MKL libraries located in the conda environment. I might > not be correct though, and perhaps there is something I misunderstood from > the conda building process... > > In case this doesn't work, I don't really know what else you can do. The > only other thing I can suggest you is removing the conda mkl package and > rebuilding petsc, petsc4py and dolfin yourself. In petsc/build.sh, you have > to change "--with-blas-lapack-dir", and in dolfin/build.sh you have to > change BLAS_DIR. (Also, you have to remove "mkl" from all the recipes). > > If you start rebuilding the packages, conda will try to build the > dependencies recursively. In case you want to avoid this, you should add my > channel to the list of default channels: > > $ conda config --add channel > https://conda.binstar.org/juanlu001/channel/fenics:1.4.0:centos > > Lastly, make sure you increment the build numbers in */meta.yaml to avoid > problems with the cached packages, as happened with boost (that one was my > fault). > > Good luck! > > Juan Luis Cano >
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