Hi, A small follow-up question. I am getting to know the FEniCS software by trying some demos. I often get errors like:
DOLFIN has not been configured with PETSc. Exiting. > DOLFIN has not been configured with SLEPc. Exiting. > DOLFIN must be compiled with CGAL to run this demo. > Can I somehow just install these libraries myself, or is it the Anaconda package maintainer who has to recompile dolfin using the appropriate version of these libraries? Maarten On 29 January 2015 at 17:54, Juan Luis Cano <[email protected]> wrote: > On 2015-01-29 17:08, Maarten wrote: > > 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 I have tried the (apparently outdated) dorsal script, the 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 > > > Oh I am so happy to read that! :D Thank you very much for your patience > and perseveration, I have learned a lot of things about compilation and > dynamic linking thanks to this and I am glad it finally helped you. > > Good luck with your Linux & FEniCS journey :) Hope this long discussion > helps others too! > > Regards, > > Juan Luis > > > > 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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