libstdc++.so.6: version `GLIBCXX_3.4.20' not found

[astrojuanlu]

I have been testing the latest gcc package from Anaconda which should fix several portability issues (conda-archive/conda-recipes#279, thanks to @stuarteberg) for building my conda recipes for FEniCS. However, I am having some problems (at least on Arch Linux and Ubuntu 14.04) where some library calls fail with this error:

libstdc++.so.6: version GLIBCXX_3.4.20' not found`

Which happens because Anaconda libstdc++.so.6 is a bit too old:

$ strings ~/.miniconda3/envs/fenics_test/lib/libstdc++.so.6 | grep GLIBCXX
LIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_FORCE_NEW

(see for instance astrojuanlu/fenics-recipes#35 and astrojuanlu/fenics-recipes#36)

Is there a way to have a newer version of the library coming with conda? cc @ccordoba12

[ccordoba12]

So is this a mismatch between our package and the one that comes in Arch/Ubuntu?

I'm sorry but I don't completely understand the problem :-)

[ccordoba12]

I meant our gcc

[astrojuanlu]

Probably so @ccordoba12. The user that reported astrojuanlu/fenics-recipes#36 is now unable to use the packages when having gcc-4.9, while everything works fine on Ubuntu 14.04 when having gcc-4.8.

This problem appeared when I started using Anaconda gcc:

$ DISPLAY=:0 LIBGL_DEBUG=verbose python demo_poisson.py
Vendor:  Continuum Analytics, Inc.
Package: mkl
Message: trial mode expires in 30 days
Solving linear variational problem.
libGL: screen 0 does not appear to be DRI3 capable
libGL: pci id for fd 4: 10de:0641, driver nouveau
libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/tls/nouveau_dri.so
libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/nouveau_dri.so
libGL: dlopen /usr/lib/x86_64-linux-gnu/dri/nouveau_dri.so failed
(/home/earanda/anaconda/envs/fenics27/lib/python2.7/site-packages/ufc/../../../libstdc++.so.6:
version `GLIBCXX_3.4.20' not found (required by
/usr/lib/x86_64-linux-gnu/dri/nouveau_dri.so))
libGL: OpenDriver: trying ${ORIGIN}/dri/tls/nouveau_dri.so
libGL: OpenDriver: trying ${ORIGIN}/dri/nouveau_dri.so
libGL: dlopen ${ORIGIN}/dri/nouveau_dri.so failed
(/home/earanda/anaconda/envs/fenics27/lib/python2.7/site-packages/ufc/../../../libstdc++.so.6:
version `GLIBCXX_3.4.20' not found (required by
/usr/lib/x86_64-linux-gnu/dri/nouveau_dri.so))
libGL: OpenDriver: trying /usr/lib/dri/tls/nouveau_dri.so
libGL: OpenDriver: trying /usr/lib/dri/nouveau_dri.so
libGL: dlopen /usr/lib/dri/nouveau_dri.so failed
(/usr/lib/dri/nouveau_dri.so: cannot open shared object file: No such file
or directory)
libGL error: unable to load driver: nouveau_dri.so
libGL error: driver pointer missing
libGL error: failed to load driver: nouveau
libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/tls/swrast_dri.so
libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so
libGL: dlopen /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so failed
(/home/earanda/anaconda/envs/fenics27/lib/python2.7/site-packages/ufc/../../../libstdc++.so.6:
version `GLIBCXX_3.4.20' not found (required by
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so))
libGL: OpenDriver: trying ${ORIGIN}/dri/tls/swrast_dri.so
libGL: OpenDriver: trying ${ORIGIN}/dri/swrast_dri.so
libGL: dlopen ${ORIGIN}/dri/swrast_dri.so failed
(/home/earanda/anaconda/envs/fenics27/lib/python2.7/site-packages/ufc/../../../libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by
/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so))
libGL: OpenDriver: trying /usr/lib/dri/tls/swrast_dri.so
libGL: OpenDriver: trying /usr/lib/dri/swrast_dri.so
libGL: dlopen /usr/lib/dri/swrast_dri.so failed
(/usr/lib/dri/swrast_dri.so: cannot open shared object file: No such file
or directory)
libGL error: unable to load driver: swrast_dri.so
libGL error: failed to load driver: swrast
X Error of failed request:  BadValue (integer parameter out of range for
operation)
  Major opcode of failed request:  156 (GLX)
  Minor opcode of failed request:  3 (X_GLXCreateContext)
  Value in failed request:  0x0
  Serial number of failed request:  58
  Current serial number in output stream:  59

As you can see, libGL is failing to load because a graphic cards driver requires a newer version of GLIBCXX.

On Arch Linux a similar problem appears, but it's mixed with the fact that it's loading boost from the system instead of the one available in Anaconda. It's an unrelated issue (?) but it eventually causes the discussed one:

$ LD_LIBRARY_PATH= python ~/.miniconda3/envs/fenics_test/share/dolfin/demo/documented/poisson/python/demo_poisson.py 
In instant.import_module_directly: Failed to import module 'dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33' from '/home/juanlu/.instant/cache';
ImportError:/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/ufc/../../../libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /usr/lib/libboost_filesystem.so.1.58.0);
Failed to import module found in cache. Modulename: 'dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33';
Path: '/home/juanlu/.instant/cache';
ImportError:/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/ufc/../../../libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /usr/lib/libboost_filesystem.so.1.58.0);
Traceback (most recent call last):
  File "/home/juanlu/.miniconda3/envs/fenics_test/share/dolfin/demo/documented/poisson/python/demo_poisson.py", line 54, in <module>
    f = Expression("10*exp(-(pow(x[0] - 0.5, 2) + pow(x[1] - 0.5, 2)) / 0.02)")
  File "/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/dolfin/functions/expression.py", line 602, in __new__
    mpi_comm=mpi_comm)
  File "/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py", line 217, in compile_expressions
    mpi_comm=mpi_comm)
  File "/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py", line 145, in compile_expression_code
    mpi_comm=mpi_comm)
  File "/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", line 64, in mpi_jit
    return local_jit(*args, **kwargs)
  File "/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/dolfin/compilemodules/compilemodule.py", line 411, in compile_extension_module
    compiled_module = instant.import_module(module_name)
  File "/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/instant/cache.py", line 171, in import_module
    return check_disk_cache(modulename, cache_dir, moduleids)
  File "/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/instant/cache.py", line 139, in check_disk_cache
    module = import_and_cache_module(path, modulename, moduleids)
  File "/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/instant/cache.py", line 87, in import_and_cache_module
    instant_assert(module is not None, "Failed to import module found in cache. Modulename: '%s';\nPath: '%s';\n%s:%s;" % (modulename, path, type(e).__name__, e))
  File "/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/instant/output.py", line 91, in instant_assert
    raise AssertionError(text)
AssertionError: Failed to import module found in cache. Modulename: 'dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33';
Path: '/home/juanlu/.instant/cache';
ImportError:/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/ufc/../../../libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /usr/lib/libboost_filesystem.so.1.58.0);

[stuarteberg]

The anaconda gcc and libgcc packages are made with gcc 4.8.5. That means they use libstdc++ version 3.4.19 (See here.)

If one of your packages is trying to find symbols from libstdc++ version 3.4.20, then you must have built that package using your own version of gcc and/or libstdc++ (i.e. you used your OS's version of libstdc++, not the version from Anaconda.

Looking at the FEniCS recipes, I notice a few issues. You should update all of your recipes to follow the rules below, at least when building C++ packages

• In meta.yaml, always include gcc as a build dependency, never a run dependency.
• If the recipe requires gcc to build, then you must list libgcc as run dependency.
• In your build.sh, make sure you are using the anaconda-provided gcc binary as your compiler. Do this by setting the CC and CXX variables at the top of your build script. For example:

CC=${PREFIX}/bin/gcc
CXX=${PREFIX}/bin/g++

./configure --prefix=${PREFIX}
make
make install

For CMake-based projects, you can set these at configure time:

mkdir build
cd build
cmake .. \
    -DCMAKE_C_COMPILER=${PREFIX}/bin/gcc \
    -DCMAKE_CXX_COMPILER=${PREFIX}/bin/g++ \
    -DCMAKE_INSTALL_PREFIX=${PREFIX} \
    ........

make
make install

Finally, regarding glibc compatibility (not C++ compatibility): It's worth noting that the Anaconda maintainers build everything on CentOS 5.11. That way, the resulting binaries always run on newer versions of Linux. I do the same for my own packages.

[stuarteberg]

On Arch Linux a similar problem appears, but it's mixed with the fact that it's loading boost from the system instead of the one available in Anaconda.

You should fix this by helping the dolphin build scripts locate the correct copy of boost. It looks like you may be able to do this via an environment variable:

https://bitbucket.org/fenics-project/dolfin/src/fe82e5a5ffa4a5625b327bfdbdd60084a6847699/CMakeLists.txt?at=master&fileviewer=file-view-default#CMakeLists.txt-306

(That's a little weird to me.) In my own recipes, I usually pass some cache variables to the cmake step, which are recognized by cmake's find_package(Boost) function. See, for example:
https://github.com/ilastik/ilastik-build-conda/blob/master/vigra/build.sh#L48

[astrojuanlu]

Thanks a lot for your advice @stuarteberg, it's very much appreciated. This was my first real world experience with compilers so a little bit of help is very valuable :) I will try and implement these changes in the following days.

[astrojuanlu]

Let's talk about these specific issues elsewhere though.

[stuarteberg]

As you can see, libGL is failing to load because a graphic cards driver requires a newer version of GLIBCXX.

As an experiment, I wonder what happens if you manually replace the anaconda/envs/fenics27/lib/libstdc++.so.6 with a symlink to your OS's copy of libstdc++.so.6. If that works, then perhaps you could come up with a hack to apply that as a post-install step for the environments you create.

[ccordoba12]

@Juanlu001, I'm afraid that even after following @stuarteberg advice you're going to keep having the same problems.

And that's because Fenics is trying to load libGL. Since it can't find it in Anaconda, it looks for it on the system, only to to find that libGL was compiled with a newer gcc :-(

[stuarteberg]

@Juanlu001, I'm afraid that even after following @stuarteberg advice you're going to keep having the same problems.

I agree with Carlos. I think your best option is to try the experiment I mentioned above, unless anyone has other ideas.

[astrojuanlu]

@Juanlu001, I'm afraid that even after following @stuarteberg advice you're going to keep having the same problems.

I agree with Carlos. I think your best option is to try the experiment I mentioned above, unless anyone has other ideas.

I see. Actually visualization support via VTK is a major blocking point for building the packages on anaconda.org, so it seems I will have to devise some hack as @stuarteberg suggested before, or state that it is not portable at all.

Thanks again for your input!