{"action":"created","issue":{"url":"https://api.github.com/repos/ContinuumIO/anaconda-issues/issues/483","labels_url":"https://api.github.com/repos/ContinuumIO/anaconda-issues/issues/483/labels{/name}","comments_url":"https://api.github.com/repos/ContinuumIO/anaconda-issues/issues/483/comments","events_url":"https://api.github.com/repos/ContinuumIO/anaconda-issues/issues/483/events","html_url":"https://github.com/ContinuumIO/anaconda-issues/issues/483","id":112166932,"number":483,"title":"libstdc++.so.6: version `GLIBCXX_3.4.20' not found","user":{"login":"Juanlu001","id":316517,"avatar_url":"https://avatars.githubusercontent.com/u/316517?v=3","gravatar_id":"","url":"https://api.github.com/users/Juanlu001","html_url":"https://github.com/Juanlu001","followers_url":"https://api.github.com/users/Juanlu001/followers","following_url":"https://api.github.com/users/Juanlu001/following{/other_user}","gists_url":"https://api.github.com/users/Juanlu001/gists{/gist_id}","starred_url":"https://api.github.com/users/Juanlu001/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Juanlu001/subscriptions","organizations_url":"https://api.github.com/users/Juanlu001/orgs","repos_url":"https://api.github.com/users/Juanlu001/repos","events_url":"https://api.github.com/users/Juanlu001/events{/privacy}","received_events_url":"https://api.github.com/users/Juanlu001/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/ContinuumIO/anaconda-issues/labels/Linux","name":"Linux","color":"009800"}],"state":"open","locked":false,"assignee":{"login":"ccordoba12","id":365293,"avatar_url":"https://avatars.githubusercontent.com/u/365293?v=3","gravatar_id":"","url":"https://api.github.com/users/ccordoba12","html_url":"https://github.com/ccordoba12","followers_url":"https://api.github.com/users/ccordoba12/followers","following_url":"https://api.github.com/users/ccordoba12/following{/other_user}","gists_url":"https://api.github.com/users/ccordoba12/gists{/gist_id}","starred_url":"https://api.github.com/users/ccordoba12/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ccordoba12/subscriptions","organizations_url":"https://api.github.com/users/ccordoba12/orgs","repos_url":"https://api.github.com/users/ccordoba12/repos","events_url":"https://api.github.com/users/ccordoba12/events{/privacy}","received_events_url":"https://api.github.com/users/ccordoba12/received_events","type":"User","site_admin":false},"milestone":null,"comments":3,"created_at":"2015-10-19T15:16:19Z","updated_at":"2015-10-19T16:14:22Z","closed_at":null,"body":"I have been testing the latest gcc package from Anaconda which should fix several portability issues (https://github.com/conda/conda-recipes/pull/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:\r\n\r\n```libstdc++.so.6: version `GLIBCXX_3.4.20' not found```\r\n\r\nWhich happens because Anaconda libstdc++.so.6 is a bit too old:\r\n\r\n```bash\r\n$ strings ~/.miniconda3/envs/fenics_test/lib/libstdc++.so.6 | grep GLIBCXX\r\nLIBCXX\r\nGLIBCXX_3.4\r\nGLIBCXX_3.4.1\r\nGLIBCXX_3.4.2\r\nGLIBCXX_3.4.3\r\nGLIBCXX_3.4.4\r\nGLIBCXX_3.4.5\r\nGLIBCXX_3.4.6\r\nGLIBCXX_3.4.7\r\nGLIBCXX_3.4.8\r\nGLIBCXX_3.4.9\r\nGLIBCXX_3.4.10\r\nGLIBCXX_3.4.11\r\nGLIBCXX_3.4.12\r\nGLIBCXX_3.4.13\r\nGLIBCXX_3.4.14\r\nGLIBCXX_3.4.15\r\nGLIBCXX_3.4.16\r\nGLIBCXX_3.4.17\r\nGLIBCXX_3.4.18\r\nGLIBCXX_3.4.19\r\nGLIBCXX_FORCE_NEW\r\n```\r\n\r\n(see for instance https://github.com/Juanlu001/fenics-recipes/issues/35 and https://github.com/Juanlu001/fenics-recipes/issues/36)\r\n\r\nIs there a way to have a newer version of the library coming with conda? cc @ccordoba12"},"comment":{"url":"https://api.github.com/repos/ContinuumIO/anaconda-issues/issues/comments/149262353","html_url":"https://github.com/ContinuumIO/anaconda-issues/issues/483#issuecomment-149262353","issue_url":"https://api.github.com/repos/ContinuumIO/anaconda-issues/issues/483","id":149262353,"user":{"login":"Juanlu001","id":316517,"avatar_url":"https://avatars.githubusercontent.com/u/316517?v=3","gravatar_id":"","url":"https://api.github.com/users/Juanlu001","html_url":"https://github.com/Juanlu001","followers_url":"https://api.github.com/users/Juanlu001/followers","following_url":"https://api.github.com/users/Juanlu001/following{/other_user}","gists_url":"https://api.github.com/users/Juanlu001/gists{/gist_id}","starred_url":"https://api.github.com/users/Juanlu001/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Juanlu001/subscriptions","organizations_url":"https://api.github.com/users/Juanlu001/orgs","repos_url":"https://api.github.com/users/Juanlu001/repos","events_url":"https://api.github.com/users/Juanlu001/events{/privacy}","received_events_url":"https://api.github.com/users/Juanlu001/received_events","type":"User","site_admin":false},"created_at":"2015-10-19T16:14:21Z","updated_at":"2015-10-19T16:14:21Z","body":"Probably so @ccordoba12. The user that reported https://github.com/Juanlu001/fenics-recipes/issues/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`.\r\n\r\nThis problem appeared when I started using Anaconda `gcc`:\r\n\r\n```\r\n$ DISPLAY=:0 LIBGL_DEBUG=verbose python demo_poisson.py\r\nVendor:  Continuum Analytics, Inc.\r\nPackage: mkl\r\nMessage: trial mode expires in 30 days\r\nSolving linear variational problem.\r\nlibGL: screen 0 does not appear to be DRI3 capable\r\nlibGL: pci id for fd 4: 10de:0641, driver nouveau\r\nlibGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/tls/nouveau_dri.so\r\nlibGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/nouveau_dri.so\r\nlibGL: dlopen /usr/lib/x86_64-linux-gnu/dri/nouveau_dri.so failed\r\n(/home/earanda/anaconda/envs/fenics27/lib/python2.7/site-packages/ufc/../../../libstdc++.so.6:\r\nversion `GLIBCXX_3.4.20' not found (required by\r\n/usr/lib/x86_64-linux-gnu/dri/nouveau_dri.so))\r\nlibGL: OpenDriver: trying ${ORIGIN}/dri/tls/nouveau_dri.so\r\nlibGL: OpenDriver: trying ${ORIGIN}/dri/nouveau_dri.so\r\nlibGL: dlopen ${ORIGIN}/dri/nouveau_dri.so failed\r\n(/home/earanda/anaconda/envs/fenics27/lib/python2.7/site-packages/ufc/../../../libstdc++.so.6:\r\nversion `GLIBCXX_3.4.20' not found (required by\r\n/usr/lib/x86_64-linux-gnu/dri/nouveau_dri.so))\r\nlibGL: OpenDriver: trying /usr/lib/dri/tls/nouveau_dri.so\r\nlibGL: OpenDriver: trying /usr/lib/dri/nouveau_dri.so\r\nlibGL: dlopen /usr/lib/dri/nouveau_dri.so failed\r\n(/usr/lib/dri/nouveau_dri.so: cannot open shared object file: No such file\r\nor directory)\r\nlibGL error: unable to load driver: nouveau_dri.so\r\nlibGL error: driver pointer missing\r\nlibGL error: failed to load driver: nouveau\r\nlibGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/tls/swrast_dri.so\r\nlibGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so\r\nlibGL: dlopen /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so failed\r\n(/home/earanda/anaconda/envs/fenics27/lib/python2.7/site-packages/ufc/../../../libstdc++.so.6:\r\nversion `GLIBCXX_3.4.20' not found (required by\r\n/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so))\r\nlibGL: OpenDriver: trying ${ORIGIN}/dri/tls/swrast_dri.so\r\nlibGL: OpenDriver: trying ${ORIGIN}/dri/swrast_dri.so\r\nlibGL: dlopen ${ORIGIN}/dri/swrast_dri.so failed\r\n(/home/earanda/anaconda/envs/fenics27/lib/python2.7/site-packages/ufc/../../../libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by\r\n/usr/lib/x86_64-linux-gnu/dri/swrast_dri.so))\r\nlibGL: OpenDriver: trying /usr/lib/dri/tls/swrast_dri.so\r\nlibGL: OpenDriver: trying /usr/lib/dri/swrast_dri.so\r\nlibGL: dlopen /usr/lib/dri/swrast_dri.so failed\r\n(/usr/lib/dri/swrast_dri.so: cannot open shared object file: No such file\r\nor directory)\r\nlibGL error: unable to load driver: swrast_dri.so\r\nlibGL error: failed to load driver: swrast\r\nX Error of failed request:  BadValue (integer parameter out of range for\r\noperation)\r\n  Major opcode of failed request:  156 (GLX)\r\n  Minor opcode of failed request:  3 (X_GLXCreateContext)\r\n  Value in failed request:  0x0\r\n  Serial number of failed request:  58\r\n  Current serial number in output stream:  59\r\n```\r\n\r\nAs you can see, libGL is failing to load because a graphic cards driver requires a newer version of `GLIBCXX`.\r\n\r\nOn Arch Linux a similar problem appears, but it's mixed with the fact that it's loading boost from the system instead of the one available in Anaconda. It's an unrelated issue (?) but it eventually causes the discussed one:\r\n\r\n```\r\n$ LD_LIBRARY_PATH= python ~/.miniconda3/envs/fenics_test/share/dolfin/demo/documented/poisson/python/demo_poisson.py \r\nIn instant.import_module_directly: Failed to import module 'dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33' from '/home/juanlu/.instant/cache';\r\nImportError:/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);\r\nFailed to import module found in cache. Modulename: 'dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33';\r\nPath: '/home/juanlu/.instant/cache';\r\nImportError:/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);\r\nTraceback (most recent call last):\r\n  File \"/home/juanlu/.miniconda3/envs/fenics_test/share/dolfin/demo/documented/poisson/python/demo_poisson.py\", line 54, in <module>\r\n    f = Expression(\"10*exp(-(pow(x[0] - 0.5, 2) + pow(x[1] - 0.5, 2)) / 0.02)\")\r\n  File \"/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/dolfin/functions/expression.py\", line 602, in __new__\r\n    mpi_comm=mpi_comm)\r\n  File \"/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py\", line 217, in compile_expressions\r\n    mpi_comm=mpi_comm)\r\n  File \"/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py\", line 145, in compile_expression_code\r\n    mpi_comm=mpi_comm)\r\n  File \"/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/dolfin/compilemodules/jit.py\", line 64, in mpi_jit\r\n    return local_jit(*args, **kwargs)\r\n  File \"/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/dolfin/compilemodules/compilemodule.py\", line 411, in compile_extension_module\r\n    compiled_module = instant.import_module(module_name)\r\n  File \"/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/instant/cache.py\", line 171, in import_module\r\n    return check_disk_cache(modulename, cache_dir, moduleids)\r\n  File \"/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/instant/cache.py\", line 139, in check_disk_cache\r\n    module = import_and_cache_module(path, modulename, moduleids)\r\n  File \"/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/instant/cache.py\", line 87, in import_and_cache_module\r\n    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))\r\n  File \"/home/juanlu/.miniconda3/envs/fenics_test/lib/python2.7/site-packages/instant/output.py\", line 91, in instant_assert\r\n    raise AssertionError(text)\r\nAssertionError: Failed to import module found in cache. Modulename: 'dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33';\r\nPath: '/home/juanlu/.instant/cache';\r\nImportError:/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);\r\n```"}}