cmake 3.9.1 seems to have been built with too new libstdc++

[ezyang]

Take a look at https://anaconda.org/anaconda/cmake/3.9.1/download/linux-64/cmake-3.9.1-hd1fb129_0.tar.bz2 which is the most recent upload for cmake on linux64:

$ strings bin/cmake | grep GLIBCXX_3.4.20
GLIBCXX_3.4.20
_ZSt24__throw_out_of_range_fmtPKcz@@GLIBCXX_3.4.20

This requires a more recent libstdc++ than Anaconda is currently shipping, see https://repo.continuum.io/pkgs/main/linux-64/libstdcxx-ng-7.2.0-h7a57d05_2.tar.bz2 (also c.f. #483)

strings /private/home/ezyang/pytorch/env/lib/libstdc++.so | grep ^GLIBCXX
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
GLIBCXX_DEBUG_MESSAGE_LENGTH
$ conda list | grep stdcxx
libstdcxx-ng              7.2.0                h7a57d05_2  

By the way, the previous patch release (visible at https://anaconda.org/anaconda/libstdcxx-ng/files ; in fact the new _2 package is not visible yet) had the necessary symbols. So, this only just started being broken three days ago, according to the timestamp on the new package version.

CC @kalefranz who is marked as the uploader for libstdcxx-ng on https://anaconda.org/anaconda/libstdcxx-ng/files

Also, the error message you get when this is broken is:

$ cmake --version
cmake: /private/home/ezyang/pytorch/env/bin/../lib/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by cmake)
cmake: /private/home/ezyang/pytorch/env/bin/../lib/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by cmake)
cmake: /private/home/ezyang/pytorch/env/bin/../lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by cmake)

[nehaljwani]

CC @msarahan

[jjhelmus]

The libstdc++.so library from the libstdcxx-ng-7.2.0-h7a57d05_2.tar.bz2 package includes 3.4.20 as well as newer symbols:

$ strings ~/anaconda3/envs/cmake2/lib/libstdc++.so | grep GLIBCXX_3.4.2
GLIBCXX_3.4.2
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
GLIBCXX_3.4.21
GLIBCXX_3.4.24
GLIBCXX_3.4.20
GLIBCXX_3.4.2
GLIBCXX_3.4.23
GLIBCXX_3.4.22

@ezyang Can you provide the output of conda list in the environment that is causing issues.

My guess is that the libstdc++.so file from the gcc-4.8.5-7.tar.bz2 package is clobbering the libstdc++.so from libstdcxx-ng-7.2.0-h7a57d05_2.tar.bz2. Is gcc 4.8.5 installed in that environment?

The gcc package should not be used with the newer libraries. If compilers are needed the gcc_linux-64 and gxx_linux-64 packages should be used.

[ezyang]

The problem is definitely from 'gcc' clobbering libstdc++. We will stop advising our users to install the 'gcc' package.