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

Question

To upload the raw-reads > 2GB to SRA on Genebank, I installed aspera connect plug-in on ubuntu 16.04. But the plug-in did not pop up as indicated by the instruction on the genebank SRA portal.

I got this error on the terminal as I initializing the plug-in locally (~/.aspera/connect/bin/asperaconnect):

lib/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /usr/lib/x86_64-linux-gnu/libproxy.so.1)
Failed to load module: /usr/lib/x86_64-linux-gnu/gio/modules/libgiolibproxy.so

I followed some of the threads, created a link to /usr/lib/libstdc++.so.6 But it did not address the problem, still showing the error message above. running strings /usr/lib/libstdc++.so.6 | grep GLIBCXX got this:

strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | 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_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_DEBUG_MESSAGE_LENGTH

GLIBCXX_3.4.20 is in the list. I don't know how to make the plug-in recognize that.

Thank you, Xp

Answer 1

On CentOS v7.9.2009 STANDARD kvm, I solved by searching for "libstdc++" on the entire machine, by using find:

find / -name "libstdc++.*" 2>/dev/null

Then, I found a new libstdc++ version on an Plesk installation on /home/virtfs/[username]/usr/lib64/c++-plesk-10.3.0/lib64/libstdc++.so.6.0.28 that meets VSCode requirements of GLIBCXX_3.4.20 and CXXABI_1.3.9 (that's why I've landed on this answer btw so sorry the off-topic).

So I made a backup of the actual /lib64/libstdc++.so.6, and did a new symlink to that Plesk lib:

ln -s /home/virtfs/[username]/usr/lib64/c++-plesk-10.3.0/lib64/libstdc++.so.6.0.28 /lib64/libstdc++.so.6

Then tried to connect to the server through VSCode Remote SSH and voila!

I don't know if it will mess up another compiler request in WHM but if that's the case, that's why I backed up the original symlink.

Answer 2

I also ran into this while installing h3. The answer by oklas helped me, but expanding on that answer. The gcc version with conda install -c anaconda gcc is 4.8.5. It is not compatible with the libstdc++.so.6.0.22. So I uninstalled it and installed a specific verision of gcc (ver 6) and it solved my problem.

Answer 3

I solved problem like this (but GLIBCXX_3.4.21 on CentOS) but it is not dependent from os. The library is part of gcc compiler so need to install or compile appropriate version of gcc. This is table of versions of gcc and versions of appropriate libstdc++:

GCC 4.9.0: libstdc++.so.6.0.20
GCC 5.1.0: libstdc++.so.6.0.21
GCC 6.1.0: libstdc++.so.6.0.22
GCC 7.1.0: libstdc++.so.6.0.23
GCC 7.2.0: libstdc++.so.6.0.24
GCC 8.0.0: libstdc++.so.6.0.25

( full list of versions is here )

It is not dependent from how to install gcc - it may be installed from package or compiled and installed from sources.

It is possible that system gcc libraries is available instead of newely installed. So need to specify environment variable where to find libraries for example in command line like this:

$ LD_LIBRARY_PATH=/usr/local/lib64 command args ...

Answer 4

Here's a solution for this problem in Ubuntu 16.04

sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install gcc-4.9
sudo apt-get upgrade libstdc++6

You can check if you get GLIBCXX desired version like this:

strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX

Answer 5

answer for lazy ppl this should fix situation in most cases

apt-get update && apt-get install sudo && \
sudo apt-get install build-essential software-properties-common -y && \
sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y && \
sudo add-apt-repository ppa:george-edison55/cmake-3.x -y && \
sudo apt-get update && \
sudo apt-get install gcc-snapshot -y && \
sudo apt-get update && \
sudo apt-get install gcc-6 g++-6 -y && \
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-6 60 --slave /usr/bin/g++ g++ /usr/bin/g++-6 && \
sudo apt-get install gcc-4.8 g++-4.8 -y && \
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 40 --slave /usr/bin/g++ g++ /usr/bin/g++-4.8 && \
sudo update-alternatives --config gcc && \
sudo apt-get update && \
sudo apt-get install cmake -y;

Answer 6

Considering that /usr/lib/x86_64-linux-gnu/libproxy.so.1 is supplied by Ubuntu, let's assume that it is compatible with the system libstdc++ library. This means that the application is not actually using that system library, but some other version. I'd suggest to check if the application sets LD_LIBRARY_PATH and if there is another copy of libstdc++.so.6 on that path. In this case, try moving it away or deleting it—the application should then switch to the system library, which is newer and should be backwards-compatible.