libstdc++.so.6 from GCC requires GLIBC_2.33 but gets linked with glibc-2.32

[pshirshov]

JNI libraries which need libstdc++.so.6 fail to load under IntelliJ IDEA.
Seems like something is wrong with gcc package or the way LD_LIBRARY_PATH is defined in the jetbrains formula.

Error messages look like

 java.lang.UnsatisfiedLinkError: java.lang.UnsatisfiedLinkError: /tmp/librocksdbjni18325293990181609010.so: 
/nix/store/jsp3h3wpzc842j0rz61m5ly71ak6qgdn-glibc-2.32-54/lib/libc.so.6: version `GLIBC_2.33' not found 
(required by /nix/store/vyqnqbp3yczrzjx2byk6p680q3mzanyw-gcc-10.3.0-lib/lib/libstdc++.so.6)

A quick search over the issues shows that other people experience similar linking issues with other software:

1. [20.03] rstudio is broken #85921 (comment)
2. Mangohud not worked #134679 (comment)

etc

At the same time everything works in FHS environments, for some reason glibc version is correct there:

❯ ls -la /usr/lib|grep libc
lrwxrwxrwx    79 nobody nogroup  1 Jan  1970  libc-2.33.so -> /nix/store/4ikqdj43z39bchjfr462izwbh2w3nbnm-javaenv-usr-target/lib/libc-2.33.so

I'm not sure if this problem is related to IDEA or stdenv/gcc, but I noticed that the formula for Android Studio uses FHS env, maybe IDEA should do that as well?

[Artturin]

How to repro?

[veprbl]

Likely a duplicate of #84043

[pshirshov]

How to repro?

Install intellij idea, create a simple java/kotlin/scala project trying to initialize rocksdb and run it. I may provide a test project if necessary.

[Ma27]

I'm not really sure if that'll trigger the problem. There is an issue template for a reason though. Please provide the information that's requested in there.

[pshirshov]

Oh, don't worry, it definitely will.

nix-info output:

❯ nix-shell -p nix-info --run "nix-info -m"
 - system: `"x86_64-linux"`
 - host os: `Linux 5.13.16, NixOS, 21.11 (Porcupine)`
 - multi-user?: `yes`
 - sandbox: `yes`
 - version: `nix-env (Nix) 2.4pre20210908_3c56f62`
 - channels(root): `"nixos-21.11pre317242.bc9b956714e, home-manager"`
 - channels(pavel): `""`
 - nixpkgs: `/nix/var/nix/profiles/per-user/root/channels/nixos`

I'm not sure if it would help anyone if I re-format the issue report according to the template, so I would probably leave it as is.

[Ma27]

OK, I see :) Would you mind creating such a simple project if possible? That'd speed up the reproduction significantly for me :)

[pshirshov]

I'm unable to reproduce the problem directly in the shell:

~ on ☁️  (eu-west-1) took 1m47s
❯ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/nix/store/0kiykyrnrpfhmjwxwx89kxr20hmf5304-gcc-10.3.0-lib/lib/

~ on ☁️  (eu-west-1)
❯ export _JAVA_OPTIONS="-Djava.library.path=`pwd`"

~ on ☁️  (eu-west-1)
❯ jshell
Picked up _JAVA_OPTIONS: -Djava.library.path=/home/pavel
|  Welcome to JShell -- Version 11.0.12
|  For an introduction type: /help intro

jshell> System.loadLibrary("rocksdbjni-linux64");

jshell>

But a project under IDEA, doing exactly the same thing, fails. Possibly the issue is not related to IDEA itself but something is wrong with graalvm formula.

I'll make a repro.

[pshirshov]

Actually I guess the most interesting question is why do I have two glibc versions in my system? I believe that shouldn't be possible with nix versioning model?..

[pshirshov]

Well, the problem is solved. Wrong glibc version had been pulled by home-manager.

[t-chab]

@pshirshov : how did you solved it ? I have the same issue with IntelliJ and I'm also using home-manager

[Artturin]

check your channels

[t-chab]

@Artturin : they seems fine to me, but perhaps I miss something, I'm a nix noob 🥵

[Artturin]

sudo nix-channel --list to list your root channels
if there is a nixos channel then you shouldn't have a nixpkgs channel in your user channels nix-channel --remove nixpkgs

[t-chab]

@Artturin : I don't have any nixos root channel. I'm currently using Nix installed on an Ubuntu 20.04 LTS

[Artturin]

do you have packages installed with nix-env?(other than home-manager) if so remove them
nix-env -q to list them
nix-env -e name

[t-chab]

Only two :

Should I remove nix ?

[Artturin]

not sure but probably not.

try garbage collecting nix-collect-garbage --delete-older-than 1m

[t-chab]

@Artturin : I now have a slighty different message, and I wonder if the problem is not related to an ubuntu package ?

Traceback (most recent call last):
  File "/usr/lib/command-not-found", line 28, in <module>
    from CommandNotFound import CommandNotFound
  File "/usr/lib/python3/dist-packages/CommandNotFound/CommandNotFound.py", line 19, in <module>
    from CommandNotFound.db.db import SqliteDatabase
  File "/usr/lib/python3/dist-packages/CommandNotFound/db/db.py", line 5, in <module>
    import apt_pkg
ImportError: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by /nix/store/7fv9v6mnlkb4ddf9kz1snknbvbfbcbx0-gcc-10.3.0-lib/lib/libstdc++.so.6)

because after purging ubuntu package command-not-found I no longer have the issue.

Thanks a lot for your help.

[coderfromhere]

How was this fixed? I don't use home-manager and I hven't installed anything with nix-env, still I'm getting the same GLIBC_2.33 not found error on my pure nix builds:

nix-build: /nix/store/jsp3h3wpzc842j0rz61m5ly71ak6qgdn-glibc-2.32-54/lib/libc.so.6: version `GLIBC_2.33' not found (required by /nix/store/7fv9v6mnlkb4ddf9kz1snknbvbfbcbx0-gcc-10.3.0-lib/lib/libstdc++.so.6)
make: *** [Makefile:113: build] Error 1

UPD: I've found the issue. My Nix shell was using the LD_LIBRARY_PATH hack explained in https://nixos.wiki/wiki/Packaging/Quirks_and_Caveats under the section ImportError: libstdc++.so.6: cannot open shared object file: No such file to fix certain issues with discoverability in interpreted langauges, and this was causing the above GLIBC_2.33 exception. Everything works if I remove the LD_LIBRARY_PATH fixed prefix.

[nixos-discourse]

This issue has been mentioned on NixOS Discourse. There might be relevant details there:

https://discourse.nixos.org/t/proper-setup-for-python-development-with-nix-and-vs-code/19011/1