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glibc warning and install wheel #11348

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busFred opened this issue Mar 19, 2025 · 7 comments
Open

glibc warning and install wheel #11348

busFred opened this issue Mar 19, 2025 · 7 comments
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@hcho3

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@busFred
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busFred commented Mar 19, 2025 •
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I'm not sure if this is more of a question or issue but i'm getting warning when importing xgboost.

(tmplafa) ~/Documents/research/afa/template-afa$ python
Python 3.13.2 | packaged by Anaconda, Inc. | (main, Feb  6 2025, 18:56:02) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import xgboost as xgbst
/home/hungtien/anaconda3/envs/tmplafa/lib/python3.13/site-packages/xgboost/core.py:377: FutureWarning: Your system has an old version of glibc (< 2.28). We will stop supporting Linux distros with glibc older than 2.28 after **May 31, 2025**. Please upgrade to a recent Linux distro (with glibc >= 2.28) to use future versions of XGBoost.
Note: You have installed the 'manylinux2014' variant of XGBoost. Certain features such as GPU algorithms or federated learning are not available. To use these features, please upgrade to a recent Linux distro with glibc 2.28+, and install the 'manylinux_2_28' variant.
  warnings.warn(

I followed instruction found on google to check glibc version installed on my system, which is higher (2.39>2.28) than what xgboost consider as old version of glibc.

(tmplafa) ~/Documents/research/afa/template-afa$ ldd --version
ldd (Ubuntu GLIBC 2.39-0ubuntu8.4) 2.39
Copyright (C) 2024 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.
(tmplafa) ~/Documents/research/afa/template-afa$ strings /usr/lib/x86_64-linux-gnu/libc.so.6|grep GLIBC_
GLIBC_2.2.5
GLIBC_2.2.6
GLIBC_2.3
GLIBC_2.3.2
GLIBC_2.3.3
GLIBC_2.3.4
GLIBC_2.4
GLIBC_2.5
GLIBC_2.6
GLIBC_2.7
GLIBC_2.8
GLIBC_2.9
GLIBC_2.10
GLIBC_2.11
GLIBC_2.12
GLIBC_2.13
GLIBC_2.14
GLIBC_2.15
GLIBC_2.16
GLIBC_2.17
GLIBC_2.18
GLIBC_2.22
GLIBC_2.23
GLIBC_2.24
GLIBC_2.25
GLIBC_2.26
GLIBC_2.27
GLIBC_2.28
GLIBC_2.29
GLIBC_2.30
GLIBC_2.31
GLIBC_2.32
GLIBC_2.33
GLIBC_2.34
GLIBC_2.35
GLIBC_2.36
GLIBC_2.38
GLIBC_2.39
GLIBC_ABI_DT_RELR
GLIBC_PRIVATE
(tmplafa) hungtien@hungtien-T480s-Linux:~/Documents/research/afa/template-afa$

I also tried reinstalling xgboost-cpu with pip but it still installs the the manylinux2014 variant.

(tmplafa) ~/Documents/research/afa/template-afa$ pip uninstall xgboost-cpu
Found existing installation: xgboost-cpu 3.0.0
Uninstalling xgboost-cpu-3.0.0:
  Would remove:
    /home/hungtien/anaconda3/envs/tmplafa/lib/python3.13/site-packages/xgboost/*
    /home/hungtien/anaconda3/envs/tmplafa/lib/python3.13/site-packages/xgboost_cpu-3.0.0.dist-info/*
    /home/hungtien/anaconda3/envs/tmplafa/lib/python3.13/site-packages/xgboost_cpu.libs/libgomp-a34b3233.so.1.0.0
Proceed (Y/n)? y
  Successfully uninstalled xgboost-cpu-3.0.0
(tmplafa) ~/Documents/research/afa/template-afa$ pip install xgboost-cpu --no-cache-dir
Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com
Collecting xgboost-cpu
  Downloading xgboost_cpu-3.0.0-py3-none-manylinux2014_x86_64.whl.metadata (2.6 kB)
Requirement already satisfied: numpy in /home/hungtien/anaconda3/envs/tmplafa/lib/python3.13/site-packages (from xgboost-cpu) (2.1.3)
Requirement already satisfied: scipy in /home/hungtien/anaconda3/envs/tmplafa/lib/python3.13/site-packages (from xgboost-cpu) (1.15.2)
Downloading xgboost_cpu-3.0.0-py3-none-manylinux2014_x86_64.whl (4.9 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.9/4.9 MB 36.0 MB/s eta 0:00:00
Installing collected packages: xgboost-cpu
Successfully installed xgboost-cpu-3.0.0
@hcho3
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hcho3 commented Mar 19, 2025

The warning should not be displayed for xgboost-cpu. We will make a new release to remove the warning.

@hcho3 hcho3 self-assigned this Mar 19, 2025
@trivialfis
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Could you please check:

ls -la ~/anaconda3/envs/tmplafa/x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6

(or something similar) for which glibc it links to? I believe it judges your libc based on the one in conda env instead of the one in the system.

@busFred
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busFred commented Mar 19, 2025

Could you please check:

ls -la ~/anaconda3/envs/tmplafa/x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6

(or something similar) for which glibc it links to? I believe it judges your libc based on the one in conda env instead of the one in the system.

I don't have [...]/sysroot/lib64 under my conda environment, but the closest thing I could find through doing a search for libc over the entire conda environment directory gives me the following
Image

I also try to look into the content of that libc10.so file:

(tmplafa) ~/Documents/research/afa/template-afa$ ls -la ~/anaconda3/envs/tmplafa/lib/python3.13/site-packages/torch/lib/libc10.so
-rwxrwxr-x 1 hungtien hungtien 1455209 Feb  7 12:35 /home/hungtien/anaconda3/envs/tmplafa/lib/python3.13/site-packages/torch/lib/libc10.so
(tmplafa) ~/Documents/research/afa/template-afa$ strings ~/anaconda3/envs/tmplafa/lib/python3.13/site-packages/torch/lib/libc10.so | grep GLIBC_
memset@@GLIBC_2.2.5
backtrace@@GLIBC_2.2.5
posix_memalign@@GLIBC_2.2.5
close@@GLIBC_2.2.5
abort@@GLIBC_2.2.5
memchr@@GLIBC_2.2.5
pthread_getname_np@@GLIBC_2.12
clock_gettime@@GLIBC_2.17
toupper@@GLIBC_2.2.5
read@@GLIBC_2.2.5
malloc@@GLIBC_2.2.5
sigfillset@@GLIBC_2.2.5
pthread_setname_np@@GLIBC_2.12
strerror_r@@GLIBC_2.2.5
gettext@@GLIBC_2.2.5
unlink@@GLIBC_2.2.5
rmdir@@GLIBC_2.2.5
pthread_cond_timedwait@@GLIBC_2.3.2
__cxa_atexit@@GLIBC_2.2.5
sysconf@@GLIBC_2.2.5
getpid@@GLIBC_2.2.5
backtrace_symbols@@GLIBC_2.2.5
free@@GLIBC_2.2.5
strlen@@GLIBC_2.2.5
pthread_create@@GLIBC_2.2.5
opendir@@GLIBC_2.2.5
mkstemp64@@GLIBC_2.2.5
__cxa_finalize@@GLIBC_2.2.5
__tls_get_addr@@GLIBC_2.3
syscall@@GLIBC_2.2.5
pthread_self@@GLIBC_2.2.5
strerror@@GLIBC_2.2.5
open64@@GLIBC_2.2.5
sigaction@@GLIBC_2.2.5
strtol@@GLIBC_2.2.5
raise@@GLIBC_2.2.5
memmove@@GLIBC_2.2.5
vsnprintf@@GLIBC_2.2.5
setenv@@GLIBC_2.2.5
getenv@@GLIBC_2.2.5
__errno_location@@GLIBC_2.2.5
qsort@@GLIBC_2.2.5
madvise@@GLIBC_2.2.5
isalpha@@GLIBC_2.2.5
__stack_chk_fail@@GLIBC_2.4
strcmp@@GLIBC_2.2.5
tolower@@GLIBC_2.2.5
clog@@GLIBC_2.2.5
pthread_rwlock_rdlock@@GLIBC_2.2.5
pthread_once@@GLIBC_2.2.5
mkdtemp@@GLIBC_2.2.5
memcmp@@GLIBC_2.2.5
calloc@@GLIBC_2.2.5
pthread_rwlock_wrlock@@GLIBC_2.2.5
strncpy@@GLIBC_2.2.5
localtime_r@@GLIBC_2.2.5
dlsym@@GLIBC_2.2.5
stderr@@GLIBC_2.2.5
sigemptyset@@GLIBC_2.2.5
__pthread_key_create@@GLIBC_2.2.5
strtoll@@GLIBC_2.2.5
pthread_rwlock_unlock@@GLIBC_2.2.5
pthread_mutex_lock@@GLIBC_2.2.5
realloc@@GLIBC_2.2.5
perror@@GLIBC_2.2.5
fprintf@@GLIBC_2.2.5
write@@GLIBC_2.2.5
pthread_mutex_unlock@@GLIBC_2.2.5
memcpy@@GLIBC_2.14
open@@GLIBC_2.2.5
strtod@@GLIBC_2.2.5
readdir64@@GLIBC_2.2.5
time@@GLIBC_2.2.5
GLIBC_2.2.5
GLIBC_2.3
GLIBC_2.3.2
GLIBC_2.12
GLIBC_2.14
GLIBC_2.4
GLIBC_2.17

BTW, based on the location of libc10.so, it seems to be installed by pytorch

@trivialfis
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Thank you for sharing, how about conda list | grep "sysroot"?

Here's my version:

$ conda list | grep "sysroot"
sysroot_linux-64          2.28                 h8bc681e_7    conda-forge

@busFred
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busFred commented Mar 19, 2025

Mine shows nothing... but here is my full conda list

(tmplafa) ~/Documents/research/afa/template-afa$ conda list
# packages in environment at /home/hungtien/anaconda3/envs/tmplafa:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_openmp_mutex             5.1                       1_gnu  
absl-py                   2.1.0                    pypi_0    pypi
aiohappyeyeballs          2.4.5                    pypi_0    pypi
aiohttp                   3.11.12                  pypi_0    pypi
aiosignal                 1.3.2                    pypi_0    pypi
antlr4-python3-runtime    4.9.3                    pypi_0    pypi
aplr                      10.8.0                   pypi_0    pypi
asttokens                 3.0.0                    pypi_0    pypi
attrs                     25.1.0                   pypi_0    pypi
bleach                    6.2.0                    pypi_0    pypi
blinker                   1.9.0                    pypi_0    pypi
bzip2                     1.0.8                h5eee18b_6  
ca-certificates           2024.12.31           h06a4308_0  
certifi                   2025.1.31                pypi_0    pypi
charset-normalizer        3.4.1                    pypi_0    pypi
click                     8.1.8                    pypi_0    pypi
cloudpickle               3.1.1                    pypi_0    pypi
comm                      0.2.2                    pypi_0    pypi
contourpy                 1.3.1                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
dash                      2.18.2                   pypi_0    pypi
dash-core-components      2.0.0                    pypi_0    pypi
dash-cytoscape            1.0.2                    pypi_0    pypi
dash-html-components      2.0.0                    pypi_0    pypi
dash-table                5.0.0                    pypi_0    pypi
debugpy                   1.8.12                   pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
dill                      0.3.9                    pypi_0    pypi
executing                 2.2.0                    pypi_0    pypi
exp-datasets              0.0.0                    pypi_0    pypi
exp-models                0.0.0                    pypi_0    pypi
expat                     2.6.4                h6a678d5_0  
external                  0.0.0                    pypi_0    pypi
farama-notifications      0.0.4                    pypi_0    pypi
filelock                  3.17.0                   pypi_0    pypi
flask                     3.0.3                    pypi_0    pypi
fonttools                 4.56.0                   pypi_0    pypi
frozenlist                1.5.0                    pypi_0    pypi
fsspec                    2025.2.0                 pypi_0    pypi
gevent                    24.11.1                  pypi_0    pypi
greenlet                  3.1.1                    pypi_0    pypi
grpcio                    1.70.0                   pypi_0    pypi
gymnasium                 1.1.1                    pypi_0    pypi
hydra-core                1.3.2                    pypi_0    pypi
hydra-joblib-launcher     1.2.0                    pypi_0    pypi
hydra-submitit-launcher   1.2.0                    pypi_0    pypi
idna                      3.10                     pypi_0    pypi
imageio                   2.37.0                   pypi_0    pypi
imbalanced-learn          0.13.0                   pypi_0    pypi
importlib-metadata        8.6.1                    pypi_0    pypi
internal                  0.0.0                    pypi_0    pypi
interpret                 0.6.9                    pypi_0    pypi
interpret-core            0.6.9                    pypi_0    pypi
ipykernel                 6.29.5                   pypi_0    pypi
ipython                   8.32.0                   pypi_0    pypi
ipywidgets                8.1.5                    pypi_0    pypi
itsdangerous              2.2.0                    pypi_0    pypi
jedi                      0.19.2                   pypi_0    pypi
jinja2                    3.1.5                    pypi_0    pypi
joblib                    1.4.2                    pypi_0    pypi
jsonpickle                4.0.1                    pypi_0    pypi
jupyter-client            8.6.3                    pypi_0    pypi
jupyter-core              5.7.2                    pypi_0    pypi
jupyterlab-widgets        3.0.13                   pypi_0    pypi
kaggle                    1.7.4.2                  pypi_0    pypi
kiwisolver                1.4.8                    pypi_0    pypi
lazy-loader               0.4                      pypi_0    pypi
ld_impl_linux-64          2.40                 h12ee557_0  
libffi                    3.4.4                h6a678d5_1  
libgcc-ng                 11.2.0               h1234567_1  
libgomp                   11.2.0               h1234567_1  
libmpdec                  4.0.0                h5eee18b_0  
libstdcxx-ng              11.2.0               h1234567_1  
libuuid                   1.41.5               h5eee18b_0  
lightning                 2.5.0.post0              pypi_0    pypi
lightning-utilities       0.12.0                   pypi_0    pypi
llvmlite                  0.44.0                   pypi_0    pypi
markdown                  3.7                      pypi_0    pypi
markupsafe                3.0.2                    pypi_0    pypi
matplotlib                3.10.1                   pypi_0    pypi
matplotlib-inline         0.1.7                    pypi_0    pypi
mpmath                    1.3.0                    pypi_0    pypi
multidict                 6.1.0                    pypi_0    pypi
multiprocess              0.70.17                  pypi_0    pypi
narwhals                  1.25.2                   pypi_0    pypi
ncurses                   6.4                  h6a678d5_0  
nest-asyncio              1.6.0                    pypi_0    pypi
networkx                  3.4.2                    pypi_0    pypi
numba                     0.61.0                   pypi_0    pypi
numpy                     2.1.3                    pypi_0    pypi
nvidia-cublas-cu12        12.4.5.8                 pypi_0    pypi
nvidia-cuda-cupti-cu12    12.4.127                 pypi_0    pypi
nvidia-cuda-nvrtc-cu12    12.4.127                 pypi_0    pypi
nvidia-cuda-runtime-cu12  12.4.127                 pypi_0    pypi
nvidia-cudnn-cu12         9.1.0.70                 pypi_0    pypi
nvidia-cufft-cu12         11.2.1.3                 pypi_0    pypi
nvidia-curand-cu12        10.3.5.147               pypi_0    pypi
nvidia-cusolver-cu12      11.6.1.9                 pypi_0    pypi
nvidia-cusparse-cu12      12.3.1.170               pypi_0    pypi
nvidia-cusparselt-cu12    0.6.2                    pypi_0    pypi
nvidia-nccl-cu12          2.21.5                   pypi_0    pypi
nvidia-nvjitlink-cu12     12.4.127                 pypi_0    pypi
nvidia-nvtx-cu12          12.4.127                 pypi_0    pypi
omegaconf                 2.3.0                    pypi_0    pypi
openssl                   3.0.15               h5eee18b_0  
orjson                    3.10.15                  pypi_0    pypi
packaging                 24.2                     pypi_0    pypi
pandas                    2.2.3                    pypi_0    pypi
parso                     0.8.4                    pypi_0    pypi
pexpect                   4.9.0                    pypi_0    pypi
pillow                    11.1.0                   pypi_0    pypi
pip                       24.2            py313h06a4308_0  
platformdirs              4.3.6                    pypi_0    pypi
plotly                    6.0.0                    pypi_0    pypi
prompt-toolkit            3.0.50                   pypi_0    pypi
propcache                 0.2.1                    pypi_0    pypi
protobuf                  5.29.3                   pypi_0    pypi
psutil                    6.1.1                    pypi_0    pypi
ptyprocess                0.7.0                    pypi_0    pypi
pure-eval                 0.2.3                    pypi_0    pypi
pyarrow                   19.0.1                   pypi_0    pypi
pygments                  2.19.1                   pypi_0    pypi
pygraphviz                1.14                     pypi_0    pypi
pyparsing                 3.2.1                    pypi_0    pypi
python                    3.13.2          hf623796_100_cp313  
python-dateutil           2.9.0.post0              pypi_0    pypi
python-graphviz           0.20.3                   pypi_0    pypi
python-slugify            8.0.4                    pypi_0    pypi
python_abi                3.13                    0_cp313  
pytorch-lightning         2.5.0.post0              pypi_0    pypi
pytz                      2025.1                   pypi_0    pypi
pyvis                     0.3.2                    pypi_0    pypi
pyyaml                    6.0.2                    pypi_0    pypi
pyzmq                     26.2.1                   pypi_0    pypi
readline                  8.2                  h5eee18b_0  
requests                  2.32.3                   pypi_0    pypi
retrying                  1.3.4                    pypi_0    pypi
salib                     1.5.1                    pypi_0    pypi
scikit-image              0.25.2                   pypi_0    pypi
scikit-learn              1.6.1                    pypi_0    pypi
scipy                     1.15.2                   pypi_0    pypi
setuptools                75.8.0          py313h06a4308_0  
shap                      0.46.0                   pypi_0    pypi
six                       1.17.0                   pypi_0    pypi
sklearn-compat            0.1.3                    pypi_0    pypi
slicer                    0.0.8                    pypi_0    pypi
sqlite                    3.45.3               h5eee18b_0  
stack-data                0.6.3                    pypi_0    pypi
standard-imghdr           3.13.0                   pypi_0    pypi
submitit                  1.5.2                    pypi_0    pypi
swig                      4.3.0                    pypi_0    pypi
sympy                     1.13.1                   pypi_0    pypi
tabulate                  0.9.0                    pypi_0    pypi
tensorboard               2.19.0                   pypi_0    pypi
tensorboard-data-server   0.7.2                    pypi_0    pypi
tensordict                0.7.2                    pypi_0    pypi
text-unidecode            1.3                      pypi_0    pypi
threadpoolctl             3.5.0                    pypi_0    pypi
tifffile                  2025.2.18                pypi_0    pypi
tk                        8.6.14               h39e8969_0  
torch                     2.6.0                    pypi_0    pypi
torchmetrics              1.6.3                    pypi_0    pypi
torchrl                   0.7.2                    pypi_0    pypi
torchvision               0.21.0                   pypi_0    pypi
tornado                   6.4.2                    pypi_0    pypi
tqdm                      4.67.1                   pypi_0    pypi
traitlets                 5.14.3                   pypi_0    pypi
triton                    3.2.0                    pypi_0    pypi
typing-extensions         4.12.2                   pypi_0    pypi
tzdata                    2025.1                   pypi_0    pypi
ucimlrepo                 0.0.7                    pypi_0    pypi
urllib3                   2.3.0                    pypi_0    pypi
wcwidth                   0.2.13                   pypi_0    pypi
webencodings              0.5.1                    pypi_0    pypi
werkzeug                  3.0.6                    pypi_0    pypi
wheel                     0.44.0          py313h06a4308_0  
widgetsnbextension        4.0.13                   pypi_0    pypi
xgboost-cpu               3.0.0                    pypi_0    pypi
xz                        5.4.6                h5eee18b_1  
yarl                      1.18.3                   pypi_0    pypi
zipp                      3.21.0                   pypi_0    pypi
zlib                      1.2.13               h5eee18b_1  
zope-event                5.0                      pypi_0    pypi
zope-interface            7.2                      pypi_0    pypi

@trivialfis
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@hcho3 Do you have any insight? Despite the xgboost-cpu, xgboost itself should not choose the 2014 version. I think that's the more significant issue.

@trivialfis
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Okay, my bad. Rereading the issue, I see that you are installing xgboost-cpu instead of xgboost. I thought you were installing xgboost and ran into a warning. Then try the xgboost-cpu.

Yes, we should create a patch release to fix that.

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