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conda-forge / linux-sysroot-feedstock

A conda-smithy repository for linux-sysroot.
BSD 3-Clause "New" or "Revised" License
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Installing more recent version of glibc on an HPC machine running older OS? #41

Closed davidrpugh closed 2 months ago

davidrpugh commented 2 years ago

My university HPC cluster runs an older version of CentOS and I need to compile software that requires a newer version of glibc than what is available on the operating system. Is this the correct package to install to insure that a newer version of glibc will be available? If so how do I check to see what version of glibc is available inside my Conda environment?


Environment (conda list):

``` $ conda list # packages in environment at /ibex/scratch/pughdr/pardiso-test/env: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_llvm conda-forge binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge binutils_linux-64 2.36 hf3e587d_1 conda-forge ca-certificates 2021.10.8 ha878542_0 conda-forge gcc_impl_linux-64 11.2.0 h82a94d6_11 conda-forge gcc_linux-64 11.2.0 h39a9532_1 conda-forge gfortran_impl_linux-64 11.2.0 h7a446d4_11 conda-forge gfortran_linux-64 11.2.0 h777b47f_1 conda-forge gxx_impl_linux-64 11.2.0 h82a94d6_11 conda-forge gxx_linux-64 11.2.0 hacbe6df_1 conda-forge kernel-headers_linux-64 2.6.32 he073ed8_14 conda-forge ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge libblas 3.9.0 12_linux64_mkl conda-forge libcblas 3.9.0 12_linux64_mkl conda-forge libffi 3.4.2 h9c3ff4c_4 conda-forge libgcc-devel_linux-64 11.2.0 h0952999_11 conda-forge libgcc-ng 11.2.0 h1d223b6_11 conda-forge libgfortran-ng 11.2.0 h69a702a_11 conda-forge libgfortran5 11.2.0 h5c6108e_11 conda-forge libgomp 11.2.0 h1d223b6_11 conda-forge liblapack 3.9.0 12_linux64_mkl conda-forge libsanitizer 11.2.0 he4da1e4_11 conda-forge libstdcxx-devel_linux-64 11.2.0 h0952999_11 conda-forge libstdcxx-ng 11.2.0 he4da1e4_11 conda-forge libzlib 1.2.11 h36c2ea0_1013 conda-forge llvm-openmp 12.0.1 h4bd325d_1 conda-forge mkl 2021.4.0 h8d4b97c_729 conda-forge mkl-service 2.4.0 py39h3811e60_0 conda-forge ncurses 6.2 h58526e2_4 conda-forge numpy 1.21.2 py39hdbf815f_0 conda-forge openssl 3.0.0 h7f98852_1 conda-forge pardiso4py 0.3.3 pyhd8ed1ab_0 conda-forge pip 21.3 pyhd8ed1ab_0 conda-forge psutil 5.8.0 py39h3811e60_1 conda-forge python 3.9.7 hf930737_3_cpython conda-forge python_abi 3.9 2_cp39 conda-forge readline 8.1 h46c0cb4_0 conda-forge scipy 1.7.1 py39hee8e79c_0 conda-forge setuptools 58.2.0 py39hf3d152e_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sqlite 3.36.0 h9cd32fc_2 conda-forge sysroot_linux-64 2.12 he073ed8_14 conda-forge tbb 2021.3.0 h4bd325d_0 conda-forge tk 8.6.11 h27826a3_1 conda-forge tzdata 2021d he74cb21_0 conda-forge wheel 0.37.0 pyhd8ed1ab_1 conda-forge xz 5.2.5 h516909a_1 conda-forge zlib 1.2.11 h36c2ea0_1013 conda-forge ```


Details about conda and system ( conda info ):

``` $ conda info active environment : /ibex/scratch/pughdr/pardiso-test/env active env location : /ibex/scratch/pughdr/pardiso-test/env shell level : 1 user config file : /home/pughdr/.condarc populated config files : /home/pughdr/.condarc conda version : 4.10.3 conda-build version : not installed python version : 3.9.5.final.0 virtual packages : __cuda=11.3=0 __linux=3.10.0=0 __glibc=2.17=0 __unix=0=0 __archspec=1=x86_64 base environment : /home/pughdr/miniconda3 (writable) conda av data dir : /home/pughdr/miniconda3/etc/conda conda av metadata url : None channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /home/pughdr/miniconda3/pkgs /home/pughdr/.conda/pkgs envs directories : /home/pughdr/miniconda3/envs /home/pughdr/.conda/envs platform : linux-64 user-agent : conda/4.10.3 requests/2.26.0 CPython/3.9.5 Linux/3.10.0-1160.24.1.el7.x86_64 centos/7.9.2009 glibc/2.17 UID:GID : 168214:1168214 netrc file : None offline mode : False ```
isuruf commented 2 years ago

No, this package is used for compiling packages only. We still use the system glibc. It's not easy to use a newer glibc and we don't have support for it in conda.

davidrpugh commented 2 years ago

Thanks for the quick response! Recently I encountered an issue where a user wanted to compile a package with Intel compilers and needed a newer version of glibc in order to do so. This is what led me to investigate what packages gxx_linux-64 was really installing and try and find the core packages that brought in the newer version of glibc.

My confusion stems from the fact that I often run into glibc errors when trying to compile CUDA extensions in packages installed via'pip into my Conda environments. Often I can solve the problem by simply installing the compiler toolchain gxx_linux-64 into my Conda environment so that these newer compilers are used instead of my system compilers. This to me suggested that installing the compiler toolchain was making a newer version of glibc available.

Any idea why installing the compiler toolchains into the Conda environment would solve errors related to glibc version mismatch if installing these toolchains doesn't actually install a new glibc version?

isuruf commented 2 years ago

Any idea why installing the compiler toolchains into the Conda environment would solve errors related to glibc version mismatch if installing these toolchains doesn't actually install a new glibc version?

No idea. Will have to see the error to give an answer.

davidrpugh commented 2 years ago

Here is a recent example that I generated while trying to install Jax.

Python 3.8.12 | packaged by conda-forge | (default, Oct 12 2021, 21:59:51) 
Type 'copyright', 'credits' or 'license' for more information
IPython 7.28.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import jax
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-cb15c4215ef7> in <module>
----> 1 import jax

~/Training/kaust-vislab/jax-gpu-data-science-project/env/lib/python3.8/site-packages/jax/__init__.py in <module>
    125 from . import image as image
    126 from . import lax as lax
--> 127 from . import nn as nn
    128 from . import numpy as numpy
    129 from . import ops as ops

~/Training/kaust-vislab/jax-gpu-data-science-project/env/lib/python3.8/site-packages/jax/nn/__init__.py in <module>
     19 from jax.numpy import tanh as tanh
     20 from . import initializers as initializers
---> 21 from jax._src.nn.functions import (
     22   celu as celu,
     23   elu as elu,

~/Training/kaust-vislab/jax-gpu-data-science-project/env/lib/python3.8/site-packages/jax/_src/nn/functions.py in <module>
     26 from jax.core import AxisName
     27 from .. import util
---> 28 from jax.scipy.special import expit
     29 from jax.scipy.special import logsumexp as _logsumexp
     30 import jax.numpy as jnp

~/Training/kaust-vislab/jax-gpu-data-science-project/env/lib/python3.8/site-packages/jax/scipy/__init__.py in <module>
     16 from . import linalg as linalg
     17 from . import ndimage as ndimage
---> 18 from . import signal as signal
     19 from . import sparse as sparse
     20 from . import special as special

~/Training/kaust-vislab/jax-gpu-data-science-project/env/lib/python3.8/site-packages/jax/scipy/signal.py in <module>
     15 # flake8: noqa: F401
     16 
---> 17 from jax._src.scipy.signal import (
     18   convolve as convolve,
     19   convolve2d as convolve2d,

~/Training/kaust-vislab/jax-gpu-data-science-project/env/lib/python3.8/site-packages/jax/_src/scipy/signal.py in <module>
     13 # limitations under the License.
     14 
---> 15 import scipy.signal as osp_signal
     16 import warnings
     17 

~/Training/kaust-vislab/jax-gpu-data-science-project/env/lib/python3.8/site-packages/scipy/signal/__init__.py in <module>
    292 from . import sigtools, windows
    293 from .waveforms import *
--> 294 from ._max_len_seq import max_len_seq
    295 from ._upfirdn import upfirdn
    296 

~/Training/kaust-vislab/jax-gpu-data-science-project/env/lib/python3.8/site-packages/scipy/signal/_max_len_seq.py in <module>
      6 import numpy as np
      7 
----> 8 from ._max_len_seq_inner import _max_len_seq_inner
      9 
     10 __all__ = ['max_len_seq']

ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /home/pughdr/Training/kaust-vislab/jax-gpu-data-science-project/env/lib/python3.8/site-packages/scipy/signal/_max_len_seq_inner.cpython-38-x86_64-linux-gnu.so)

If I exit IPython and then run the following command.

export LD_LIBRARY_PATH=$ENV_PREFIX/lib:$LD_LIBRARY_PATH

The the error will go away. I attributed this to the fact that there is a version of libstdc++.so.6 that is able to use the required version of GLIBCXX in my Conda environment.

ls $ENV_PREFIX/lib/libstdc++.so
libstdc++.so         libstdc++.so.6       libstdc++.so.6.0.29

Here is my Conda environment.

conda list
# packages in environment at /home/pughdr/Training/kaust-vislab/jax-gpu-data-science-project/env:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
_py-xgboost-mutex         2.0                       cpu_0    conda-forge
abseil-cpp                20210324.2           h9c3ff4c_0    conda-forge
absl-py                   0.15.0             pyhd8ed1ab_0    conda-forge
aiohttp                   3.7.4.post0      py38h497a2fe_0    conda-forge
alembic                   1.7.4              pyhd8ed1ab_0    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
anyio                     3.3.4            py38h578d9bd_0    conda-forge
argh                      0.26.2                py38_1001    conda-forge
argon2-cffi               21.1.0           py38h497a2fe_0    conda-forge
arrow-cpp                 5.0.0           py38h94c96a7_8_cpu    conda-forge
astroid                   2.8.4            py38h578d9bd_0    conda-forge
astunparse                1.6.3                    pypi_0    pypi
async-timeout             3.0.1                   py_1000    conda-forge
async_generator           1.10                       py_0    conda-forge
attrs                     21.2.0             pyhd8ed1ab_0    conda-forge
autopage                  0.4.0              pyhd8ed1ab_0    conda-forge
autopep8                  1.5.6              pyhd8ed1ab_0    conda-forge
aws-c-cal                 0.5.11               h95a6274_0    conda-forge
aws-c-common              0.6.2                h7f98852_0    conda-forge
aws-c-event-stream        0.2.7               h3541f99_13    conda-forge
aws-c-io                  0.10.5               hfb6a706_0    conda-forge
aws-checksums             0.1.11               ha31a3da_7    conda-forge
aws-sdk-cpp               1.8.186              hb4091e7_3    conda-forge
babel                     2.9.1              pyh44b312d_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
binutils_impl_linux-64    2.36.1               h193b22a_2    conda-forge
binutils_linux-64         2.36                 hf3e587d_1    conda-forge
bleach                    4.1.0              pyhd8ed1ab_0    conda-forge
blinker                   1.4                        py_1    conda-forge
bokeh                     2.3.3                    pypi_0    pypi
brotlipy                  0.7.0           py38h497a2fe_1001    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2021.10.26           h06a4308_2  
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                4.2.4              pyhd8ed1ab_0    conda-forge
certifi                   2021.10.8        py38h578d9bd_0    conda-forge
cffi                      1.14.6           py38h3931269_1    conda-forge
chardet                   4.0.0            py38h578d9bd_1    conda-forge
charset-normalizer        2.0.0              pyhd8ed1ab_0    conda-forge
chex                      0.0.8                    pypi_0    pypi
clang                     5.0                      pypi_0    pypi
click                     8.0.3            py38h578d9bd_0    conda-forge
cliff                     3.9.0              pyhd8ed1ab_0    conda-forge
cloudpickle               2.0.0              pyhd8ed1ab_0    conda-forge
cmaes                     0.8.2              pyh44b312d_0    conda-forge
cmd2                      2.2.0            py38h578d9bd_0    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
colorcet                  2.0.6              pyhd8ed1ab_0    conda-forge
colorlog                  6.5.0            py38h578d9bd_0    conda-forge
configparser              5.0.2              pyhd8ed1ab_0    conda-forge
cryptography              35.0.0           py38h3e25421_1    conda-forge
cudatoolkit               11.1.1               h6406543_9    conda-forge
cudatoolkit-dev           11.1.1           py38h497a2fe_0    conda-forge
cudnn                     8.2.1.32             h86fa8c9_0    conda-forge
cupy                      9.5.0            py38hbc4b76f_0    conda-forge
curl                      7.79.1               h2574ce0_1    conda-forge
cycler                    0.10.0                     py_2    conda-forge
cytoolz                   0.11.0           py38h497a2fe_3    conda-forge
dask                      2021.10.0          pyhd8ed1ab_0    conda-forge
dask-core                 2021.10.0          pyhd8ed1ab_0    conda-forge
dask-glm                  0.2.0                      py_1    conda-forge
dask-labextension         5.1.0              pyhd8ed1ab_0    conda-forge
dask-ml                   2021.10.17         pyhd8ed1ab_0    conda-forge
dataclasses               0.8                pyhc8e2a94_3    conda-forge
datashader                0.13.0             pyh6c4a22f_0    conda-forge
datashape                 0.5.4                      py_1    conda-forge
dbus                      1.13.18              hb2f20db_0  
debugpy                   1.4.1            py38h709712a_0    conda-forge
decorator                 5.1.0              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
distributed               2021.10.0        py38h578d9bd_0    conda-forge
dm-haiku                  0.0.4                    pypi_0    pypi
dm-tree                   0.1.6                    pypi_0    pypi
docker-pycreds            0.4.0                      py_0    conda-forge
entrypoints               0.3             py38h32f6830_1002    conda-forge
expat                     2.4.1                h9c3ff4c_0    conda-forge
fastrlock                 0.8              py38h709712a_0    conda-forge
featuretools              1.0.0              pyhd8ed1ab_0    conda-forge
fedjax                    0.0.7                    pypi_0    pypi
flake8                    3.9.0              pyhd3eb1b0_0  
flatbuffers               1.12                     pypi_0    pypi
fontconfig                2.13.1            hba837de_1005    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
fsspec                    2021.10.1          pyhd8ed1ab_0    conda-forge
future                    0.18.2           py38h578d9bd_3    conda-forge
gast                      0.4.0                    pypi_0    pypi
gcc_impl_linux-64         11.2.0              h82a94d6_11    conda-forge
gcc_linux-64              11.2.0               h39a9532_1    conda-forge
gettext                   0.21.0               hf68c758_0  
gflags                    2.2.2             he1b5a44_1004    conda-forge
gh                        2.2.0                ha8f183a_0    conda-forge
giflib                    5.2.1                h516909a_2    conda-forge
git                       2.33.1          pl5321hc30692c_0    conda-forge
gitdb                     4.0.9              pyhd8ed1ab_0    conda-forge
gitpython                 3.1.24             pyhd8ed1ab_0    conda-forge
glib                      2.70.0               h780b84a_1    conda-forge
glib-tools                2.70.0               h780b84a_1    conda-forge
glog                      0.5.0                h48cff8f_0    conda-forge
google-auth               1.35.0             pyh6c4a22f_0    conda-forge
google-auth-oauthlib      0.4.6              pyhd8ed1ab_0    conda-forge
google-pasta              0.2.0                    pypi_0    pypi
gql                       2.0.0              pyh9f0ad1d_0    conda-forge
graphql-core              2.3.2              pyh9f0ad1d_0    conda-forge
greenlet                  1.1.2            py38h709712a_0    conda-forge
grpc-cpp                  1.40.0               h05f19cf_2    conda-forge
grpcio                    1.41.1           py38hdd6454d_0    conda-forge
gst-plugins-base          1.18.5               hf529b03_0    conda-forge
gstreamer                 1.18.5               h76c114f_0    conda-forge
gxx_impl_linux-64         11.2.0              h82a94d6_11    conda-forge
gxx_linux-64              11.2.0               hacbe6df_1    conda-forge
h5py                      3.1.0                    pypi_0    pypi
hdf5                      1.12.1          nompi_h2750804_101    conda-forge
heapdict                  1.0.1                      py_0    conda-forge
holoviews                 1.14.6             pyhd8ed1ab_0    conda-forge
hvplot                    0.7.3              pyh6c4a22f_0    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
idna                      3.2                pyhd3eb1b0_0  
imbalanced-learn          0.8.1              pyhd8ed1ab_0    conda-forge
importlib-metadata        4.8.1            py38h578d9bd_0    conda-forge
importlib_resources       5.3.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.4.2            py38he5a9106_0    conda-forge
ipython                   7.28.0           py38he5a9106_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
isort                     5.9.3              pyhd8ed1ab_0    conda-forge
jax                       0.2.24                   pypi_0    pypi
jaxlib                    0.1.73+cuda11.cudnn82          pypi_0    pypi
jbig                      2.1               h7f98852_2003    conda-forge
jedi                      0.17.2           py38h578d9bd_1    conda-forge
jinja2                    3.0.2              pyhd8ed1ab_0    conda-forge
joblib                    1.1.0              pyhd8ed1ab_0    conda-forge
jpeg                      9d                   h516909a_0    conda-forge
json5                     0.9.6              pyhd3eb1b0_0  
jsonschema                4.1.2              pyhd8ed1ab_0    conda-forge
jupyter-lsp               1.5.0              pyhd8ed1ab_0    conda-forge
jupyter-server-mathjax    0.2.3              pyhd8ed1ab_0    conda-forge
jupyter-server-proxy      3.1.0              pyhd8ed1ab_0    conda-forge
jupyter_client            7.0.6              pyhd8ed1ab_0    conda-forge
jupyter_core              4.9.0            py38h578d9bd_0    conda-forge
jupyter_server            1.11.1             pyhd8ed1ab_0    conda-forge
jupyterlab                3.2.1              pyhd8ed1ab_0    conda-forge
jupyterlab-git            0.33.0             pyhd8ed1ab_0    conda-forge
jupyterlab-lsp            3.9.1              pyhd8ed1ab_0    conda-forge
jupyterlab-nvdashboard    0.6.0              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_server         2.8.2              pyhd8ed1ab_0    conda-forge
keras                     2.6.0                    pypi_0    pypi
keras-preprocessing       1.1.2                    pypi_0    pypi
kernel-headers_linux-64   2.6.32              he073ed8_14    conda-forge
kiwisolver                1.3.2            py38h1fd1430_0    conda-forge
krb5                      1.19.2               hcc1bbae_2    conda-forge
lazy-object-proxy         1.6.0            py38h497a2fe_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      3.0                  h9c3ff4c_0    conda-forge
libblas                   3.9.0           12_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h7f98852_5    conda-forge
libbrotlidec              1.0.9                h7f98852_5    conda-forge
libbrotlienc              1.0.9                h7f98852_5    conda-forge
libcblas                  3.9.0           12_linux64_openblas    conda-forge
libclang                  11.1.0          default_ha53f305_1    conda-forge
libcurl                   7.79.1               h2574ce0_1    conda-forge
libdeflate                1.8                  h7f98852_0    conda-forge
libedit                   3.1.20210714         h7f8727e_0  
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               h9b69904_4    conda-forge
libffi                    3.4.2                h9c3ff4c_4    conda-forge
libgcc-devel_linux-64     11.2.0              h0952999_11    conda-forge
libgcc-ng                 11.2.0              h1d223b6_11    conda-forge
libgfortran-ng            11.2.0              h69a702a_11    conda-forge
libgfortran5              11.2.0              h5c6108e_11    conda-forge
libglib                   2.70.0               h174f98d_1    conda-forge
libgomp                   11.2.0              h1d223b6_11    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0           12_linux64_openblas    conda-forge
libllvm11                 11.1.0               hf817b99_2    conda-forge
libnghttp2                1.43.0               h812cca2_1    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libogg                    1.3.5                h27cfd23_1  
libopenblas               0.3.18          pthreads_h8fe5266_0    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.37               hed695b0_2    conda-forge
libpq                     13.3                 hd57d9b9_1    conda-forge
libprotobuf               3.18.1               h780b84a_0    conda-forge
libsanitizer              11.2.0              he4da1e4_11    conda-forge
libsodium                 1.0.18               h516909a_1    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-devel_linux-64  11.2.0              h0952999_11    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_11    conda-forge
libthrift                 0.15.0               he6d91bd_1    conda-forge
libtiff                   4.3.0                h6f004c6_2    conda-forge
libutf8proc               2.6.1                h7f98852_0    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libvorbis                 1.3.7                he1b5a44_0    conda-forge
libwebp                   1.2.1                h3452ae3_0    conda-forge
libwebp-base              1.2.1                h7f98852_0    conda-forge
libxcb                    1.14                 h7b6447c_0  
libxgboost                1.5.0                h9c3ff4c_0    conda-forge
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.12               h72842e0_0    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
lightgbm                  3.2.1            py38h709712a_0    conda-forge
llvmlite                  0.37.0           py38h4630a5e_0    conda-forge
locket                    0.2.1            py38h06a4308_1  
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
mako                      1.1.5              pyhd8ed1ab_0    conda-forge
markdown                  3.3.4              pyhd8ed1ab_0    conda-forge
markupsafe                2.0.1            py38h497a2fe_0    conda-forge
matplotlib                3.4.3            py38h578d9bd_1    conda-forge
matplotlib-base           3.4.3            py38hf4fb855_1    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
mccabe                    0.6.1                      py_1    conda-forge
mistune                   0.8.4           py38h497a2fe_1004    conda-forge
msgpack-python            1.0.2            py38h1fd1430_1    conda-forge
multidict                 5.2.0            py38h497a2fe_0    conda-forge
multipledispatch          0.6.0                      py_0    conda-forge
mysql-common              8.0.27               ha770c72_0    conda-forge
mysql-libs                8.0.27               hfa10184_0    conda-forge
nbclassic                 0.3.3              pyhd8ed1ab_0    conda-forge
nbclient                  0.5.4              pyhd8ed1ab_0    conda-forge
nbconvert                 6.2.0            py38h578d9bd_0    conda-forge
nbdime                    3.1.1              pyhd8ed1ab_0    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
nccl                      2.11.4.1             h97a9cb7_0    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
nest-asyncio              1.5.1              pyhd8ed1ab_0    conda-forge
notebook                  6.4.5              pyha770c72_0    conda-forge
nspr                      4.30                 h9c3ff4c_0    conda-forge
nss                       3.69                 hb5efdd6_1    conda-forge
numba                     0.54.1           py38h4bf6c61_0    conda-forge
numpy                     1.19.5           py38h9894fe3_2    conda-forge
nvidia-ml                 7.352.0                    py_0    conda-forge
oauthlib                  3.1.1              pyhd8ed1ab_0    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openssl                   1.1.1l               h7f98852_0    conda-forge
opt-einsum                3.3.0                    pypi_0    pypi
optax                     0.0.9                    pypi_0    pypi
optuna                    2.10.0             pyhd8ed1ab_0    conda-forge
orc                       1.7.0                h68e2c4e_0    conda-forge
packaging                 21.0               pyhd8ed1ab_0    conda-forge
pandas                    1.3.4            py38h43a58ef_0    conda-forge
pandas-bokeh              0.5.5                    pypi_0    pypi
pandoc                    2.15                 h7f98852_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
panel                     0.12.4             pyhd8ed1ab_0    conda-forge
param                     1.12.0             pyh6c4a22f_0    conda-forge
parquet-cpp               1.5.1                         1    conda-forge
parso                     0.7.1              pyh9f0ad1d_0    conda-forge
partd                     1.2.0              pyhd8ed1ab_0    conda-forge
pathtools                 0.1.2                      py_1    conda-forge
pbr                       5.6.0              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pcre2                     10.37                h032f7d1_0    conda-forge
perl                      5.32.1          1_h7f98852_perl5    conda-forge
pexpect                   4.8.0            py38h32f6830_1    conda-forge
pickleshare               0.7.5           py38h32f6830_1002    conda-forge
pillow                    8.4.0            py38h5aabda8_0  
pip                       21.3.1             pyhd8ed1ab_0    conda-forge
platformdirs              2.3.0              pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0            py38h578d9bd_1    conda-forge
prettytable               2.2.1              pyhd8ed1ab_0    conda-forge
prometheus_client         0.11.0             pyhd8ed1ab_0    conda-forge
promise                   2.3              py38h578d9bd_4    conda-forge
prompt-toolkit            3.0.21             pyha770c72_0    conda-forge
protobuf                  3.18.1           py38h709712a_0    conda-forge
psutil                    5.8.0            py38h497a2fe_1    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
py-xgboost                1.5.0            py38h578d9bd_0    conda-forge
pyarrow                   5.0.0           py38h1bc9799_8_cpu    conda-forge
pyasn1                    0.4.8                      py_0    conda-forge
pyasn1-modules            0.2.8                      py_0  
pycodestyle               2.6.0              pyh9f0ad1d_0    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pyct                      0.4.8                    py38_0  
pydocstyle                6.1.1              pyhd8ed1ab_0    conda-forge
pyflakes                  2.2.0              pyh9f0ad1d_0    conda-forge
pygments                  2.10.0             pyhd8ed1ab_0    conda-forge
pyjwt                     2.3.0              pyhd8ed1ab_0    conda-forge
pylint                    2.11.1             pyhd8ed1ab_0    conda-forge
pynndescent               0.5.5              pyh6c4a22f_0    conda-forge
pynvml                    11.0.0             pyhd8ed1ab_0    conda-forge
pyopenssl                 21.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.3              pyhd8ed1ab_0    conda-forge
pyperclip                 1.8.2              pyhd8ed1ab_2    conda-forge
pyqt                      5.12.3           py38h578d9bd_7    conda-forge
pyqt-impl                 5.12.3           py38h7400c14_7    conda-forge
pyqt5-sip                 4.19.18          py38h709712a_7    conda-forge
pyqtchart                 5.12             py38h7400c14_7    conda-forge
pyqtwebengine             5.12.1           py38h7400c14_7    conda-forge
pyrsistent                0.17.3           py38h497a2fe_2    conda-forge
pysocks                   1.7.1            py38h578d9bd_3    conda-forge
python                    3.8.12          hb7a2778_2_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-jsonrpc-server     0.4.0              pyh9f0ad1d_0    conda-forge
python-language-server    0.36.2             pyhd8ed1ab_0    conda-forge
python_abi                3.8                      2_cp38    conda-forge
pytz                      2021.3             pyhd8ed1ab_0    conda-forge
pyu2f                     0.1.5              pyhd8ed1ab_0    conda-forge
pyviz_comms               2.1.0              pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py38h497a2fe_0    conda-forge
pyzmq                     22.3.0           py38h2035c66_0    conda-forge
qt                        5.12.9               hda022c4_4    conda-forge
re2                       2021.09.01           h9c3ff4c_0    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
requests                  2.26.0             pyhd8ed1ab_0    conda-forge
requests-oauthlib         1.3.0              pyh9f0ad1d_0    conda-forge
requests-unixsocket       0.2.0                      py_0    conda-forge
rope                      0.21.0             pyhd8ed1ab_0    conda-forge
rsa                       4.7.2              pyh44b312d_0    conda-forge
rx                        1.6.1                      py_0    conda-forge
s2n                       1.0.10               h9b69904_0    conda-forge
scikit-learn              1.0.1            py38hacb3eff_1    conda-forge
scipy                     1.7.1            py38h56a6a73_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
sentry-sdk                1.4.3              pyhd8ed1ab_0    conda-forge
setuptools                58.2.0           py38h578d9bd_0    conda-forge
shap                      0.40.0           py38h43a58ef_0    conda-forge
shortuuid                 1.0.1            py38h578d9bd_4    conda-forge
simpervisor               0.4                pyhd8ed1ab_0    conda-forge
six                       1.15.0                   pypi_0    pypi
slicer                    0.0.7              pyhd8ed1ab_0    conda-forge
smmap                     3.0.5              pyh44b312d_0    conda-forge
snappy                    1.1.8                he1b5a44_3    conda-forge
sniffio                   1.2.0            py38h578d9bd_1    conda-forge
snowballstemmer           2.1.0              pyhd8ed1ab_0    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
sqlalchemy                1.4.26           py38h497a2fe_0    conda-forge
sqlite                    3.36.0               h9cd32fc_2    conda-forge
stevedore                 3.5.0            py38h578d9bd_0    conda-forge
subprocess32              3.5.4                      py_1    conda-forge
sysroot_linux-64          2.12                he073ed8_14    conda-forge
tabulate                  0.8.9                    pypi_0    pypi
tbb                       2021.4.0             h4bd325d_0    conda-forge
tblib                     1.7.0              pyhd8ed1ab_0    conda-forge
tensorboard               2.6.0              pyhd8ed1ab_1    conda-forge
tensorboard-data-server   0.6.0            py38h3e25421_0    conda-forge
tensorboard-plugin-wit    1.8.0              pyh44b312d_0    conda-forge
tensorflow                2.6.0                    pypi_0    pypi
tensorflow-estimator      2.6.0                    pypi_0    pypi
termcolor                 1.1.0                    pypi_0    pypi
terminado                 0.12.1           py38h578d9bd_0    conda-forge
testpath                  0.5.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             3.0.0              pyh8a188c0_0    conda-forge
tk                        8.6.11               h27826a3_1    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
toolz                     0.11.1                     py_0    conda-forge
tornado                   6.1              py38h497a2fe_1    conda-forge
tqdm                      4.62.3             pyhd8ed1ab_0    conda-forge
traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge
typing-extensions         3.7.4.3                  pypi_0    pypi
ujson                     4.2.0            py38h709712a_0    conda-forge
umap-learn                0.5.1            py38h578d9bd_1    conda-forge
urllib3                   1.26.7             pyhd8ed1ab_0    conda-forge
wandb                     0.12.1             pyhd8ed1ab_0    conda-forge
watchdog                  0.10.4           py38h578d9bd_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          0.58.0           py38h06a4308_4  
werkzeug                  2.0.1              pyhd8ed1ab_0    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
woodwork                  0.8.2              pyhd8ed1ab_0    conda-forge
wrapt                     1.12.1           py38h497a2fe_3    conda-forge
xarray                    0.19.0             pyhd8ed1ab_1    conda-forge
xeus                      2.2.0                hab3612f_0    conda-forge
xeus-python               0.13.5           py38hcf90354_0    conda-forge
xeus-python-shell         0.1.7              pyhd8ed1ab_0    conda-forge
xgboost                   1.5.0            py38h578d9bd_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h516909a_0    conda-forge
yapf                      0.31.0             pyhd8ed1ab_0    conda-forge
yarl                      1.7.0            py38h497a2fe_0    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zict                      2.0.0                      py_0    conda-forge
zipp                      3.6.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
zstd                      1.5.0                ha95c52a_0    conda-forge

Do you have any ideas as to what is going on here?

isuruf commented 2 years ago

You should use jax from conda-forge too. It depends on the order that libstdc++.so is loaded in. For eg: if you import jax first which links to the older libstdc++ from the system, that will get loaded instead of the one from conda env that scipy depends on. If you import scipy first, then it'll work.

davidrpugh commented 2 years ago

I would if I could but the current jax and jaxlib available via Conda don’t yet support GPUs. There is an open ticket for this but it is stuck for some reason.

Just to confirm I understand, this error message has nothing to do with glibc version but rather the libstdc++ version? Also glibc is never distributed by Conda? The README of this package specifically mentions glibc which is what made me think that this was how you change the version of glibc on your Conda environment.

Thanks again for your help!

Sent from my iPhone

On Oct 28, 2021, at 20:41, Isuru Fernando @.***> wrote:

 You should use jax from conda-forge too. It depends on the order that libstdc++.so is loaded in. For eg: if you import jax first which links to the older libstdc++ from the system, that will get loaded instead of the one from conda env that scipy depends on. If you import scipy first, then it'll work.

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isuruf commented 2 years ago

Just to confirm I understand, this error message has nothing to do with glibc version but rather the libstdc++ version?

Yes.

Also glibc is never distributed by Conda?

Yes. glibc in this package is used only when compiling packages. glibc in the user's OS is used at runtime.