James Scott
Reputation: 181
Python AWS Lambda Error "libgomp.so.1: cannot open shared object file: No such file or directory" from AWS EFS file system mounted on Ubuntu
I have an AWS lambda function connected to an AWS EFS mounted on a EC2 instance of Ubunutu 18. I am getting this error below when importing a LightGBM model i believe.
{
"errorMessage": "libgomp.so.1: cannot open shared object file: No such file or directory",
"errorType": "OSError",
"stackTrace": [
" File \"/var/lang/lib/python3.8/imp.py\", line 234, in load_module\n return load_source(name, filename, file)\n",
" File \"/var/lang/lib/python3.8/imp.py\", line 171, in load_source\n module = _load(spec)\n",
" File \"<frozen importlib._bootstrap>\", line 702, in _load\n",
" File \"<frozen importlib._bootstrap>\", line 671, in _load_unlocked\n",
" File \"<frozen importlib._bootstrap_external>\", line 848, in exec_module\n",
" File \"<frozen importlib._bootstrap>\", line 219, in _call_with_frames_removed\n",
" File \"/var/task/lambda_function.py\", line 9, in <module>\n from supervised.automl import AutoML\n",
" File \"/mnt/access/supervised/__init__.py\", line 3, in <module>\n from supervised.automl import AutoML\n",
" File \"/mnt/access/supervised/automl.py\", line 3, in <module>\n from supervised.base_automl import BaseAutoML\n",
" File \"/mnt/access/supervised/base_automl.py\", line 21, in <module>\n from supervised.algorithms.registry import AlgorithmsRegistry\n",
" File \"/mnt/access/supervised/algorithms/registry.py\", line 74, in <module>\n import supervised.algorithms.lightgbm\n",
" File \"/mnt/access/supervised/algorithms/lightgbm.py\", line 8, in <module>\n import lightgbm as lgb\n",
" File \"/mnt/access/lightgbm/__init__.py\", line 8, in <module>\n from .basic import Booster, Dataset\n",
" File \"/mnt/access/lightgbm/basic.py\", line 43, in <module>\n _LIB = _load_lib()\n",
" File \"/mnt/access/lightgbm/basic.py\", line 34, in _load_lib\n lib = ctypes.cdll.LoadLibrary(lib_path[0])\n",
" File \"/var/lang/lib/python3.8/ctypes/__init__.py\", line 451, in LoadLibrary\n return self._dlltype(name)\n",
" File \"/var/lang/lib/python3.8/ctypes/__init__.py\", line 373, in __init__\n self._handle = _dlopen(self._name, mode)\n"
]
}
My package list installed
ubuntu@ip-***-**-**-***:~/mounted/access$ ls
ConfigSpace category_encoders-2.2.2.dist-info examples matplotlib plotlywidget scikit_plot-0.3.7.dist-info tabulate.py
ConfigSpace-0.4.19.dist-info click fsspec matplotlib-3.4.2-py3.8-nspkg.pth pluggy scikitplot tblib
Cython click-8.0.1.dist-info fsspec-2021.5.0.dist-info matplotlib-3.4.2.dist-info pluggy-0.13.1.dist-info scipy tblib-1.7.0.dist-info
Cython-0.29.23.dist-info cliff graphviz mljar_supervised-0.10.4.dist-info prettytable scipy-1.6.1.dist-info testing
HeapDict-1.0.1.dist-info cliff-3.8.0.dist-info graphviz-0.16.dist-info mpl_toolkits prettytable-2.1.0.dist-info scipy-1.6.3.dist-info threadpoolctl-2.1.0.dist-info
Mako-1.1.4.dist-info cloudpickle greenlet msgpack psutil scipy.libs threadpoolctl.py
Markdown-3.3.4.dist-info cloudpickle-1.3.0.dist-info greenlet-1.1.0.dist-info msgpack-1.0.2.dist-info psutil-5.8.0.dist-info seaborn tlz
MarkupSafe-2.0.1.dist-info cloudpickle-1.6.0.dist-info heapdict.py numba py seaborn-0.11.1.dist-info toml
PIL cmaes include numba-0.48.0.dist-info py-1.10.0.dist-info setuptools toml-0.10.2.dist-info
Pillow-8.2.0.dist-info cmaes-0.8.2.dist-info iniconfig numba-0.53.1.dist-info pyarrow setuptools-57.0.0.dist-info toolz
Pillow.libs cmd2 iniconfig-1.1.1.dist-info numpy pyarrow-4.0.1.dist-info shap toolz-0.11.1.dist-info
PyYAML-5.4.1.dist-info cmd2-1.5.0.dist-info intel_openmp-2021.2.0.dist-info numpy-1.20.3.dist-info pylab.py shap-0.36.0.dist-info tornado
SQLAlchemy-1.4.17.dist-info colorama joblib numpy.libs pynisher share tornado-6.1.dist-info
__pycache__ colorama-0.4.4.dist-info joblib-1.0.1.dist-info optuna pynisher-0.6.4.dist-info six-1.16.0.dist-info tqdm
_distutils_hack colorlog kiwisolver-1.3.1.dist-info optuna-2.7.0.dist-info pyparsing-2.4.7.dist-info six.py tqdm-4.61.0.dist-info
_plotly_future_ colorlog-5.0.1.dist-info kiwisolver.cpython-38-x86_64-linux-gnu.so packaging pyparsing.py sklearn wcwidth
_plotly_utils colour-0.1.5.dist-info lazy_import packaging-20.9.dist-info pyperclip sklearn-0.0.dist-info wcwidth-0.2.5.dist-info
_pytest colour.py lazy_import-0.2.2.dist-info pandas pyperclip-1.8.2.dist-info slicer wheel
_yaml cycler-0.10.0.dist-info liac_arff-2.5.0.dist-info pandas-1.2.0.dist-info pyrfr slicer-0.0.7.dist-info wheel-0.36.2.dist-info
alembic cycler.py licensing pandas-1.2.4.dist-info pyrfr-0.8.2.dist-info smac wordcloud
alembic-1.6.5.dist-info cython.py lightgbm partd pytest smac-0.13.1.dist-info wordcloud-1.8.1.dist-info
apt.txt dask lightgbm-3.0.0.dist-info partd-1.2.0.dist-info pytest-6.2.4.dist-info somefile.txt xgboost
arff.py dask-2021.6.0.dist-info llvmlite patsy python_dateutil-2.8.1.dist-info sortedcontainers xgboost-1.3.3.dist-info
attr dateutil llvmlite-0.31.0.dist-info patsy-0.5.1.dist-info python_editor-1.0.4.dist-info sortedcontainers-2.4.0.dist-info xgboost-1.4.2.dist-info
attrs-21.2.0.dist-info distributed llvmlite-0.36.0.dist-info pbr pytz sqlalchemy xgboost.libs
auto_sklearn-0.12.6.dist-info distributed-2021.6.0.dist-info local pbr-5.6.0.dist-info pytz-2021.1.dist-info statsmodels yaml
autosklearn distutils-precedence.pth locket pip pyximport statsmodels-0.12.2.dist-info zict
bin dtreeviz locket-0.2.1.dist-info pip-21.1.2.dist-info retrying-1.3.3.dist-info stevedore zict-2.0.0.dist-info
catboost dtreeviz-1.3.dist-info mako pkg_resources retrying.py stevedore-3.3.0.dist-info
catboost-0.24.4.dist-info editor.py markdown plotly scikit_learn-0.24.2.dist-info supervised
category_encoders etc markupsafe plotly-4.14.3.dist-info scikit_learn.libs tabulate-0.8.7.dist-info
if anyone knows how to resolves this error or if more information is needed please help!
Function Logs
START RequestId: 576d0bf7-1cdb-4f98-bd6d-ba807d0af0bb Version: $LATEST
OpenBLAS WARNING - could not determine the L2 cache size on this system, assuming 256k
/mnt/access/joblib/_multiprocessing_helpers.py:45: UserWarning: [Errno 38] Function not implemented. joblib will operate in serial mode
warnings.warn('%s. joblib will operate in serial mode' % (e,))
OpenBLAS WARNING - could not determine the L2 cache size on this system, assuming 256k
[WARNING] 2021-06-05T00:57:04.711Z Matplotlib created a temporary config/cache directory at /tmp/matplotlib-bw2u754h because the default path (/home/sbx_user1051/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
[ERROR] OSError: libgomp.so.1: cannot open shared object file: No such file or directory
Traceback (most recent call last):
File "/var/lang/lib/python3.8/imp.py", line 234, in load_module
return load_source(name, filename, file)
File "/var/lang/lib/python3.8/imp.py", line 171, in load_source
module = _load(spec)
File "<frozen importlib._bootstrap>", line 702, in _load
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 848, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/var/task/lambda_function.py", line 9, in <module>
import lightgbm
File "/mnt/access/lightgbm/__init__.py", line 8, in <module>
from .basic import Booster, Dataset, register_logger
File "/mnt/access/lightgbm/basic.py", line 95, in <module>
_LIB = _load_lib()
File "/mnt/access/lightgbm/basic.py", line 86, in _load_lib
lib = ctypes.cdll.LoadLibrary(lib_path[0])
File "/var/lang/lib/python3.8/ctypes/__init__.py", line 451, in LoadLibrary
return self._dlltype(name)
File "/var/lang/lib/python3.8/ctypes/__init__.py", line 373, in __init__
self._handle = _dlopen(self._name, mode)END RequestId: 576d0bf7-1cdb-4f98-bd6d-ba807d0af0bb
REPORT RequestId: 576d0bf7-1cdb-4f98-bd6d-ba807d0af0bb Duration: 22908.85 ms Billed Duration: 22909 ms Memory Size: 5000 MB Max Memory Used: 243 MB
Unknown application error occurred
This is the log from the AWS lambda function, i have libgomp1 installed on my ec2 Ubuntu envirorment however im not to sure if the problem is in lambda or ubuntu. I can do an import of lightgbm just fine
Upvotes: 5
Views: 2614
Answers (1)
nuri
Reputation: 240
It's worth noting that the versions of libgomp.so and glibc can vary depending on the Amazon Lambda runtime version.
For more information, refer to https://repost.aws/questions/QUrXOioL46RcCnFGyELJWKLw/glibc-2-27-on-amazon-linux-2.
To address this, you can create a custom AWS Lambda layer by provisioning an Amazon Linux 2 instance on an EC2, downloading the required libgomp.so and glibc packages, and packaging them into a Lambda layer. Ensure that the AWS Lambda layer objects are located under the /lib folder, as specified in the documentation: https://docs.aws.amazon.com/lambda/latest/dg/packaging-layers.html.
Once this layer is added, the Lightgbm library should be importable in your Lambda environment.
here my layer for python 3.8! AWS-Lambda-Layers-v0.zip
Upvotes: 0
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