Traceback (most recent call last):
File "./bert/run_classifier.py", line 981, in <module>
tf.app.run()
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/platform/app.py", line 40, in run
_run(main=main, argv=argv, flags_parser=_parse_flags_tolerate_undef)
File "/usr/local/lib/python3.5/dist-packages/absl/app.py", line 299, in run
_run_main(main, args)
File "/usr/local/lib/python3.5/dist-packages/absl/app.py", line 250, in _run_main
sys.exit(main(argv))
File "./bert/run_classifier.py", line 808, in main
tf.gfile.MakeDirs(FLAGS.output_dir)
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/lib/io/file_io.py", line 438, in recursive_create_dir
recursive_create_dir_v2(dirname)
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/lib/io/file_io.py", line 453, in recursive_create_dir_v2
pywrap_tensorflow.RecursivelyCreateDir(compat.as_bytes(path))
tensorflow.python.framework.errors_impl.PermissionDeniedError: /MRPC-output; Permission denied
I am following the BERT example on the Google Cloud platform. (https://cloud.google.com/tpu/docs/tutorials/bert?hi)
In the last process, after input the next code, I got an error that permission denied.
python3 ./bert/run_classifier.py \
--task_name=${TASK_NAME} \
--do_train=true \
--do_eval=true \
--data_dir=$GLUE_DIR/${TASK_NAME} \
--vocab_file=$BERT_BASE_DIR/vocab.txt \
--bert_config_file=$BERT_BASE_DIR/bert_config.json \
--init_checkpoint=$BERT_BASE_DIR/bert_model.ckpt \
--max_seq_length=128 \
--train_batch_size=32 \
--learning_rate=2e-5 \
--num_train_epochs=3.0 \
--output_dir=${STORAGE_BUCKET}/${TASK_NAME}-output/ \
--use_tpu=True \
--tpu_name=$TPU_NAME
what should I do?
Thanks for your answer in advance.
Related
Description
When I tried to deploy an egg file to the scrapyd server within a docker container, it always returned a DistributionNotFound error for each external package.
I tried both with curl and scrapyd-deploy
Steps to Reproduce
python setup.py bdist_uberegg -r requirements.txt
curl http://localhost:13334/addversion.json -F project=pr_reviews -F version=1.0.0 -F egg=.\dist\project-1.0-py3.10.egg
or
scrapyd-deploy --include-dependencies
Actual behavior: [What actually happens]
$ curl http://localhost:13334/addversion.json -F project=pr_reviews -F version=re1 -F egg=#".\dist\project-1.0-py3.10.egg"
{"node_name": "e9e273febed8", "status": "error", "message": "/usr/local/lib/python3.9/dist-packages/scrapy/utils/project.py:81: ScrapyDeprecationWarning: Use of environment variables prefixed with SCRAPY_ to override settings is deprecated. The following environment variables are currently defined: EGG_VERSION\n warnings.warn(\nTraceback (most recent call last):\n File \"/usr/lib/python3.9/runpy.py\", line 197, in _run_module_as_main\n return _run_code(code, main_globals, None,\n File \"/usr/lib/python3.9/runpy.py\", line 87, in _run_code\n exec(code, run_globals)\n File \"/usr/local/lib/python3.9/dist-packages/scrapyd/runner.py\", line 46, in <module>\n main()\n File \"/usr/local/lib/python3.9/dist-packages/scrapyd/runner.py\", line 43, in main\n execute()\n File \"/usr/local/lib/python3.9/dist-packages/scrapy/cmdline.py\", line 144, in execute\n cmd.crawler_process = CrawlerProcess(settings)\n File \"/usr/local/lib/python3.9/dist-packages/scrapy/crawler.py\", line 290, in __init__\n super().__init__(settings)\n File \"/usr/local/lib/python3.9/dist-packages/scrapy/crawler.py\", line 167, in __init__\n self.spider_loader = self._get_spider_loader(settings)\n
File \"/usr/local/lib/python3.9/dist-packages/scrapy/crawler.py\", line 161, in _get_spider_loader\n return loader_cls.from_settings(settings.frozencopy())\n File \"/usr/local/lib/python3.9/dist-packages/scrapy/spiderloader.py\", line 67, in from_settings\n return cls(settings)\n File \"/usr/local/lib/python3.9/dist-packages/scrapy/spiderloader.py\", line 24, in __init__\n self._load_all_spiders()\n File \"/usr/local/lib/python3.9/dist-packages/scrapy/spiderloader.py\", line 51, in _load_all_spiders\n for module in walk_modules(name):\n File \"/usr/local/lib/python3.9/dist-packages/scrapy/utils/misc.py\", line 88, in walk_modules\n submod = import_module(fullpath)\n File \"/usr/lib/python3.9/importlib/__init__.py\", line 127, in import_module\n return _bootstrap._gcd_import(name[level:], package, level)\n File \"<frozen importlib._bootstrap>\", line 1030, in _gcd_import\n File \"<frozen importlib._bootstrap>\", line 1007, in _find_and_load\n File \"<frozen importlib._bootstrap>\", line 986, in _find_and_load_unlocked\n File \"<frozen importlib._bootstrap>\", line 664, in _load_unlocked\n File \"<frozen importlib._bootstrap>\", line 627, in _load_backward_compatible\n File \"<frozen zipimport>\", line 259, in load_module\n File \"/tmp/pr_reviews-re1-vukl7x51.egg/pr_reviews/spiders/ReviewCrawler.py\", line 2, in <module>\n File \"<frozen importlib._bootstrap>\", line 1007, in _find_and_load\n File \"<frozen importlib._bootstrap>\", line 986, in _find_and_load_unlocked\n File \"<frozen importlib._bootstrap>\", line 664, in _load_unlocked\n File \"<frozen importlib._bootstrap>\", line 627, in _load_backward_compatible\n File \"<frozen zipimport>\", line 259, in load_module\n File \"/tmp/pr_reviews-re1-vukl7x51.egg/pr_reviews/items.py\", line 4, in <module>\n File \"<frozen importlib._bootstrap>\", line 1007, in _find_and_load\n File \"<frozen importlib._bootstrap>\", line 986, in _find_and_load_unlocked\n File \"<frozen importlib._bootstrap>\", line 664, in _load_unlocked\n File \"<frozen importlib._bootstrap>\", line 627, in _load_backward_compatible\n File \"<frozen zipimport>\", line 259, in load_module\n File \"/tmp/pr_reviews-re1-vukl7x51.egg/pycountry/__init__.py\", line 13, in <module>\n File \"/usr/local/lib/python3.9/dist-packages/pkg_resources/__init__.py\", line 478, in get_distribution\n dist = get_provider(dist)\n File \"/usr/local/lib/python3.9/dist-packages/pkg_resources/__init__.py\", line 354, in get_provider\n return working_set.find(moduleOrReq) or require(str(moduleOrReq))[0]\n File \"/usr/local/lib/python3.9/dist-packages/pkg_resources/__init__.py\", line 909, in require\n needed = self.resolve(parse_requirements(requirements))\n File \"/usr/local/lib/python3.9/dist-packages/pkg_resources/__init__.py\", line 795, in resolve\n raise DistributionNotFound(req, requirers)\npkg_resources.DistributionNotFound: The 'pycountry' distribution was not found and is required by the application\n"}
setup.py
from setuptools import setup, find_packages
setup(
name='project',
version='1.0',
packages=find_packages(),
install_requires=[
"itemadapter",
"langdetect",
"pycountry",
"scrapy",
"setuptools",
"scrapy_zyte_smartproxy",
"scrapy_user_agents"
],
entry_points={'scrapy': ['settings = pr_reviews.settings']},
)
requirements.txt
itemadapter==0.6.0
langdetect==1.0.9
pycountry==22.3.5
scrapy==2.6.1
setuptools==63.1.0
scrapy_zyte_smartproxy==2.1.0
scrapy_user_agents==0.1.1
Scrapd server
FROM ubuntu:20.04
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update -qq \
&& apt-get install -y tini git python3.9 python3.9-dev python3.9-distutils curl python3.9-venv build-essential libxml2-dev libxslt1-dev zlib1g-dev libffi-dev libssl-dev nginx apache2-utils \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
RUN python3.9 get-pip.py
ADD requirements.txt /
RUN python3.9 -m pip install -r /requirements.txt
RUN python3.9 -m pip install -e git+https://github.com/necrophcodr/chaperone.git#egg=chaperone
RUN mkdir /etc/chaperone.d
COPY ./scrapyd.conf /etc/scrapyd/
VOLUME /etc/scrapyd/ /var/lib/scrapyd/
EXPOSE 6800
ENTRYPOINT ["tini", "--"]
CMD ["scrapyd", "--pidfile="]
I am deploying a Docker container with AWS Lambda which executes a machine learning model. But whenever I attempt to load the saved checkpoints, I am getting a permission denied message when attempting to read the local filesystem or a no directory found based on where I am storing the model...?
Here is the relevant Dockerfile:
FROM public.ecr.aws/lambda/python:3.8
# copy requirements.txt file to the container
COPY requirements.txt ./
# upgrade pip and install the python requirements from requirements.txt
RUN python3.8 -m pip install \
--upgrade pip
RUN python3.8 -m pip install \
-r requirements.txt
# Copy function code
COPY app.py ./
# Install the runtime interface client
RUN python3.8 -m pip install \
awslambdaric
# clean up image for small container
RUN find . -type d -name "tests" -exec rm -rf {} +
RUN find . -type d -name "__pycache__" -exec rm -rf {} +
RUN find . -type d -name "include" -exec rm -rf {} +
RUN rm -rf ./{caffe2,wheel,wheel-*,pkg_resources,boto*,aws*,pip,pip-*,pipenv,setuptools}
RUN rm -rf ./{*.egg-info,*.dist-info}
RUN find . -name \*.pyc -delete
RUN find . -type d -name "test" -exec rm -rf {} +
RUN ls -R -al
# update linux libraries
RUN yum update -y
# install python3 and unzip
RUN yum install -y python3 unzip
# pull model files
RUN mkdir ./model
RUN curl https://somewhere.com/model.zip -o ./model/model.zip
RUN unzip ./model/model.zip -d ./model
RUN chmod 644 ./model
RUN chmod -R 644 ./model/*
RUN rm ./model/model.zip
WORKDIR ./
ENTRYPOINT [ "python3", "-m", "awslambdaric" ]
CMD [ "app.lambda_handler" ]
And the app.py:
from __future__ import print_function
import json, time
import urllib.request
from jose import jwk, jwt
from jose.utils import base64url_decode
from sentence_transformers import SentenceTransformer, util
model = ModelFunction('/model')
def lambda_handler(event, context):
body = json.loads(event['body'])
token = body['jwttoken']
utterance = body['utterance']
comparestring = body['comparestring']
# generate embeddings for each phrase
embeddings1 = model.encode(utterance, convert_to_tensor=True)
embeddings2 = model.encode(comparestring, convert_to_tensor=True)
# compute score
score = util.embeddings(embeddings1, embeddings2)
# output score
print("Score:")
print(score.item())
return {
"statusCode": 200,
"score": json.dums(score.item())
}
# the following is useful to make this script executable in both
# AWS Lambda and any other local environments
if __name__ == '__main__':
event = {
'token': '',
'email': 'somewhere#somewhere.com'}
lambda_handler(event, None)
A couple of the relevant error messages:
[ERROR] PermissionError: [Errno 13] Permission denied: './model/modules.json'
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/app.py", line 8, in <module>
model = model('./model')
File "/var/lang/lib/python3.8/site-packages/model/model.py", line 115, in __init__
with open(os.path.join(model_path, 'modules.json')) as fIn:
and
[ERROR] FileNotFoundError: [Errno 2] No such file or directory: '/home/sbx_user1051/.cache/model'
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/app.py", line 8, in <module>
model = model('/model')
File "/var/lang/lib/python3.8/site-packages/model/model.py", line 101, in __init__
shutil.rmtree(model_path)
File "/var/lang/lib/python3.8/shutil.py", line 709, in rmtree
onerror(os.lstat, path, sys.exc_info())
File "/var/lang/lib/python3.8/shutil.py", line 707, in rmtree
orig_st = os.lstat(path)
Any ideas? I think I am not storing the model checkpoints in the correct directory? The above logs have been somewhat scrubbed due to NDA etc.
Try running:
chmod 644 $(find . -type f)
chmod 755 $(find . -type d)
on the files you're trying to deploy.
As the AWS Docs say, there may be a permissions issue if the files aren't set to be executable by any user.
Good day all!
I have written a very simple Ansible Role to update all packages to Suse Leap 15.2:
- name: All packages updated
package:
name: "*"
state: latest
but it seems that the Zypper module has a problem with it:
TASK [system_update : All packages updated] ***************************************************************************************************************************************************************************************************
task path: /home/merlin/ansible-kt-linux/roles/system_update/tasks/main.yml:10
<localhost> ESTABLISH LOCAL CONNECTION FOR USER: merlin
<localhost> EXEC /bin/sh -c 'echo ~merlin && sleep 0'
<localhost> EXEC /bin/sh -c '( umask 77 && mkdir -p "` echo /home/merlin/.ansible/tmp/ansible-tmp-1617094154.778992-48329012899811 `" && echo ansible-tmp-1617094154.778992-48329012899811="` echo /home/merlin/.ansible/tmp/ansible-tmp-1617094154.778992-48329012899811 `" ) && sleep 0'
Using module file /usr/lib/python3.6/site-packages/ansible/modules/packaging/os/zypper.py
<localhost> PUT /home/merlin/.ansible/tmp/ansible-local-5239dx5tukgw/tmpvf5upp37 TO /home/merlin/.ansible/tmp/ansible-tmp-1617094154.778992-48329012899811/AnsiballZ_zypper.py
<localhost> EXEC /bin/sh -c 'chmod u+x /home/merlin/.ansible/tmp/ansible-tmp-1617094154.778992-48329012899811/ /home/merlin/.ansible/tmp/ansible-tmp-1617094154.778992-48329012899811/AnsiballZ_zypper.py && sleep 0'
<localhost> EXEC /bin/sh -c 'sudo -H -S -n -u root /bin/sh -c '"'"'echo BECOME-SUCCESS-qfmrjmpwqhyapufsdqunaohtmlxjucdk ; /usr/bin/python /home/merlin/.ansible/tmp/ansible-tmp-1617094154.778992-48329012899811/AnsiballZ_zypper.py'"'"' && sleep 0'
<localhost> EXEC /bin/sh -c 'rm -f -r /home/merlin/.ansible/tmp/ansible-tmp-1617094154.778992-48329012899811/ > /dev/null 2>&1 && sleep 0'
The full traceback is:
Traceback (most recent call last):
File "/home/merlin/.ansible/tmp/ansible-tmp-1617094154.778992-48329012899811/AnsiballZ_zypper.py", line 102, in <module>
_ansiballz_main()
File "/home/merlin/.ansible/tmp/ansible-tmp-1617094154.778992-48329012899811/AnsiballZ_zypper.py", line 94, in _ansiballz_main
invoke_module(zipped_mod, temp_path, ANSIBALLZ_PARAMS)
File "/home/merlin/.ansible/tmp/ansible-tmp-1617094154.778992-48329012899811/AnsiballZ_zypper.py", line 40, in invoke_module
runpy.run_module(mod_name='ansible.modules.packaging.os.zypper', init_globals=None, run_name='__main__', alter_sys=True)
File "/usr/lib64/python2.7/runpy.py", line 188, in run_module
fname, loader, pkg_name)
File "/usr/lib64/python2.7/runpy.py", line 82, in _run_module_code
mod_name, mod_fname, mod_loader, pkg_name)
File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/tmp/ansible_zypper_payload_jYlnfB/ansible_zypper_payload.zip/ansible/modules/packaging/os/zypper.py", line 195, in <module>
ImportError: No module named xml
fatal: [localhost]: FAILED! => {
"changed": false,
"module_stderr": "Traceback (most recent call last):\n File \"/home/merlin/.ansible/tmp/ansible-tmp-1617094154.778992-48329012899811/AnsiballZ_zypper.py\", line 102, in <module>\n _ansiballz_main()\n File \"/home/merlin/.ansible/tmp/ansible-tmp-1617094154.778992-48329012899811/AnsiballZ_zypper.py\", line 94, in _ansiballz_main\n invoke_module(zipped_mod, temp_path, ANSIBALLZ_PARAMS)\n File \"/home/merlin/.ansible/tmp/ansible-tmp-1617094154.778992-48329012899811/AnsiballZ_zypper.py\", line 40, in invoke_module\n runpy.run_module(mod_name='ansible.modules.packaging.os.zypper', init_globals=None, run_name='__main__', alter_sys=True)\n File \"/usr/lib64/python2.7/runpy.py\", line 188, in run_module\n fname, loader, pkg_name)\n File \"/usr/lib64/python2.7/runpy.py\", line 82, in _run_module_code\n mod_name, mod_fname, mod_loader, pkg_name)\n File \"/usr/lib64/python2.7/runpy.py\", line 72, in _run_code\n exec code in run_globals\n File \"/tmp/ansible_zypper_payload_jYlnfB/ansible_zypper_payload.zip/ansible/modules/packaging/os/zypper.py\", line 195, in <module>\nImportError: No module named xml\n",
"module_stdout": "",
"msg": "MODULE FAILURE\nSee stdout/stderr for the exact error",
"rc": 1
}
PLAY RECAP ************************************************************************************************************************************************************************************************************************************
localhost : ok=2 changed=0 unreachable=0 failed=1 skipped=0 rescued=0 ignored=0
unfortunately I can't read from this what exactly the problem is. Do any of you know the problem?
solved it with shell:
- name: "Install python-xml on Suse"
shell: zypper -n install python-xml
[QTL-seq:2019-10-09 09:13:37] !!ERROR!! bcftools concat -a -O z -o Chikpea_qtl/30_vcf/qtlseq.vcf.gz Chikpea_qtl/30_vcf/qtlseq.*.vcf.gz >> Chikpea_qtl/log/bcftools.log 2>&1
Failed to open Chikpea_qtl/30_vcf/qtlseq.NW_004516646.1.vcf.gz: could not load index
Traceback (most recent call last):
File "/home/jthakur/Desktop/Software/QTL-seq/qtlseq/mpileup.py", line 191, in concat
check=True)
File "/home/jthakur/anaconda2/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'bcftools concat -a -O z -o Chikpea_qtl/30_vcf/qtlseq.vcf.gz Chikpea_qtl/30_vcf/qtlseq.*.vcf.gz >> Chikpea_qtl/log/bcftools.log 2>&1' returned non-zero exit status 255.
Traceback (most recent call last):
File "/home/jthakur/anaconda2/bin/qtlseq", line 11, in
load_entry_point('qtlseq', 'console_scripts', 'qtlseq')()
File "/home/jthakur/Desktop/Software/QTL-seq/qtlseq/qtlseq.py", line 192, in main
QTLseq(args).run()
File "/home/jthakur/Desktop/Software/QTL-seq/qtlseq/qtlseq.py", line 123, in mpileup
mp.run()
File "/home/jthakur/Desktop/Software/QTL-seq/qtlseq/mpileup.py", line 232, in run
self.concat()
File "/home/jthakur/Desktop/Software/QTL-seq/qtlseq/mpileup.py", line 194, in concat
sys.exit()
NameError: name 'sys' is not defined
I got this shell script from a blog about how to equip git with gitosis.
But i got a "No such file or directory" error after running the script.
[git#209285 ~]$ sudo -H -u git gitosis-init < ~/id_rsa.pub
Traceback (most recent call last):
File "/usr/local/bin/gitosis-init", line 9, in <module>
load_entry_point('gitosis==0.2', 'console_scripts', 'gitosis-init')()
File "/usr/local/lib/python2.7/site-packages/gitosis-0.2-py2.7.egg/gitosis/app.py", line 24, in run
return app.main()
File "/usr/local/lib/python2.7/site-packages/gitosis-0.2-py2.7.egg/gitosis/app.py", line 38, in main
self.handle_args(parser, cfg, options, args)
File "/usr/local/lib/python2.7/site-packages/gitosis-0.2-py2.7.egg/gitosis/init.py", line 138, in handle_args
user=user,
File "/usr/local/lib/python2.7/site-packages/gitosis-0.2-py2.7.egg/gitosis/init.py", line 75, in init_admin_repository
template=resource_filename('gitosis.templates', 'admin')
File "/usr/local/lib/python2.7/site-packages/gitosis-0.2-py2.7.egg/gitosis/repository.py", line 63, in init
close_fds=True,
File "/usr/local/lib/python2.7/subprocess.py", line 522, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/local/lib/python2.7/subprocess.py", line 710, in __init__
errread, errwrite)
File "/usr/local/lib/python2.7/subprocess.py", line 1335, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
I am puzzled,as the man manual says that:
-H The -H (HOME) option sets the HOME environment variable to the homedir of the target user (root by default) as specified in passwd(5). By default, sudo
does not modify HOME (see set_home and always_set_home in sudoers(5)).
,which is cited from linux manual.
The -H option just sets the HOME environment variable to the homedir of the target user as specified in passwd.
However i specified "/home/git" as homedir for git user in my /etc/passwd file.
apache:x:48:48:Apache:/var/www:/sbin/nologin
git:x:100:101:git version control:/home/git:/bin/bash
duanduan:x:101:500::/home/duanduan:/bin/bash
But why i still got this message? or was incorrect my comprehension of the description in manual?
Append for comments:
And it seems like before with specifying a absolute path.Maybe, it's not the cause.
sudo -H -u git gitosis-init < /home/git/id_rsa.pub
Traceback (most recent call last):
File "/usr/local/bin/gitosis-init", line 9, in <module>
load_entry_point('gitosis==0.2', 'console_scripts', 'gitosis-init')()
File "/usr/local/lib/python2.7/site-packages/gitosis-0.2-py2.7.egg/gitosis/app.py", line 24, in run
return app.main()
File "/usr/local/lib/python2.7/site-packages/gitosis-0.2-py2.7.egg/gitosis/app.py", line 38, in main
self.handle_args(parser, cfg, options, args)
File "/usr/local/lib/python2.7/site-packages/gitosis-0.2-py2.7.egg/gitosis/init.py", line 138, in handle_args
user=user,
File "/usr/local/lib/python2.7/site-packages/gitosis-0.2-py2.7.egg/gitosis/init.py", line 75, in init_admin_repository
template=resource_filename('gitosis.templates', 'admin')
File "/usr/local/lib/python2.7/site-packages/gitosis-0.2-py2.7.egg/gitosis/repository.py", line 63, in init
close_fds=True,
File "/usr/local/lib/python2.7/subprocess.py", line 522, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/local/lib/python2.7/subprocess.py", line 710, in __init__
errread, errwrite)
File "/usr/local/lib/python2.7/subprocess.py", line 1335, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
I guess it is because ~ is expanded by bash before transferring to sudo as a argument, why not try to specify a absolute path for you public key file?