pip version
20.3.3
Python version
python:3.9.1
OS
Linux
Dockerfile:
FROM python:3.9.1
COPY --from=openjdk:11 /usr/local/openjdk-11 /usr/local/openjdk-11
RUN pip config set global.index-url https://pypi.doubanio.com/simple/
&& pip config set global.trusted-host pypi.doubanio.com
&& pip install Mako requests pymatgen apscheduler
ENV JAVA_HOME=/usr/local/openjdk-11
ENV PATH=${JAVA_HOME}/bin:$PATH
RUN java --version
docker info
?> ~/storage docker info 10:03:46
Client:
Context: default
Debug Mode: false
Plugins:
app: Docker App (Docker Inc., v0.9.1-beta3)
buildx: Build with BuildKit (Docker Inc., v0.5.1-docker)
Server:
Containers: 16
Running: 3
Paused: 0
Stopped: 13
Images: 40
Server Version: 20.10.3
Storage Driver: aufs
Root Dir: /home/matcloudplus/storage/docker/lib/aufs
Backing Filesystem: nfs
Dirs: 110
Dirperm1 Supported: true
Logging Driver: json-file
Cgroup Driver: cgroupfs
Cgroup Version: 1
Plugins:
Volume: local
Network: bridge host ipvlan macvlan null overlay
Log: awslogs fluentd gcplogs gelf journald json-file local logentries splunk syslog
Swarm: inactive
Runtimes: io.containerd.runc.v2 io.containerd.runtime.v1.linux runc
Default Runtime: runc
Init Binary: docker-init
containerd version: 269548fa27e0089a8b8278fc4fc781d7f65a939b
runc version: ff819c7e9184c13b7c2607fe6c30ae19403a7aff
init version: de40ad0
Security Options:
apparmor
seccomp
Profile: default
Kernel Version: 4.15.0-135-generic
Operating System: Ubuntu 18.04.5 LTS
OSType: linux
Architecture: x86_64
CPUs: 64
Total Memory: 125.9GiB
Name: iZ8vbgfaf2ya4gtguw9w0cZ
ID: JPSR:2ODB:X3IU:5UX3:2HUB:2Q3W:G3V3:2L5K:6MHF:3MCY:Y53N:UZMT
Docker Root Dir: /home/matcloudplus/storage/docker/lib
Debug Mode: false
Registry: https://index.docker.io/v1/
Labels:
Experimental: false
Insecure Registries:
127.0.0.0/8
Registry Mirrors:
https://6xnlqfhs.mirror.aliyuncs.com/
Live Restore Enabled: false
WARNING: No swap limit support
WARNING: the aufs storage-driver is deprecated, and will be removed in a future release.
Description
I installed docker in the system to build an image with both java and python3 environment. On other machines, such operations and building images are all successful. However, I found that the hard disk space in my linux system is insufficient, so I created a new directory and used
sudo mount -t nfs -o vers=3,nolock,proto=tcp,rsize=1048576,wsize=1048576,hard,timeo=600,retrans=2, noresvport /dev/vdb1 /home/matcloudplus/storage/ Mount the hard disk Loaded to my /home/matcloudplus/storage/ directory, and used the /home/matcloudplus/storage/docker/lib directory under this directory to replace the original /var/lib/docker, the following is my daemon.json content
{
"graph": "/home/matcloudplus/storage/docker/lib",
"registry-mirrors": ["https://6xnlqfhs.mirror.aliyuncs.com"]
}
Everything seems to be normal. However, when I build the image on this server, it fails all the time. When I execute the RUN command in the above dockerfile, it fails. When I cancel the mount of the hard disk and restart the docker, it just fails. The build can be successful, which makes me very puzzled. I mounted the NAS hard drive of the ALiYun service provider. When this happens, I don’t know whether to ask docker, python, pip, or aliyun, so I can only Post it again, I can’t solve this problem. The image I use requires that my hard disk occupancy rate not be higher than 75%, and my own physical machine has already exceeded this threshold. I must use a new hard disk, but this problem I can't solve it
Expected behavior
When the hard disk is not mounted，Normally build, the image is successfully built，log：
Collecting tabulate
Downloading https://pypi.doubanio.com/packages/c4/f4/770ae9385990f5a19a91431163d262182d3203662ea2b5739d0fcfc080f1/tabulate-0.8.7-py3-none-any.whl (24 kB)
Building wheels for collected packages: Mako, pymatgen, retrying, future, mpmath
Building wheel for Mako (setup.py): started
Building wheel for Mako (setup.py): finished with status 'done'
Created wheel for Mako: filename=Mako-1.1.4-py2.py3-none-any.whl size=75675 sha256=65b71013508748308ac6795ce732c697388739cb9ad90217d13dee87e47a31f2
Stored in directory: /root/.cache/pip/wheels/59/4e/c7/9fab27cd9efbe0dbb72e7e155d1ccf96d5931c736eda76cd0d
Building wheel for pymatgen (setup.py): started
Building wheel for pymatgen (setup.py): finished with status 'done'
Created wheel for pymatgen: filename=pymatgen-2020.12.31-cp39-cp39-linux_x86_64.whl size=3946314 sha256=2bca8de80e6d129150c469ec62ca89a16a6aec89163be47a04bbfd364554452c
Stored in directory: /root/.cache/pip/wheels/59/75/87/d05efc208d74bce8a0368eebca2b7ba743f8add4c0ef46aa15
Building wheel for retrying (setup.py): started
Building wheel for retrying (setup.py): finished with status 'done'
Created wheel for retrying: filename=retrying-1.3.3-py3-none-any.whl size=11429 sha256=f73b6fae347f496e483274ef684d39b01d0e7b7509a248119e6d7a5b0a81ad8a
Stored in directory: /root/.cache/pip/wheels/96/4f/f9/49a8cf51d87d8eed926bdcd198468532fdf4e97d71cbadaa0d
Building wheel for future (setup.py): started
Building wheel for future (setup.py): finished with status 'done'
Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=7ee0e3e98c43aa36e843e3eca94a3760efb5500cc2dda66fd63a233a704005ce
Stored in directory: /root/.cache/pip/wheels/31/fb/97/91bc10cc2d76a2a525e0716f4ae611f74f6b8ca977aba9bebb
Building wheel for mpmath (setup.py): started
Building wheel for mpmath (setup.py): finished with status 'done'
Created wheel for mpmath: filename=mpmath-1.1.0-py3-none-any.whl size=532239 sha256=ff74e68dccfa4fea248fb7279eac281af476fc5463c296437a126e113bbd35f1
Stored in directory: /root/.cache/pip/wheels/fe/8a/3e/0f28f6c7965cfb700cb048787ab4a8fb82f6660b6332e0feb8
Successfully built Mako pymatgen retrying future mpmath
Installing collected packages: six, urllib3, retrying, pytz, python-dateutil, pyparsing, pillow, numpy, mpmath, kiwisolver, idna, future, decorator, cycler, chardet, certifi, uncertainties, tzlocal, tabulate, sympy, spglib, scipy, ruamel.yaml, requests, plotly, pandas, palettable, networkx, monty, matplotlib, MarkupSafe, pymatgen, Mako, apscheduler
Successfully installed Mako-1.1.4 MarkupSafe-1.1.1 apscheduler-3.7.0 certifi-2020.12.5 chardet-4.0.0 cycler-0.10.0 decorator-4.4.2 future-0.18.2 idna-2.10 kiwisolver-1.3.1 matplotlib-3.3.4 monty-4.0.2 mpmath-1.1.0 networkx-2.5 numpy-1.20.0 palettable-3.3.0 pandas-1.2.1 pillow-8.1.0 plotly-4.14.3 pymatgen-2020.12.31 pyparsing-2.4.7 python-dateutil-2.8.1 pytz-2021.1 requests-2.25.1 retrying-1.3.3 ruamel.yaml-0.16.12 scipy-1.6.0 six-1.15.0 spglib-1.16.1 sympy-1.7.1 tabulate-0.8.7 tzlocal-2.1 uncertainties-3.1.5 urllib3-1.26.3
WARNING: You are using pip version 20.3.3; however, version 21.0.1 is available.
You should consider upgrading via the '/usr/local/bin/python -m pip install --upgrade pip' command.
Removing intermediate container 380de1ed68d3
---> 32f9302b1fd7
Step 4/6 : ENV JAVA_HOME=/usr/local/openjdk-11
---> Running in 4abf3207a04d
Removing intermediate container 4abf3207a04d
---> c70e2887ef66
Step 5/6 : ENV PATH=${JAVA_HOME}/bin:$PATH
---> Running in 044967fbf774
Removing intermediate container 044967fbf774
---> 60657ed0dc1c
Step 6/6 : RUN java --version
---> Running in 7f702a5f4068
openjdk 11.0.9.1 2020-11-04
OpenJDK Runtime Environment 18.9 (build 11.0.9.1+1)
OpenJDK 64-Bit Server VM 18.9 (build 11.0.9.1+1, mixed mode)
Removing intermediate container 7f702a5f4068
---> 332449747adb
Successfully built 332449747adb
How to Reproduce
- Install docker
- Build the image without mounting the hard disk-----success
- Close docker
- Mount the hard drive
- Edit daemon.json or configure docker's root dir path by editing sudo vim /lib/systemd/system/docker.service
- Restart docker, build the image ---- failed during pipi install
Mount a new hard disk to a directory on the host server where docker is located, configure the root directory of docker in daemon.json, pay attention to use df -h to check whether the mount is successful, and then use the dockerfile I provided to build
Failed log
copying build/lib/past/types/olddict.py -> build/bdist.linux-x86_64/wheel/past/types
copying build/lib/past/types/oldstr.py -> build/bdist.linux-x86_64/wheel/past/types
creating build/bdist.linux-x86_64/wheel/past/utils
copying build/lib/past/utils/__init__.py -> build/bdist.linux-x86_64/wheel/past/utils
running install_egg_info
Copying src/future.egg-info to build/bdist.linux-x86_64/wheel/future-0.18.2-py3.9.egg-info
running install_scripts
error: [Errno 39] Directory not empty: 'build/bdist.linux-x86_64/wheel/future-0.18.2-py3.9.egg-info'
----------------------------------------
ERROR: Failed building wheel for future
Running setup.py clean for future
Building wheel for mpmath (setup.py): started
Building wheel for mpmath (setup.py): finished with status 'error'
ERROR: Command errored out with exit status 1:
command: /usr/local/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-la7pwtyg/mpmath_cb46a0d0b3b34439b0f615d573ce8497/setup.py'"'"'; __file__='"'"'/tmp/pip-install-la7pwtyg/mpmath_cb46a0d0b3b34439b0f615d573ce8497/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'
'"'"', '"'"'
'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-tmkv5wvf
......
copying build/lib/mpmath/visualization.py -> build/bdist.linux-x86_64/wheel/mpmath
running install_egg_info
running egg_info
creating mpmath.egg-info
writing mpmath.egg-info/PKG-INFO
writing dependency_links to mpmath.egg-info/dependency_links.txt
writing top-level names to mpmath.egg-info/top_level.txt
writing manifest file 'mpmath.egg-info/SOURCES.txt'
reading manifest file 'mpmath.egg-info/SOURCES.txt'
writing manifest file 'mpmath.egg-info/SOURCES.txt'
Copying mpmath.egg-info to build/bdist.linux-x86_64/wheel/mpmath-1.1.0-py3.9.egg-info
running install_scripts
adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
error: [Errno 39] Directory not empty: 'build/bdist.linux-x86_64/wheel/mpmath-1.1.0-py3.9.egg-info'
----------------------------------------
ERROR: Failed building wheel for mpmath
Running setup.py clean for mpmath
Successfully built Mako
Failed to build pymatgen retrying future mpmath
Installing collected packages: six, urllib3, retrying, pytz, python-dateutil, pyparsing, pillow, numpy, mpmath, kiwisolver, idna, future, decorator, cycler, chardet, certifi, uncertainties, tzlocal, tabulate, sympy, spglib, scipy, ruamel.yaml, requests, plotly, pandas, palettable, networkx, monty, matplotlib, MarkupSafe, pymatgen, Mako, apscheduler
Running setup.py install for retrying: started
Running setup.py install for retrying: finished with status 'done'
DEPRECATION:
