I want to use the new platform Openshift 3 but I can't install lxml for Weblate with pip when build process is launch.
In logs the last line is "Running setup.py install for lxml" but no more error
How can I found what happened ?
Thanks
Some of the packages around data analytics when compiled with compiler optimisations can chew up too much memory and hit the default memory limit for builds. Try following steps outlined in:
Pandas on OpenShift v3
Is less likely, but just in case is the version of pip used, add a file .s2i/environment and in it add:
UPGRADE_PIP_TO_LATEST=1
This will ensure that latest version of pip is installed first. This can be required sometimes where a package provides a wheel file. Older version of pip used may ignore the binary wheel or get confused in other ways.
Thanks #Graham I followed this instruction Pandas on OpenShift v3 to edit YAML build configuration
resources:
limits:
memory: 1Gi
Related
Currently I am in a process of upgrading the Apache Beam version from 2.27.0 to 2.32.0 but when I start my jobs on Dataflow runner the job stucks during the worker-startup and it never finish installing dependencies. The python version is 3.7
This is what I see in the logs
INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime
After initial analysis it looks like this is the issue with pip dependencies backtracking and it keeps on downloading and installing dependencies. These are some warnings in the logs
INFO: pip is looking at multiple versions of google-auth to determine which version is compatible with other requirements.
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead:
This is the setup.py for the Beam
import setuptools
REQUIRED_PACKAGES = [
"numpy==1.21.4",
"pandas==0.25.3",
"dateparser==1.1.0",
"python-dateutil==2.8.2",
"pytz==2021.3",
"google-api-core==1.14.0",
"google-cloud-storage==1.36.1",
"fastavro==0.22.10",
]
setuptools.setup(
name="data-workflows",
version="0.1.0",
install_requires=REQUIRED_PACKAGES,
packages=setuptools.find_packages(),
)
The pipelines used to run fine in the Beam version 2.27.0. I am not sure if these warnings are the cause of the issue. Could someone please help me to identify the root cause of this problem?
I tried to install dgl(https://github.com/dmlc/dgl)
There were several ways to install it.(https://docs.dgl.ai/install/index.html#install-from-source)
pip
conda
from git source
from whl
and I failed with error message when I tried pip
$ pip install dgl-cu101
ERROR: Could not find a version that satisfies the requirement dgl-cu101 (from versions: none)
ERROR: No matching distribution found for dgl-cu101
even pip search spot the package
$ pip search dgl
dgl (0.4.1) - Deep Graph Library
dgl-bots.py (1.1.0) - A python wrapper for https://bots.discord.gl
dgl-cu100 (0.4.1) - Deep Graph Library
dgl-cu92 (0.4.1) - Deep Graph Library
dgl-cu90 (0.4.1) - Deep Graph Library
dgl-cu101 (0.4.1) - Deep Graph Library
dgl-cu102 (0.5a200108) - Deep Graph Library
conda also does not work
$ conda install -c dglteam dgl-cuda10.1
Solving environment: failed
PackagesNotFoundError:
The following packages are not available from current channels:
- dgl-cuda10.1
Current channels:
- https://conda.anaconda.org/dglteam/linux-ppc64le
- https://conda.anaconda.org/dglteam/noarch
- https://repo.anaconda.com/pkgs/main/linux-ppc64le
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/free/linux-ppc64le
- https://repo.anaconda.com/pkgs/free/noarch
- https://repo.anaconda.com/pkgs/r/linux-ppc64le
- https://repo.anaconda.com/pkgs/r/noarch
- https://repo.anaconda.com/pkgs/pro/linux-ppc64le
- https://repo.anaconda.com/pkgs/pro/noarch
- https://conda.anaconda.org/conda-forge/linux-ppc64le
- https://conda.anaconda.org/conda-forge/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
install with source code is not available option because I am the remote client to the server and has no root access
install with whl seems nice but also occurred error.(https://pypi.org/project/dgl/#files)
$ pip install dgl_cu101-0.4.1-cp37-cp37m-manylinux1_x86_64.whl
ERROR: dgl_cu101-0.4.1-cp37-cp37m-manylinux1_x86_64.whl is not a supported wheel on this platform.
I read almost every articles and most of them said it would be the environment problem,
but as far as I know, they match!
My env server
CentOS 7
python 3.7
64 bit
minsky
4 GPUs
designed for ML
My env client
macos
iterm2
no root access
access from different city
How can I solve this problem?
Please help.
Your conda channel
https://conda.anaconda.org/dglteam/linux-ppc64le
gives the clue. Your system seems to be based on a ppc64le CPU, not the most frequently seen x86_64.
As you can see On the conda page, only linux-64 (i.e. x86_64) is available. Same goes for the pypi project.
So your setup does not match.
install with source code is not available option because I am the remote client to the server and has no root access
You should not need root access to compile the source code. The requirements listed in the guide are
gcc-c++ python3-devel make cmake
which, if not available yet could be installed using conda:
conda install -c conda-forge make cmake libgcc
I have been trying to install obspy and have been running into a lot of problems. I want to install obspy which has a dependency on pyproj. But apparently obspy only works with pyproj 1.9.5.1, which I tried installing using pip (pip3 install pyproj==1.9.5.1), but only got the errors like-
_proj.c:7488:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
Digging deeper I found that it might be a Cython problem, and installing pyproj directly from github might help, because it would apparently make Cython recompile all the necessary files. Something along the lines of -
pip3 install git+https://github.com/jswhit/pyproj.git
However this one gives the error -
ERROR: Minimum supported proj version is 6.2.0, installed version is 5.2.0.
I di try installing a higher version of libproj-dev (sudo apt install libproj-dev=6.2.0) however it shows that there is no candidate for 6.2.0. I tried downloading the deb file and installing from that using -
sudo apt-get install ~/Downloads/libproj-dev_6.2.0-1_amd64.deb
which just leads to the error -
The following packages have unmet dependencies:
libproj-dev : Depends: libproj15 (= 6.2.0-1) but it is not installable
E: Unable to correct problems, you have held broken packages.
But I think this is not the right way to install for me anyway, since I need a specific version. Hence I tried installing directly from the tarball of the release -
pip3 install https://github.com/pyproj4/pyproj/archive/v1.9.5.1rel.tar.gz
Which leads to the first error I had, evidently due to Cython.
With errors on everything I tried to do to fix this, I am not sure what even is relevant to my problem now.
Any help is appreciated, and if this site is not the correct place for this question, please help me migrate it to its proper destination.
I am on Ubuntu 18.10.
The problem is, that Cython-generated c-files don't work for Python-3.7 if generated with Cython versions up to 0.27.3 (at least): The setup.py of pyproj (at least in the version 1.9.5.1) doesn't regenerate the_proj.c, which is generated with Cython 0.23.2 and thus the installation cannot succeed.
You have the following options:
stay on Python3.6 where everything works out of the box.
regenerate _proj.c with a current Cython-version.
For the second option:
download and unzip your prefered version from https://github.com/pyproj4/pyproj/releases/tag/v1.9.5.1rel and switch to the created folder pyproj-1.9.5.1rel.
check, that the cython-version is >=0.27.3. via cython --version.
regenerate the _proj.c file via cython -3 _proj.pyx (_proj.pyx looks like Python3-code, but also language_level=2 (i.e. cython -2 _proj.pyx) will probably work.
install running pip install .
pyproj 1.9.5.1 was release at Jan 7, 2016. At that time, the latest version Python was 3.5. In my tests. pyproj 1.9.5.1 failed to be installed on Python 3.7.4, but succeeded on Python 3.5.7.
You need to create a environment with Python 3.5 by pyenv or conda.
References
pyproj 1.9.5.1 release
Python release history
When i use pydicom in python3.6, there are some problem:
import pydicom
import matplotlib.pyplot as plt
import os
import pylab
filePath = "/Users/zhuangrui/Documents/Python/Dicom/dicoms/zhang_bo/0001.dcm"
dataSet_1 = pydicom.dcmread(filePath)
plt.imshow(dataSet_1.pixel_array)
plt.show()
here is the problem:
How can this problem be solved？ Thank you very much！
I've faced with the same problem, after doing some research on the suggested link above. I've managed to solve it by updating to the latest pydicom module "1.2.0" and installing gdcm. You can update the pydicom with
pip install -U git+https://github.com/pydicom/pydicom.git
You can find the latest gdcm here and this link explains the installation.
I use anaconda and it's easier to install the gdcm package and solve the problem. If you use anaconda
just type inside from your environment:
conda install pydicom --channel conda-forge to get pydicom's latest and
conda install -c conda-forge gdcm
to get the gdcm. This resolves the problem. Hope these will help.
With pydicom, you need an appropriate image handler also installed to handle compressed image types.
For JPEG lossless, in theory the following should work: jpeg_ls, gdcm, or Pillow with jpeg plugin. All of these also require Numpy to be installed. See the discussion at https://github.com/pydicom/pydicom/issues/532.
There is also a pull request in progress to add more descriptive error messages for what image handlers are needed for different images.
Problem:
I was trying to read medical images with .dcm extension. But was getting an error on Windows as well as on Ubuntu. I find a solution which will work on both the machined.
The error I got on Ubuntu is: NotImplementedError: this transfer syntax JPEG 2000 Image Compression (Lossless Only), can not be read because Pillow lacks the jpeg 2000 decoder plugin
(Note for Windows I was getting a different error but I am sure it's because of the same issue i.e. Pillow does not support JPEG 2000 format)
Platforma Information:
I am using: Python 3.6, Anaconda and Ubuntu, 15 GB RAM
RAM is important:
The solution I applied is the same as Ali explained above. But I want to add this installation may take time (depending on RAM you are using). On ubuntu where I am using 15 GB RAM on Cloud platform taken less time and on Windows on a local machine having 4 GB RAM taken a lot of time.
Solution
Anaconda is necessary. Why?
Please check the official doc of pydicom (https://pydicom.github.io/pydicom/dev/getting_started.html) its mentioned "To install pydicom along with image handlers for compressed pixel data, we encourage you to use Miniconda or Anaconda" (Note for Windows I was getting a different error)
If you are using Ubuntu directly open Terminal. If you are using Windows then on Anaconda Navigator go to Environment from here start terminal. Execute the following commands on it:
pip install -U git+https://github.com/pydicom/pydicom.git
conda install pydicom --channel conda-forge
conda install -c conda-forge gdcm
Cross Check:
Now use .dcm file for which we got the Error. Try to use the following code in Python notebook
filename = 'FileName.dcm'
ds = pydicom.dcmread(filename)
plt.imshow(ds.pixel_array, cmap=plt.cm.bone)
It should print the output. Also try this code:
ds.pixel_array
This will give you the array containing values.
I am installing Oracle 11g on the my system RHEL7.2 64bit,But in this step,I can not continue to install it,Because I can not find a file on my system,It is 'libgmp.so.3'.
So,like the picture,I can not install anything else.Because I had installed a higher level 'gmp' on my system.It is useless when I make a softlink to a higher level file.
What can I do?
try
yum clean all
this is will clear the yum cache .
Try first install mpfr-2.4.1-6.el6.x86_64.rpm
See http://www.oracle.com/technetwork/articles/servers-storage-admin/ginnydbinstallonlinux-488779.html. (It is for Oracle Linux 6.0, but it describes your problem)
# yum install oracle-rdbms-server-11gR2-preinstall
........
---> Package mpfr.x86_64 0:2.4.1-6.el6 will be installed
--> Running transaction check
---> Package kernel-uek-headers.x86_64 0:2.6.32-300.32.1.el6uek will be installed
---> Package ppl.x86_64 0:0.10.2-11.el6 will be installed
Also see brief installation guide how to install libraries https://oracle-base.com/articles/11g/oracle-db-11gr2-installation-on-oracle-linux-7
And of course big installation guide if nothing has helped https://docs.oracle.com/cd/E11882_01/install.112/e24326/toc.htm#BHCFACHG