I can not install VTK by anaconda in Mac OS X. I use
conda install -c anaconda vtk=6.3.0
Python 2.7 but get the following error:
UnsatisfiableError: The following specifications were found to be in conflict: - python 3.6* - vtk 6.3.0* -> python 2.7* -> openssl 1.0.1* Use "conda info " to see the dependencies for each package.
But I've updated Python to 3.6, and the same error.
Conda Search
$ conda search vtk
Fetching package metadata ...........
vtk 5.10.1 py27_0 defaults
5.10.1 py27_1 defaults
6.3.0 py27_0 defaults
6.3.0 py27_1 defaults
Create the choicest env
$ conda create -n vtk python=2.7 vtk=6.3.0
Fetching package metadata ...........
Solving package specifications: .
Package plan for installation in environment /home/sidon/opt/anaconda3/envs/vtk:
The following NEW packages will be INSTALLED:
openssl: 1.0.2k-1
pip: 9.0.1-py27_1
python: 2.7.13-0
readline: 6.2-2
setuptools: 27.2.0-py27_0
sqlite: 3.13.0-0
tk: 8.5.18-0
vtk: 6.3.0-py27_1
wheel: 0.29.0-py27_0
zlib: 1.2.8-3
Proceed ([y]/n)? y
vtk-6.3.0-py27 100% |#############################################################################################| Time: 0:00:15 1.97 MB/s
#
# To activate this environment, use:
# > source activate vtk
#
# To deactivate this environment, use:
# > source deactivate vtk
#
Active the new env
$ source activate vtk
Test
$ python -c "import vtk; print vtk.vtkSphereSource()"
vtkSphereSource (0xcfdcc0)
Debug: Off
Modified Time: 39
Reference Count: 2
Registered Events: (none)
Executive: 0xae5e00
ErrorCode: Success
Information: 0xf6e210
AbortExecute: Off
Progress: 0
Progress Text: (None)
Theta Resolution: 8
Phi Resolution: 8
Theta Start: 0
Phi Start: 0
Theta End: 360
Phi End: 180
Radius: 0.5
Center: (0, 0, 0)
LatLong Tessellation: 0
Output Points Precision: 0
I would suggest installing directly from the wheel file. You can get the VTK wheel file from here (wheel file directory site). This site has pretty much every wheel file so it is your friend! just search for it and you will see a bunch of .whl VTK files.
just download the wheel file that matches your anaconda python root version (either 3.5, 3.6, 2.7 etc.) and either 32 or 64 bit (depending on your python version).
To install from a wheel file, open a terminal in the directory the wheel is in and type
pip install "your_wheel_file_name"
If you want to install it for a conda environment, just activate the environment first (activate "env_name") and then install from the wheel file.
Try this out for me:
conda create --name vtk_test python=2.7 vtk
This will create a new environment with VTK, Python and their dependencies inside.
Related
In a simple test, I tried to create a basic Conda environment, export that environment to a YAML file, and re-create the environment from the YAML file on the exact same computing instance.
No matter what I try, the re-create step hangs up (fails) with no error message (timeout)
This is on an AWS EC2 Linux instance.
Command sequence as follows:
conda create -n myenv python=3.10.4
conda activate myenv
conda list ## output is shown below
conda env export > newenv.yml ## yml contents are shown below...so far so good
conda deactivate
conda env create -n newenv --f newenv.yml ## this is where it hangs up/freezes
<output> Collecting package metadata (repodata.json): -
<output> Collecting package metadata (repodata.json): - Killed ## after about 5mins
I have also tried multiple variations where I remove myenv before trying to re-create it using the same name (myenv). Folder permissions to the anaconda3/envs folder are 775 and there is no problem creating the environment. I have already updated, cleaned, and re-initialized Conda and have re-booted my instance multiple times.
Any help/ideas would be greatly appreciated. This is my first Python project.
Conda list output
(myenv) [ec2-user#ip-172-31-93-141 ~]$ conda list
# packages in environment at /home/ec2-user/anaconda3/envs/myenv:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2022.9.24 ha878542_0 conda-forge
ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
libsqlite 3.40.0 h753d276_0 conda-forge
libstdcxx-ng 12.2.0 h46fd767_19 conda-forge
libuuid 1.41.5 h5eee18b_0
libzlib 1.2.13 h166bdaf_4 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
openssl 1.1.1s h0b41bf4_1 conda-forge
pip 22.3.1 pyhd8ed1ab_0 conda-forge
python 3.10.4 h12debd9_0
readline 8.1.2 h0f457ee_0 conda-forge
setuptools 65.5.1 pyhd8ed1ab_0 conda-forge
sqlite 3.40.0 h4ff8645_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tzdata 2022g h191b570_0 conda-forge
wheel 0.38.4 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.13 h166bdaf_4 conda-forge
YAML file output
name: myenv
channels:
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- bzip2=1.0.8=h7f98852_4
- ca-certificates=2022.9.24=ha878542_0
- ld_impl_linux-64=2.39=hcc3a1bd_1
- libffi=3.3=h58526e2_2
- libgcc-ng=12.2.0=h65d4601_19
- libgomp=12.2.0=h65d4601_19
- libsqlite=3.40.0=h753d276_0
- libstdcxx-ng=12.2.0=h46fd767_19
- libuuid=1.41.5=h5eee18b_0
- libzlib=1.2.13=h166bdaf_4
- ncurses=6.3=h27087fc_1
- openssl=1.1.1s=h0b41bf4_1
- pip=22.3.1=pyhd8ed1ab_0
- python=3.10.4=h12debd9_0
- readline=8.1.2=h0f457ee_0
- setuptools=65.5.1=pyhd8ed1ab_0
- sqlite=3.40.0=h4ff8645_0
- tk=8.6.12=h27826a3_0
- tzdata=2022g=h191b570_0
- wheel=0.38.4=pyhd8ed1ab_0
- xz=5.2.6=h166bdaf_0
- zlib=1.2.13=h166bdaf_4
prefix: /home/ec2-user/anaconda3/envs/myenv
Possibly a channel mixing issue. I see python and libuuid come from defaults (i.e., main, anaconda) channel, whereas everything else is Conda Forge. If you have channel_priority: strict, then any packages in conda-forge channel (which is given priority by the YAML because it is first), will mask any packages of the same name in the lower priority channel (defaults).
Concretely, Conda is told to find python with a specific build (h12debd9_0) that is only available on defaults, but because conda-forge has python packages available, only those will be considered. The hanging is probably just Conda trying to "explain" why it can't find a solution.
Immediate Workaround
If this is the issue, then changing the channel priority to flexible should get it working.
conda config --set channel_priority flexible
Better: Avoid mixing channels
If you instead started from conda-forge to begin with, then everything should be fine. Conda Forge is entirely self-sufficient these days. Whereas Anaconda users often need to use Conda Forge packages to fill in the gaps. This practice (which is encouraged by Anaconda documentation with little warning about how problematic it is) generates a substantial portion of user issues.
Personally, I recommend a base install of Mambaforge. It puts conda-forge as the default, installs a minimum of packages in the base environment, and comes with Mamba for fast environment solving.
The problem turned out to be a memory issue (as in, lack thereof). I was trying to do this on an AWS EC2 instance that was on the t2.micro free tier. This instance only had 1GB of memory (RAM) and buried in the feedback I got from the dmesg command (run from the terminal after the command failed) I noticed an "Out of Memory" line. I increased the instance size and the problem went away. Thanks for the help!
I created a virtual environment with virtualenv python3.7_env. after source home/${username}/python3.7_env/bin/activate. i checked the current python version and pip version with which python and which pip, the environment seems to be ran normally as follows.
(python3.7_env) jin#jin-t480:~/python3.7_env/bin$ which python
/home/jin/python3.7_env/bin/python
(python3.7_env) jin#jin-t480:~/python3.7_env/bin$ which pip
/home/jin/python3.7_env/bin/pip
(python3.7_env) jin#jin-t480:~/python3.7_env/bin$ pip list
Package Version
------------------------------- -------
actionlib 1.11.16
angles 1.9.12
base-local-planner 1.14.8
bondpy 1.8.3
camera-calibration 1.12.23
camera-calibration-parsers 1.11.13
catkin 0.7.20
controller-manager 0.13.5
controller-manager-msgs 0.13.5
controller-manager-tests 0.13.5
cv-bridge 1.12.8
...
...
wheel 0.35.1
wiimote 1.13.0
xacro 1.11.3
why the virtualenv includes ros-packages?
I had the same issue, and was able to resolve it by removing
source /opt/ros/hydro/setup.bash
line from my .bashrc. Now my venvs are normal again.
I'm trying to install some packages on a remote machine (with GPUs) that is not connected to the internet.
(Some people have suggested I should be using Docker and I may well do that but here's one last chance to get this working).
FYI: I'm following the instructions here.
What I've done so far:
Downloaded Anaconda Anaconda3-2019.03-Linux-x86_64.sh file and installed it on the remote machine
$ conda --version
conda 4.6.14
Then downloaded the desired package from here and moved it to the remote machine.
$ ls pkgs-for-anaconda/linux-64/*tensorflow*
pkgs-for-anaconda/linux-64/tensorflow-gpu-1.9.0-hf154084_0.tar.bz2
Setup a new channel which is the file path on the local file system.
$ conda config --prepend channels file:///home/billtubbs/pkgs-for-anaconda
Excerpt from config to confirm this worked:
channels:
- file:///home/billtubbs/pkgs-for-anaconda
- defaults
Install the package
$ conda install pkgs-for-anaconda/linux-64/tensorflow-gpu-1.9.0-hf154084_0.tar.bz2
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Index the packages
$ conda index pkgs-for-anaconda/
Subdir: noarch: 100%|████████████████████████████████████| 2/2 [00:00<00:00, 81.80it/s]
(base) [billtubbs#localhost ~]$ ch: 0it [00:00, ?it/s]s]05 [00:00<00:00, 750741.03it/s]
Is the issue that it looked in no noarch instead of linux-64?
Try to install the package
When I use the following to create a new environment with the desired package:
$ conda create -n tf tensorflow-gpu
I get:
Collecting package metadata: done
Solving environment: failed
PackagesNotFoundError: The following packages are not available from current channels:
- tensorflow-gpu -> _tflow_190_select==0.0.1=gpu
- tensorflow-gpu -> tensorflow==1.9.0
Current channels:
- file:///home/billtubbs/pkgs-for-anaconda/linux-64
- file:///home/billtubbs/pkgs-for-anaconda/noarch
- https://repo.anaconda.com/pkgs/main/linux-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/free/linux-64
- https://repo.anaconda.com/pkgs/free/noarch
- https://repo.anaconda.com/pkgs/r/linux-64
- https://repo.anaconda.com/pkgs/r/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.
What I don't understand is that it shows my channel exists. And it even seems to be looking for the right version (1.9.0). But it says it can't find it.
Just to confirm, I did the following:
$ conda search tensorflow-gpu==1.9.0
Loading channels: done
# Name Version Build Channel
tensorflow-gpu 1.9.0 hf154084_0 pkgs-for-anaconda
tensorflow-gpu 1.9.0 hf154084_0 pkgs/main
Anyone know what I am doing wrong?
UPDATE:
Here is some of the output from
$ conda list --show-channel-urls
...
sympy 1.3 py37_0 defaults
tblib 1.3.2 py37_0 defaults
tensorflow-gpu 1.9.0 hf154084_0 file:///home/billtubbs/pkgs-for-anaconda
terminado 0.8.1 py37_1 defaults
testpath 0.4.2 py37_0 defaults
I will recommend you that you uninstall the current version of anaconda that you have, when I downloaded the last version of anaconda i got some problems, I remenber that I could'nt install for example tensorflow or matplotlib..
The best version to work with tensorflow or matplotlib is having one anaconda with python 3.6. Try to install Anaconda3-4.4.0-Windows-x86_64 or Anaconda3-4.4.0-Linux-x86_64.sh which was released in 2017-05-26.
Anacoda versions
And then try to install tensorflow, matplotlib, pandas, numpy but before run
conda update conda
To update some packages of anaconda.
And you will install those the packages/libraries without problems,
Best Regards.
PD: I also tried to install docker however I got more problems than using python with pip, that's why I think anaconda is the best solution.
I am trying to use the ECMWF GRIB_API to access GRIB files from Python. I get this error
Traceback (most recent call last):
File "/home/martin/markj/JustImportGRIB.py", line 1, in <module>
from gribapi import *
ImportError: No module named gribapi
One line of code :)
from gribapi import *
I am using Anaconda Python 2.7.12, Linux Centos 64-bit, installed as user and not added Anaconda to the path if that's relevant - the system Python (2.6) is on the path. I installed GRIB_API from the Pingu Carsti channel which was the top Google hit. The conda install did not report any errors.
[martin#bonnie ~]$ anaconda2/bin/conda install -c pingucarsti grib_api=1.10.4
Fetching package metadata .........
Solving package specifications: ..........
Package plan for installation in environment /home/martin/anaconda2:
The following packages will be downloaded:
package | build
---------------------------|-----------------
grib_api-1.10.4 | 3 1.7 MB pingucarsti
The following NEW packages will be INSTALLED:
grib_api: 1.10.4-3 pingucarsti
Proceed ([y]/n)? y
Fetching packages ...
grib_api-1.10. 100% |################################| Time: 0:00:01 1.24 MB/s
Extracting packages ...
[ COMPLETE ]|###################################################| 100%
Linking packages ...
[ COMPLETE ]|###################################################| 100%
I found some bug reports about this error being caused by a bug in the ECMWF GRIB_API, but I don't know enough about Anaconda (or perhaps Python) to figure out how to apply the workarounds.
I read GRIB files in Python with pygrib. I have successfully installed it inside a conda virtual environment (Miniconda2 on Ubuntu 16.04). Here is what has worked for me:
Install system dependencies for pygrib:
sudo apt-get install libjpeg9
sudo apt-get install libgrib-api-dev
Install pygrib and ecmwf_grib from conda-forge channel.
conda install -c conda-forge pygrib ecmwf_grib
Try conda-forge's build at python-eccodes (note: that's not eccodes which is the C library).
How it is built: https://github.com/conda-forge/python-eccodes-feedstock/blob/master/recipe/meta.yaml
The ECMWF's ecCodes library is the next version of their GRIB API, and is extremely similar to the old GRIB API.
pelson> conda create -n gribby -c conda-forge python-eccodes
Fetching package metadata .............
Solving package specifications: .
Package plan for installation in environment /Users/pelson/miniconda/envs/gribby:
The following NEW packages will be INSTALLED:
ca-certificates: 2017.7.27.1-0 conda-forge
curl: 7.54.1-0 conda-forge
eccodes: 2.4.0-0 conda-forge
hdf4: 4.2.12-0 conda-forge
hdf5: 1.8.18-1 conda-forge
intel-openmp: 2018.0.0-h68bdfb3_7 defaults
jasper: 1.900.1-4 conda-forge
jpeg: 9b-1 conda-forge
krb5: 1.14.2-0 conda-forge
libgfortran: 3.0.1-h93005f0_2 defaults
libnetcdf: 4.4.1.1-8 conda-forge
libpng: 1.6.28-1 conda-forge
libssh2: 1.8.0-1 conda-forge
mkl: 2018.0.0-h5ef208c_6 defaults
ncurses: 5.9-10 conda-forge
numpy: 1.13.3-py27h62f9060_0 defaults
openssl: 1.0.2l-0 conda-forge
python: 2.7.14-0 conda-forge
python-eccodes: 2.4.0-py27_1 conda-forge
readline: 6.2-0 conda-forge
sqlite: 3.13.0-1 conda-forge
tk: 8.5.19-2 conda-forge
zlib: 1.2.8-3 conda-forge
#
# To activate this environment, use:
# > source activate gribby
#
# To deactivate an active environment, use:
# > source deactivate
#
pelson> source activate gribby
python(gribby) pelson> python
Python 2.7.14 | packaged by conda-forge | (default, Oct 5 2017, 23:08:53)
[GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import gribapi
>>> gribapi.__version__
'2.4.0'
So I'm building a package with conda on Win7:
conda skeleton pypi $pkgname
conda build $pkgname
binstar upload ./conda-bld/win-64/$pkgname-py27_0.tar.bz2
conda install -c https://conda.binstar.org/myname $pkgname
With python2k, this works like a charm. However, using python3k this fails because the patch package is not available for python3k. Error (example for docopt):
$ conda skeleton pypi docopt
Using url https://pypi.python.org/packages/source/d/docopt/docopt-0.6.2.tar.gz (25 KB) for docopt.
Downloading docopt (use --no-download to skip this step)
Using cached download
Unpacking docopt...
done
working in C:\cygwin64\tmp\tmpy7erx8vyconda_skeleton_docopt-0.6.2.tar.gz
Fetching package metadata: ......
Solving package specifications: .
Applying patch: 'C:\\cygwin64\\tmp\\tmpy7erx8vyconda_skeleton_docopt-0.6.2.tar.gz\\pypi-distutils.patch'
Error:
Did not find 'patch' in: C:\Python\Anaconda3\envs\_build\Scripts;C:\Python\Anaconda3\Scripts;C:\cygwin\bin;C:\cygwin64\usr\local\bin;C:\cygwin64\bin;C:\Python\Python3\Lib\site-packages\PyQt4;C:\ProgramData\Oracle\Java\javapath;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0;C:\Program Files (x86)\ATI Technologies\ATI.ACE\Core-Static;C:\Program Files\MiKTeX 2.9\miktex\bin\x64;C:\cygwin64\bin;C:\Program Files (x86)\AMD\ATI.ACE\Core-Static;C:\Python\Anaconda3;C:\Python\Anaconda3\Scripts;C:\cygwin64\lib\lapack
You can install 'patch' using apt-get, yum (Linux), Xcode (MacOSX), or conda, cygwin (Windows)
When trying to install patch:
$conda search ^patch$
Fetching package metadata: ....
patch 1.12.11 py27_0 defaults
No patch package for python3k - does this mean no package building for me?
You can reuse the same recipe that you built with Python 2. Or you can create an environment with patch (conda create -n patch patch) and put it on your PATH. Or you can install patch from http://gnuwin32.sourceforge.net/packages/patch.htm.