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Installation of MDAnalysis on 32 bit systems #1364

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ashkurti opened this Issue May 23, 2017 · 26 comments

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@ashkurti

ashkurti commented May 23, 2017

I tried and get the following error:

conda install mdanalysis
Fetching package metadata ...............


PackageNotFoundError: Package not found: Conda could not find '

I have installed conda by doing the following:

wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86.sh
bash Miniconda2-latest-Linux-x86.sh -b -p $HOME/miniconda2
export PATH=$HOME/miniconda2/bin:$PATH
echo "export PATH=$HOME/miniconda2/bin:$PATH" >> ~/.bashrc

and my linux operating system is:

Linux ubuntu-VirtualBox 3.8.0-35-generic #50-Ubuntu SMP Tue Dec 3 01:25:33 UTC 2013 i686 i686 i686 GNU/Linux
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kain88-de May 23, 2017

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http://www.mdanalysis.org/pages/installation_quick_start/

conda config --add channels conda-forge
conda install mdanalysis

or short

conda  install -c conda-forge mdanalysis
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kain88-de commented May 23, 2017

http://www.mdanalysis.org/pages/installation_quick_start/

conda config --add channels conda-forge
conda install mdanalysis

or short

conda  install -c conda-forge mdanalysis
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orbeckst May 23, 2017

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The important thing is to add the conda-forge channel because the MDAnalysis conda packages reside there, together with all dependencies@kain88-de worked hard to make sure that everything that MDAnalysis needs is available as a conda package.

You only have to do the --add channels once for your conda installation.

Please let us know if this works or if there are any other issues.

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orbeckst commented May 23, 2017

The important thing is to add the conda-forge channel because the MDAnalysis conda packages reside there, together with all dependencies@kain88-de worked hard to make sure that everything that MDAnalysis needs is available as a conda package.

You only have to do the --add channels once for your conda installation.

Please let us know if this works or if there are any other issues.

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ashkurti May 24, 2017

Thanks @orbeckst and @kain88-de for your suggestions.

I have tried what you suggest, as I also had run into the links indicated by @kain88-de without success. I also have retried it and this is what I get:

ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ source activate venv_slabit
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda config --add channels conda-forge
Warning: 'conda-forge' already in 'channels' list, moving to the top
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda install mdanalysis
Fetching package metadata ...............


PackageNotFoundError: Package not found: Conda could not find '


(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda  install -c conda-forge mdanalysis
Fetching package metadata ...............


PackageNotFoundError: Package not found: Conda could not find '


(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ 

Any suggestions on what might be going wrong here. Thanks :)

ashkurti commented May 24, 2017

Thanks @orbeckst and @kain88-de for your suggestions.

I have tried what you suggest, as I also had run into the links indicated by @kain88-de without success. I also have retried it and this is what I get:

ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ source activate venv_slabit
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda config --add channels conda-forge
Warning: 'conda-forge' already in 'channels' list, moving to the top
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda install mdanalysis
Fetching package metadata ...............


PackageNotFoundError: Package not found: Conda could not find '


(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda  install -c conda-forge mdanalysis
Fetching package metadata ...............


PackageNotFoundError: Package not found: Conda could not find '


(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ 

Any suggestions on what might be going wrong here. Thanks :)

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@ashkurti what platform is this running on? What does conda search mdanalysis return?

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richardjgowers commented May 24, 2017

@ashkurti what platform is this running on? What does conda search mdanalysis return?

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@ashkurti can you run conda config --show and paste the output.

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kain88-de commented May 24, 2017

@ashkurti can you run conda config --show and paste the output.

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ashkurti May 24, 2017

@richardjgowers

(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda search mdanalysis
Fetching package metadata ...............
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$

@kain88-de :

(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda config --show
add_anaconda_token: True
add_pip_as_python_dependency: True
allow_softlinks: True
always_copy: False
always_softlink: False
always_yes: False
auto_update_conda: True
binstar_upload: None
changeps1: True
channel_alias: https://conda.anaconda.org
channel_priority: True
channels:
  - conda-forge
  - MDAnalysis
  - mdanalysis
  - defaults
client_ssl_cert: 
client_ssl_cert_key: 
create_default_packages: []
debug: False
default_channels:
  - https://repo.continuum.io/pkgs/free
  - https://repo.continuum.io/pkgs/r
  - https://repo.continuum.io/pkgs/pro
disallow: []
envs_dirs:
  - /home/ubuntu/miniconda2/envs
  - /home/ubuntu/.conda/envs
json: False
offline: False
proxy_servers: {}
quiet: False
shortcuts: True
show_channel_urls: None
ssl_verify: True
track_features: []
update_dependencies: True
use_pip: True
verbosity: 0
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ 

ashkurti commented May 24, 2017

@richardjgowers

(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda search mdanalysis
Fetching package metadata ...............
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$

@kain88-de :

(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda config --show
add_anaconda_token: True
add_pip_as_python_dependency: True
allow_softlinks: True
always_copy: False
always_softlink: False
always_yes: False
auto_update_conda: True
binstar_upload: None
changeps1: True
channel_alias: https://conda.anaconda.org
channel_priority: True
channels:
  - conda-forge
  - MDAnalysis
  - mdanalysis
  - defaults
client_ssl_cert: 
client_ssl_cert_key: 
create_default_packages: []
debug: False
default_channels:
  - https://repo.continuum.io/pkgs/free
  - https://repo.continuum.io/pkgs/r
  - https://repo.continuum.io/pkgs/pro
disallow: []
envs_dirs:
  - /home/ubuntu/miniconda2/envs
  - /home/ubuntu/.conda/envs
json: False
offline: False
proxy_servers: {}
quiet: False
shortcuts: True
show_channel_urls: None
ssl_verify: True
track_features: []
update_dependencies: True
use_pip: True
verbosity: 0
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ 

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ashkurti May 24, 2017

@richardjgowers as to the platform:

(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ uname -a
Linux ubuntu-VirtualBox 3.8.0-35-generic #50-Ubuntu SMP Tue Dec 3 01:25:33 UTC 2013 i686 i686 i686 GNU/Linux
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ 

ashkurti commented May 24, 2017

@richardjgowers as to the platform:

(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ uname -a
Linux ubuntu-VirtualBox 3.8.0-35-generic #50-Ubuntu SMP Tue Dec 3 01:25:33 UTC 2013 i686 i686 i686 GNU/Linux
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ 
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@ashkurti this is weird. Can you please remove the MDAnalysis channels from your config file in ~/.condarc

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kain88-de commented May 24, 2017

@ashkurti this is weird. Can you please remove the MDAnalysis channels from your config file in ~/.condarc

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ashkurti May 24, 2017

@kain88-de I removed MDAnalysis channels and then followed again the previous steps (and nothing changed :( :

(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda  install -c conda-forge mdanalysis
Fetching package metadata ...........


PackageNotFoundError: Package not found: Conda could not find '


(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ cat ~/.condarc
channels:
  - defaults
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda config --add channels conda-forge
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ cat ~/.condarc
channels:
  - conda-forge
  - defaults
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda install mdanalysis
Fetching package metadata ...........


PackageNotFoundError: Package not found: Conda could not find '


(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ 

ashkurti commented May 24, 2017

@kain88-de I removed MDAnalysis channels and then followed again the previous steps (and nothing changed :( :

(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda  install -c conda-forge mdanalysis
Fetching package metadata ...........


PackageNotFoundError: Package not found: Conda could not find '


(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ cat ~/.condarc
channels:
  - defaults
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda config --add channels conda-forge
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ cat ~/.condarc
channels:
  - conda-forge
  - defaults
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda install mdanalysis
Fetching package metadata ...........


PackageNotFoundError: Package not found: Conda could not find '


(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ 
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OK this is weird. I'm not sure what is going on there. I sometimes had luck with such weird errors in conda by reinstalling it. My guess is here also conda because your error message looks cut off.

For example when I try to install a non existing package I get the following error.

thinki ~ » conda install mdanalysisssss
Fetching package metadata .................


PackageNotFoundError: Package missing in current linux-64 channels: 
  - mdanalysisssss

Close matches found; did you mean one of these?

    mdanalysisssss: mdanalysis, mdanalysistests
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kain88-de commented May 24, 2017

OK this is weird. I'm not sure what is going on there. I sometimes had luck with such weird errors in conda by reinstalling it. My guess is here also conda because your error message looks cut off.

For example when I try to install a non existing package I get the following error.

thinki ~ » conda install mdanalysisssss
Fetching package metadata .................


PackageNotFoundError: Package missing in current linux-64 channels: 
  - mdanalysisssss

Close matches found; did you mean one of these?

    mdanalysisssss: mdanalysis, mdanalysistests
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what version of conda your you running?

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kain88-de commented May 24, 2017

what version of conda your you running?

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run conda -V

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kain88-de commented May 24, 2017

run conda -V

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ashkurti May 24, 2017

(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda -V
conda 4.3.14
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ 

ashkurti commented May 24, 2017

(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda -V
conda 4.3.14
(venv_slabit) ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ 
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I'm running 4.3.17. The point release shouldn't change anything but maybe it does.

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kain88-de commented May 24, 2017

I'm running 4.3.17. The point release shouldn't change anything but maybe it does.

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ashkurti May 24, 2017

what platform are you running on?

ashkurti commented May 24, 2017

what platform are you running on?

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ashkurti commented May 24, 2017

uname -a

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I'm running on Fedora. But that shouldn't make any difference. @richardjgowers runs ubuntu and it works for him as well. I've asked the conda-forge people for help.

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kain88-de commented May 24, 2017

I'm running on Fedora. But that shouldn't make any difference. @richardjgowers runs ubuntu and it works for him as well. I've asked the conda-forge people for help.

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isuruf May 24, 2017

You need 4.3.16 or above. See conda/conda#4860 (comment)

isuruf commented May 24, 2017

You need 4.3.16 or above. See conda/conda#4860 (comment)

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ashkurti May 24, 2017

@isuruf As I want to automatically install conda (as part of a package I am working on) I am getting the conda installation script from https://repo.continuum.io/miniconda/
The latest conda version from those scripts dated less than two weeks ago is 4.3.14.

Any suggestions? Maybe I can install this version then, include a command for update? Anywhere I can find the script to install a 4.3.16 or above version of conda. Thanks :)

ashkurti commented May 24, 2017

@isuruf As I want to automatically install conda (as part of a package I am working on) I am getting the conda installation script from https://repo.continuum.io/miniconda/
The latest conda version from those scripts dated less than two weeks ago is 4.3.14.

Any suggestions? Maybe I can install this version then, include a command for update? Anywhere I can find the script to install a 4.3.16 or above version of conda. Thanks :)

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isuruf May 24, 2017

Here's a script from ContinuumIO, https://conda.io/docs/travis.html. Note that they recommend updating conda even when downloading a fresh version of miniconda.

UPDATED

isuruf commented May 24, 2017

Here's a script from ContinuumIO, https://conda.io/docs/travis.html. Note that they recommend updating conda even when downloading a fresh version of miniconda.

UPDATED

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@isuruf thanks

@ashkurti running conda update --all after installing it might help.

I'll close this since it's not related to MDAnalysis

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kain88-de commented May 24, 2017

@isuruf thanks

@ashkurti running conda update --all after installing it might help.

I'll close this since it's not related to MDAnalysis

@kain88-de kain88-de closed this May 24, 2017

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ashkurti May 24, 2017

I am still not managing to find out mdanalysis within conda.

So even after updating conda to 4.3.18 it is not managing to find mdanalysis, and specifically the following happens:

ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda config --add channels conda-forge
Warning: 'conda-forge' already in 'channels' list, moving to the top
ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda install mdanalysis=0.15.0
Fetching package metadata ...........

PackageNotFoundError: Package missing in current linux-32 channels: 
  - mdanalysis 0.15.0*

ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda install mdanalysis
Fetching package metadata ...........

PackageNotFoundError: Package missing in current linux-32 channels: 
  - mdanalysis

ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda -V
conda 4.3.18
ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ 

ashkurti commented May 24, 2017

I am still not managing to find out mdanalysis within conda.

So even after updating conda to 4.3.18 it is not managing to find mdanalysis, and specifically the following happens:

ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda config --add channels conda-forge
Warning: 'conda-forge' already in 'channels' list, moving to the top
ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda install mdanalysis=0.15.0
Fetching package metadata ...........

PackageNotFoundError: Package missing in current linux-32 channels: 
  - mdanalysis 0.15.0*

ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda install mdanalysis
Fetching package metadata ...........

PackageNotFoundError: Package missing in current linux-32 channels: 
  - mdanalysis

ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ conda -V
conda 4.3.18
ubuntu@ubuntu-VirtualBox:~/test_slabit/slabit$ 
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ashkurti May 24, 2017

The thing is that apparently the Ubuntu image I am using for testing in my virtual machine is a 32 bit one apparently and therefore it cannot find mdanalysis within the linux-32 channel. At this point, is there a specific reason for MDAnalysis to be only supported for 64 bit linux platforms.

ashkurti commented May 24, 2017

The thing is that apparently the Ubuntu image I am using for testing in my virtual machine is a 32 bit one apparently and therefore it cannot find mdanalysis within the linux-32 channel. At this point, is there a specific reason for MDAnalysis to be only supported for 64 bit linux platforms.

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Yeah we don't ship 32bit prebuild binaries. There is also a recent bug report that the library doesn't work on 32bit in some parts.

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kain88-de commented May 24, 2017

Yeah we don't ship 32bit prebuild binaries. There is also a recent bug report that the library doesn't work on 32bit in some parts.

@richardjgowers richardjgowers changed the title from How to install mdanalysis with conda to Installation of MDAnalysis on 32 bit systems May 26, 2017

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@ashkurti we don't really support 32 bit systems, mostly because none of the developers have access/need a 32 bit system. If it's something you specifically need, we can guide you through how to make a conda package for this, but there might be some bugs you have to fix too (eg #1362).

Related discussion on dev board

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richardjgowers commented May 26, 2017

@ashkurti we don't really support 32 bit systems, mostly because none of the developers have access/need a 32 bit system. If it's something you specifically need, we can guide you through how to make a conda package for this, but there might be some bugs you have to fix too (eg #1362).

Related discussion on dev board

@orbeckst orbeckst added the 32 bit label May 26, 2017

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Just as an update: despite #1364 (comment) there are nevertheless some efforts going on to make it work on 32-bit, see issue #1362 (and related #1389) and PR #1393 as well as PR #1392 for setting up the testing.

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orbeckst commented Jun 12, 2017

Just as an update: despite #1364 (comment) there are nevertheless some efforts going on to make it work on 32-bit, see issue #1362 (and related #1389) and PR #1393 as well as PR #1392 for setting up the testing.

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