ETE: cannot connect to X server #101

JohnReid · 2015-04-23T17:54:50Z

ETE exits python when I try to render a tree without an X server. This is a real shame as I want to run it on a server (without X) to serve tree images from. Is there any way around this?

jhcepas · 2015-04-23T19:42:01Z

Sorry, this is a known issue. The only way to get the renderer working is having an X server. It is actually a limitation of Qt4, which ETE uses for drawing. A minimal X system would be enough, or even using a forwarded X display.

We know this is quite annoying and we are working on an Qt4-free renderer.

JohnReid · 2015-04-24T06:50:54Z

Thanks for the reply. Is it possible for it to raise an Exception rather than exit python? I might try to use xvfb as a headless dummy Xserver.

jhcepas · 2015-04-24T07:35:10Z

The exit call seems to be raised by qt4, so all we can do is to check before importing the library. Shouldn't be difficult, I will look into it.

Let us know if xvfb works, never tried before.
Thanks!

JohnReid · 2015-04-24T14:51:03Z

xvfb worked a dream. After installation as an Ubuntu package, I could just preface my webserver command line with xvfb-run and a dummy Xserver was created that allowed ete2 to render my images. Thanks for ete2 and the feedback on this issue.

matsen · 2015-12-10T23:24:44Z

This worked great for me. Thanks, @JohnReid !

gregcaporaso · 2016-03-28T15:30:18Z

check before importing the library

@jhcepas, could you describe how you would do that check? I'm building some plots as part of IAB, and when I execute my tests via TravisCI they fail due to the missing xserver. I'd like to just check and skip rendering the plots if the xserver isn't available.

Thanks!

gregcaporaso · 2016-03-28T19:25:38Z

I got this working in my TravisCI build by starting the xserver there (thanks for the tip @jairideout!). Here's how I'm doing that, in case it's useful for others.

jhcepas · 2016-03-29T09:34:49Z

@gregcaporaso , we use xvfb also under TravisCI

ete/.travis.yml

Line 36 in a734959

- "sh -e /etc/init.d/xvfb start"

mgalardini · 2016-06-08T14:30:48Z

Hi,

just wanted to state my support to find an alternate renderer that doesn't rely on an X server; I would have problems to run xvfb on our cluster, so something that is less of a workaround would be preferable.

Thanks for the great work.
Marco

anatoly108 · 2017-04-25T13:03:57Z

Well, despite our best efforts we couldn't use ETE on Amazon EC2 instance because it relies on X server. For us this is the reason to forget ETE

jhcepas · 2017-04-25T13:53:38Z

I just tried the following commands on an Amazon EC2 instance running Ubuntu server 14.04.2 LTS:

apt-get install xvfb
wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O Miniconda-latest-Linux-x86_64.sh
bash Miniconda-latest-Linux-x86_64.sh -b -p ~/anaconda_ete/
export PATH=~/anaconda_ete/bin:$PATH; 
conda install -c etetoolkit ete3 ete3_external_apps
xvfb-run ete3 view -t '(a, b); ' -o test.png

and everything ran ok. No need of an X server.

andrewsanchez · 2017-11-10T09:45:46Z

Here is a success story for compiling xvfb without root access on RHEL:
https://ericdraken.com/running-xvfb-on-a-shared-host-without-x/

thdpuydt · 2018-05-31T13:39:11Z

This fix from following anaconda thread works for me:

ContinuumIO/anaconda-issues#1806

In [1]: import os
In [2]: os.environ['QT_QPA_PLATFORM']='offscreen'
In [3]: import ete3

andrewsanchez · 2018-07-29T22:45:44Z

Any idea how to suppress the error output that results from running with this setting (as discussed at ContinuumIO/anaconda-issues#1806) on a remote server with no x server or x 11 forwarding?

os.environ['QT_QPA_PLATFORM']='offscreen'

Here is the error output I get:

QFontDatabase: Cannot find font directory ~/miniconda3/envs/env/lib/fonts - is Qt installed correctly?

jhcepas · 2018-07-30T08:41:32Z

is the error coming directly from ete3? qt messages should only appear when using graphics features in ete. Also, using xvfb is workaround for servers without x11

…

On 30 July 2018 at 00:45, Andrew Sanchez ***@***.***> wrote: Any idea how to suppress the error output that results from running with this setting (as discussed at ContinuumIO/anaconda-issues#1806 <ContinuumIO/anaconda-issues#1806>) on a remote server with no x server or x 11 forwarding? - os.environ['QT_QPA_PLATFORM']='offscreen' Here is the error output I get: QFontDatabase: Cannot find font directory ~/miniconda3/envs/env/lib/fonts - is Qt installed correctly? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#101 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAJ_SnsLwcZ2fmA9Gxf5MENVNIlOAXEFks5uLjsYgaJpZM4EHJ_A> .

andrewsanchez · 2018-07-30T18:13:55Z

Yes, it's from ete3 after generating .svg trees. It resulted after setting `os.environ['QT_QPA_PLATFORM']='offscreen'` My goal in using that setting was to avoid relying on xvfb/x11. xvfb worked great, but in the interest of ease of reproducibility, I'd like to avoid requiring others to install xvfb. I can research the problem/open an issue with pyqt if that makes more sense, unless you have any ideas. Thanks! On Mon, Jul 30, 2018 at 1:41 AM, Jaime Huerta-Cepas < notifications@github.com> wrote:

…

is the error coming directly from ete3? qt messages should only appear when using graphics features in ete. Also, using xvfb is workaround for servers without x11 On 30 July 2018 at 00:45, Andrew Sanchez ***@***.***> wrote: > Any idea how to suppress the error output that results from running with > this setting (as discussed at ContinuumIO/anaconda-issues#1806 > <ContinuumIO/anaconda-issues#1806>) on a remote > server with no x server or x 11 forwarding? > > - os.environ['QT_QPA_PLATFORM']='offscreen' > > Here is the error output I get: > > QFontDatabase: Cannot find font directory ~/miniconda3/envs/env/lib/fonts - is Qt installed correctly? > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#101 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/AAJ_SnsLw cZ2fmA9Gxf5MENVNIlOAXEFks5uLjsYgaJpZM4EHJ_A> > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#101 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALKp6jATH7MHbupB3PF3MLHxEgOtTCIaks5uLsa-gaJpZM4EHJ_A> .

jhcepas · 2018-07-31T06:15:26Z

I see, then I am afraid that you will need xvfb. At least I could not find any other way.
Even SVG features in ete3 use Qt directives, and Qt requieres an xserver to work.

orangeSi · 2018-11-15T02:16:21Z

Any idea how to suppress the error output that results from running with this setting (as discussed at ContinuumIO/anaconda-issues#1806) on a remote server with no x server or x 11 forwarding?

os.environ['QT_QPA_PLATFORM']='offscreen'

Here is the error output I get:
QFontDatabase: Cannot find font directory ~/miniconda3/envs/env/lib/fonts - is Qt installed correctly?

I solved this error by

download https://github.com/openwebos/qt/tree/master/lib/fonts to get fonts directory 
mv fonts to xx/envs/your_envname/lib/

wsdewitt · 2022-03-08T17:48:38Z

As an alternative to XVFB, I've had had success setting the following environment variables:

export QT_QPA_PLATFORM=offscreen
export XDG_RUNTIME_DIR=/tmp/runtime-runner

JohnReid closed this as completed Apr 24, 2015

gregcaporaso mentioned this issue Mar 28, 2016

conditional rendering of trees isn't possible in IPython Notebooks? #204

Closed

cswarth mentioned this issue Nov 14, 2016

Need pipeline from partis output to visualization matsengrp/cft#15

Closed

unode mentioned this issue May 9, 2018

ete3 cannot be used on hosted Jupyter instances #352

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

ETE: cannot connect to X server #101

ETE: cannot connect to X server #101

JohnReid commented Apr 23, 2015

jhcepas commented Apr 23, 2015

JohnReid commented Apr 24, 2015

jhcepas commented Apr 24, 2015

JohnReid commented Apr 24, 2015

matsen commented Dec 10, 2015

gregcaporaso commented Mar 28, 2016

gregcaporaso commented Mar 28, 2016

jhcepas commented Mar 29, 2016

mgalardini commented Jun 8, 2016

anatoly108 commented Apr 25, 2017 •

edited

Loading

jhcepas commented Apr 25, 2017 •

edited

Loading

andrewsanchez commented Nov 10, 2017

thdpuydt commented May 31, 2018

andrewsanchez commented Jul 29, 2018

jhcepas commented Jul 30, 2018 via email

andrewsanchez commented Jul 30, 2018 via email

jhcepas commented Jul 31, 2018

orangeSi commented Nov 15, 2018 •

edited

Loading

wsdewitt commented Mar 8, 2022

ETE: cannot connect to X server #101

ETE: cannot connect to X server #101

Comments

JohnReid commented Apr 23, 2015

jhcepas commented Apr 23, 2015

JohnReid commented Apr 24, 2015

jhcepas commented Apr 24, 2015

JohnReid commented Apr 24, 2015

matsen commented Dec 10, 2015

gregcaporaso commented Mar 28, 2016

gregcaporaso commented Mar 28, 2016

jhcepas commented Mar 29, 2016

mgalardini commented Jun 8, 2016

anatoly108 commented Apr 25, 2017 • edited Loading

jhcepas commented Apr 25, 2017 • edited Loading

andrewsanchez commented Nov 10, 2017

thdpuydt commented May 31, 2018

andrewsanchez commented Jul 29, 2018

jhcepas commented Jul 30, 2018 via email

andrewsanchez commented Jul 30, 2018 via email

jhcepas commented Jul 31, 2018

orangeSi commented Nov 15, 2018 • edited Loading

wsdewitt commented Mar 8, 2022

anatoly108 commented Apr 25, 2017 •

edited

Loading

jhcepas commented Apr 25, 2017 •

edited

Loading

orangeSi commented Nov 15, 2018 •

edited

Loading