Can't see GUI in Ubuntu #11
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We will look at this. Sorry for the delay.
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On Jul 29, 2017, at 1:15 PM, Eduardo Garza-Villarreal ***@***.***> wrote:
I have Linux Ubuntu 16.04 LTS Xenial. It seems I cannot get the GUI even with the instructions given. Any help is appreciated.
Here is the code and the error:
sudo docker run -i --rm --privileged -e DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix -v /tmp:/scratch -v /media/egarza/INP_MRI_Backup/projects/INP/addimex_tms/data/mri/nifti:/bids_dataset -v /media/egarza/INP_MRI_Backup/projects/INP/addimex_tms/data/mri/outputs:/outputs bids/cpac /bids_dataset /outputs GUI No protocol specified Namespace(analysis_level='GUI', aws_input_creds=None, aws_output_creds=None, bids_dir='/bids_dataset', data_config_file=None, mem_gb=None, mem_mb=None, n_cpus='1', output_dir='/outputs', participant_label=None, participant_ndx=None, pipeline_file='/cpac_resources/default_pipeline.yaml', save_working_dir=False) Starting CPAC GUI Unable to access the X Display, is $DISPLAY set properly?
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No problem, sir. I tried several fixes such as [this] (http://fabiorehm.com/blog/2014/09/11/running-gui-apps-with-docker/), but no luck. Thanks Ed |
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Are you willing to try installing singilarity? It should just work
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On Aug 1, 2017, at 11:31 AM, Eduardo Garza-Villarreal ***@***.***> wrote:
No problem, sir. I tried several fixes such as this [http://fabiorehm.com/blog/2014/09/11/running-gui-apps-with-docker/], but no luck.
Thanks
Ed
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I did that already, then tried to import the docker2singularity cpac with no luck. I get an error. Let me paste that error. |
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I have a singularity image you can download. I will send info later today.
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On Aug 1, 2017, at 11:42 AM, Eduardo Garza-Villarreal ***@***.***> wrote:
sudo docker run --privileged -ti --rm -v /var/run/docker.sock:/var/run/docke r.sock -v /home/egarza/MRI/apps/singularity_images:/output singularityware/docker2singularity bids/cpac Size: 5533 MB for the singularity container (1/9) Creating an empty image... Creating a sparse image with a maximum size of 5533MiB... Using given image size of 5533 Formatting image (/sbin/mkfs.ext3) Done. Image can be found at: /tmp/bids_cpac-2017-03-29-71120146c4f4.img (2/9) Importing filesystem... (3/9) Bootstrapping... (4/9) Adding run script... (5/9) Setting ENV variables... Singularity: sexec (U=0,P=146)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh (6/9) Adding mount points... Singularity: sexec (U=0,P=152)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh (7/9) Fixing permissions... Singularity: sexec (U=0,P=158)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh We're running on BusyBox/Buildroot Singularity: sexec (U=0,P=201)> Command=exec, Container=/tmp/bids_cpac-2017-03-29-71120146c4f4.img, CWD=/, Arg1=/bin/sh find:/proc/2/task/2/fd/11': No such file or directory
find: /proc/2/task/2/fd/11': No such file or directory find:/proc/2/task/2/fdinfo/11': No such file or directory
find: /proc/2/task/2/fdinfo/11': No such file or directory find:/proc/2/fd/11': No such file or directory
find: /proc/2/fd/11': No such file or directory find:/proc/2/fdinfo/11': No such file or directory
find: /proc/2/fdinfo/11': No such file or directory
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Cool, thanks. |
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As a follow-up, my student just installed bids/cpac in his Macbook Pro OSX El Capitan. We did all the instructions to get the Display, and we get the same error with Display. |
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Tried with singularity and GUI worked like a charm. Now, I tried to make and save a subjects list and gave me the same error as with the full CPAC: Is there a conflict between cpacs? Thanks Ed |
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Still can't save the data nor pipeline files using the GUI with singularity. I opted for editing the regular pipeline, but it would greatly help our work if we could do it from the GUI at some point, specially for teaching reasons. Thanks |
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I am having the same issue with an ubuntu machine (14.04.5 LTS). The issue being: "Unable to access the X Display, is $DISPLAY set properly?" Has there been any resolution to using docker? |
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i have been able to use it following these instructions:
https://github.com/bids-apps/cpac#running-docker-container-on-linux
make sure that you are correctly passing the DISPLAY environment variable
into the container
…On Fri, Jun 29, 2018 at 1:09 PM Zarrar Shehzad ***@***.***> wrote:
I am having the same issue with an ubuntu machine (14.04.5 LTS). The issue
being: "Unable to access the X Display, is $DISPLAY set properly?" Has
there been any resolution to using docker?
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or try singularity, it just works
On Fri, Jun 29, 2018 at 1:10 PM Cameron Craddock <[email protected]>
wrote:
… i have been able to use it following these instructions:
https://github.com/bids-apps/cpac#running-docker-container-on-linux
make sure that you are correctly passing the DISPLAY environment variable
into the container
On Fri, Jun 29, 2018 at 1:09 PM Zarrar Shehzad ***@***.***>
wrote:
> I am having the same issue with an ubuntu machine (14.04.5 LTS). The
> issue being: "Unable to access the X Display, is $DISPLAY set properly?"
> Has there been any resolution to using docker?
>
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> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <#11 (comment)>, or mute
> the thread
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> .
>
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University of Texas at Austin
Director, Computational NeuroImaging Lab
<http://computational-neuroimaging-lab.org/>
Founding Chair, Organization for Human Brain Mapping Open Science Special
Interest Group
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preprocessed versions of the ABIDE and ADHD200 neuroimaging datasets.
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Hi Cam, We still get the same error with Docker. In different computers with Ubuntu. |
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OK, i will look into this again.
…On Fri, Jun 29, 2018 at 1:56 PM Eduardo Garza-Villarreal < ***@***.***> wrote:
Hi Cam,
We still get the same error with Docker. In different computers with
Ubuntu.
Singularity works with the GUI but we are still unable to save the YML
file.
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Google Scholar Citations
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GitHub <https://github.com/ccraddock>
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Check out my recent blog Open Science Resources for Contributing to Brain
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Share that Brain @ the International Neuroimaging Datasharing Initiative
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The Preprocessed Connectomes Project
<http://preprocessed-connectomes-project.org/> is now sharing preprocessed
versions of the ABIDE and ADHD200 neuroimaging datasets.
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I have the reverse problem. I can save the YAML file with singularity but when I try to run preprocessing, it doesn't do anything. Well it shows one line (below) but then nothing is run.
But if I run with participant mode instead of GUI using the yaml files saved by the GUI, then it runs for me with singularity. |
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Which singularity container are you using?
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On Jun 30, 2018, at 5:55 PM, Zarrar Shehzad ***@***.***> wrote:
I have the reverse problem. I can save the YAML file with singularity but when I try to run preprocessing, it doesn't do anything. Well it shows one line (below) but then nothing is run.
strategy_entries: [['_compcor_ncomponents_5_selector_pc10.linear0.wm0.global0.motion1.quadratic0.gm0.compcor1.csf0', '_target_angle_deg_90', '_threshold_0.2']]
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The one I made by converting the CPAC docker to singularity. |
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Ok. What version of the docket container
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On Jun 30, 2018, at 9:40 PM, Zarrar Shehzad ***@***.***> wrote:
The one I made by converting the CPAC docker to singularity.
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I was able to get the GUI to work using x11docker (https://github.com/mviereck/x11docker). Would you mind trying that? This sample worked for me: x11docker --bids/cpac /tmp /tmp GUI |
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I am able to run the GUI that way, I include the --homedir flag and it works. I can save the Subject file, but when I try to Generate the Subject YAML it tells me this:
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I will look into this further. In the meantime, can you generate your data config file using the 'test_config' flag to the CPAC app? Also, you appear to be using an older version of CPAC (the logo is different), perhaps you could try with a newer version? |
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Everything works for me now in singularity. There was a path issue for the inputs that wasn't being displayed. |
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@czarrar would you please elaborate so that we can fix the error reporting in future versions? |
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When running in the 'participant' instead of 'GUI' option, I saw that I had improper BIDS paths that was causing an issue. In the 'GUI' setting, when I ran the analysis, it didn't show this error or any of the output that comes with CPAC. However, when I fixed the path issue, then going through the 'GUI' ran fine. Hope this helps. |
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I downloaded the latest bids/cpac. Now it does not give me the error, but it also does not Generate the Data Config file. And still, the CPAC looks as if it crashed but it is still responsive. Very strange. |
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Made Singularity GUI work using the instructions. Now I did not have a problem converting the docker image to singularity and it all opened fine. I do have a problem, but I made it another Issue. It may seem this new issue is similar to the Docker issue with x11docker as it has to do more with the Path Search. |
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I have Linux Ubuntu 16.04 LTS Xenial. It seems I cannot get the GUI even with the instructions given. Any help is appreciated.
Here is the code and the error:
sudo docker run -i --rm --privileged -e DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix -v /tmp:/scratch -v /media/egarza/INP_MRI_Backup/projects/INP/addimex_tms/data/mri/nifti:/bids_dataset -v /media/egarza/INP_MRI_Backup/projects/INP/addimex_tms/data/mri/outputs:/outputs bids/cpac /bids_dataset /outputs GUI No protocol specified Namespace(analysis_level='GUI', aws_input_creds=None, aws_output_creds=None, bids_dir='/bids_dataset', data_config_file=None, mem_gb=None, mem_mb=None, n_cpus='1', output_dir='/outputs', participant_label=None, participant_ndx=None, pipeline_file='/cpac_resources/default_pipeline.yaml', save_working_dir=False) Starting CPAC GUI Unable to access the X Display, is $DISPLAY set properly?The text was updated successfully, but these errors were encountered: