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Error running example #58

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malcolmudeozor opened this issue Mar 24, 2021 · 21 comments
Open

Error running example #58

malcolmudeozor opened this issue Mar 24, 2021 · 21 comments

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@malcolmudeozor
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malcolmudeozor commented Mar 24, 2021 •
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Hello! I am getting an error when trying to run the prfsynth image in the example. I am wondering if i need install a matlab container image inorder for the docker command to run properly.

Here is a snapshot of my terminal as I run prfsynth if it helps.

`Setting up environment variables

LD_LIBRARY_PATH is .:/opt/mcr/v95//runtime/glnxa64:/opt/mcr/v95//bin/glnxa64:/opt/mcr/v95//sys/os/glnxa64:/opt/mcr/v95//sys/opengl/lib/glnxa64
Number of workers:

NumWorkers =

 8

Starting parallel pool (parpool) using the 'local' profile ...

Error using parpool (line 113)
Parallel pool failed to start with the following error.

Error in pmForwardModelCalculate (line 57)

Error in synthBOLDgenerator (line 184)

Caused by:
Error using parallel.internal.pool.InteractiveClient>iThrowWithCause (line 676)
Failed to initialize the interactive session.
Error using parallel.internal.pool.InteractiveClient>iThrowIfBadParallelJobStatus (line 790)
The interactive communicating job failed with no message.

parallel:cluster:PoolCreateFailed

real 3m1.451s
user 1m29.344s
sys 1m9.530s
[garikoitz/prfsynth] An error occurred during execution of the Matlab executable. Exiting!
`

I'm not sure if this is sufficient info to solve my problem but anything will help.
@garikoitz
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garikoitz commented Mar 25, 2021 via email

@malcolmudeozor
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malcolmudeozor commented Mar 25, 2021 •
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Hi! Thanks for such a speedy response. I am launching docker from terminal on my mac. Also, I am using zsh.

What I am trying to do is the simple wiki example actually.

Here is the entire command with the resulting error. I have also attached the config file as .txt file. When i run the docker command however, i use the json version of that file

prfsynth_sub-001_sess-20200320 copy.txt

(base) homeDir / % docker run --rm -it
-v $basedir/prfsynth_sub-001_sess-20200320.json:/flywheel/v0/input/config.json
-v $basedir:/flywheel/v0/output
garikoitz/prfsynth
[garikoitz/prfsynth] Initialized.
[garikoitz/prfsynth] See detailed usage here: https://github.com/vistalab/PRFmodel/wiki/prf-Synthesize:-how-to-edit-json-file

Setting up environment variables

LD_LIBRARY_PATH is .:/opt/mcr/v95//runtime/glnxa64:/opt/mcr/v95//bin/glnxa64:/opt/mcr/v95//sys/os/glnxa64:/opt/mcr/v95//sys/opengl/lib/glnxa64
Number of workers:

NumWorkers =

 8

Starting parallel pool (parpool) using the 'local' profile ...

Error using parpool (line 113)
Parallel pool failed to start with the following error.

Error in pmForwardModelCalculate (line 57)

Error in synthBOLDgenerator (line 184)

Caused by:
Error using parallel.internal.pool.InteractiveClient>iThrowWithCause (line 676)
Failed to initialize the interactive session.
Error using parallel.internal.pool.InteractiveClient>iThrowIfBadParallelJobStatus (line 790)
The interactive communicating job failed with no message.

parallel:cluster:PoolCreateFailed

real 3m28.087s
user 1m32.405s
sys 2m58.570s
[garikoitz/prfsynth] An error occurred during execution of the Matlab executable. Exiting!
(base) udeozormi@MH02183913MACLT / %

@garikoitz
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garikoitz commented Mar 25, 2021 via email

@malcolmudeozor
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You're exactly right. I ran it to create the initial json and it worked fine. After that i followed the steps in the wiki to edit the name of the file and edit its contents. I do indeed have write access to basedir. Also, I tried running the command with bash and got the same error.

Are there any specific Matlab requirements? On my machine, I have only the newest version of matlab (including the parallel toolbox). Do you think there could there be a problem with the version i have?

Lastly, thank you very much for taking time out to help me solve my problem. I am pretty sure the error is coming from my end, so i really appreciate your help.

@garikoitz
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garikoitz commented Mar 29, 2021 via email

@malcolmudeozor
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I am attaching a text file with the exact order of commands that I ran. Ofc, you will need to edit the file to put in your respective username and edit the json like you explained in the example.

dockerCommands copy.txt

@garikoitz
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garikoitz commented Mar 29, 2021 via email

@malcolmudeozor
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yes, that is the one that is failing.

dockerImagesVersions.txt

@garikoitz
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garikoitz commented Mar 29, 2021 via email

@malcolmudeozor
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Got the same error unfortunately. I also see that both prfsynth versions have the exact same image ID; im not sure if you expected that or not. Did my series of commands look correct in the txt file that I sent?

Also, I am not in a huge rush to figure this out, so please do not let me absorb too much of your time.

@garikoitz
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garikoitz commented Mar 29, 2021 via email

@malcolmudeozor
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Great! thanks for being so helpful.

@garikoitz
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garikoitz commented Apr 2, 2021 via email

@malcolmudeozor
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Turning off parallel toolbox worked! Thanks so much! Let me know when you see this message so i can go ahead and close the issue.

@garikoitz
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garikoitz commented Apr 5, 2021 via email

@malcolmudeozor
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malcolmudeozor commented Apr 5, 2021 •
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I haven't tried yet. My goal is to finish running the example and then run real data for my PI. I can let you know what happens then. I will also turn parallel toolbox back on when running analyze and report to see if it works there and let you know.

@malcolmudeozor
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Hello! So I was able to successfully run both analyze and report and report containers. I first ran analyze-vista which worked fine. then i ran analyze-aprf (which used parallel toolbox) and it worked fine as well. This leads me to believe that my synth container specifically is not working correctly when prarallel toolbox is on. Lastly, my output files look a bit wonky. Again, it seems like this problem is deriving from the synth module (Id: d9b64480cf1e)
CloudPlots_4x4_Noise_mid

@garikoitz
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garikoitz commented Apr 8, 2021 via email

@malcolmudeozor
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malcolmudeozor commented Apr 12, 2021 •
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Hello, Im just looking at this again, and I do get data for aprf as the tool with vista_twogammas as the HRF. Its just that i dont get data for conical HRF for either vista or aprf. I checked the synth json and HRF "type" only contains "vista_two gammas". Not sure why PRFreport printed a graph for canonical HRF at all. Does this still sound unusual?

@garikoitz
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garikoitz commented Apr 12, 2021 via email

@DantePk420
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i Am struggling to execute and i get LD_LIBRARY_PATH is .:/opt/mcr/v95//runtime/glnxa64:/opt/mcr/v95//bin/glnxa64:/opt/mcr/v95//sys/os/glnxa64:/opt/mcr/v95//sys/opengl/lib/glnxa64
Assertion failed: p_rcu_reader->depth != 0 (/qemu/include/qemu/rcu.h: rcu_read_unlock: 101)
Aborted

real 0m22.111s
user 0m20.706s
sys 0m1.036s
[garikoitz/prfsynth] An error occurred during execution of the Matlab executable. Exiting!
Would be great if you could help me on the same

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@garikoitz @malcolmudeozor @DantePk420