Sure, I was not aware that this was an older version. I downloaded it on the 15th of august.
Aaron Tanenbaum
________________________________
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of paul mccarthy <[log in to unmask]>
Sent: Wednesday, August 31, 2022 10:10 AM
To: [log in to unmask] <[log in to unmask]>
Subject: Re: [FSL] fslpython install hangs on stage two..
* External Email - Caution *
Hi Aaron,
Would you be able to install the latest version of FSL instead (6.0.5.2), as it should not have this problem/
Paul
On Wed, 31 Aug 2022 at 12:38, Tanenbaum, Aaron <[log in to unmask]<mailto:[log in to unmask]>> wrote:
I forgot to mention fsl version from etc/fslversion is 6.0.5:9e026117
Aaron Tanenbaum
________________________________
From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Tanenbaum, Aaron <[log in to unmask]<mailto:[log in to unmask]>>
Sent: Wednesday, August 31, 2022 5:53 AM
To: [log in to unmask]<mailto:[log in to unmask]> <[log in to unmask]<mailto:[log in to unmask]>>
Subject: Re: [FSL] fslpython install hangs on stage two..
* External Email - Caution *
We recently installed Ubuntu 20.04.4 on this system. The system has 256Gb of ram.
Aaron Tanenbaum
________________________________
From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of paul mccarthy <[log in to unmask]<mailto:[log in to unmask]>>
Sent: Wednesday, August 31, 2022 3:08 AM
To: [log in to unmask]<mailto:[log in to unmask]> <[log in to unmask]<mailto:[log in to unmask]>>
Subject: Re: [FSL] fslpython install hangs on stage two..
* External Email - Caution *
Hi Aaron,
What version of FSL are you installing? This has been a problem in previous releases, but I wouldn't have expected it to happen for the latest version (6.0.5.2).
Also, how much RAM does your target system have? Conda can use quite a lot of memory, so you might be suffering from swapping.
Paul
On Tue, 30 Aug 2022 at 17:40, Tanenbaum, Aaron <[log in to unmask]<mailto:[log in to unmask]>> wrote:
I tried to set up the fslpython env manually running the command
fslpython/bin/conda env create -f etc/fslconf/fslpython_environment.yml
This command does hang too. Furthermore this command does give a few warning, se below. these are just warning so probably harmless.
WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 2.*, but conda is ignoring the .* and treating it as 2
WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.*, but conda is ignoring the .* and treating it as 1
| WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 3.6.*, but conda is ignoring the .* and treating it as 3.6
Aaron Tanenbaum
________________________________
From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Tanenbaum, Aaron <[log in to unmask]<mailto:[log in to unmask]>>
Sent: Tuesday, August 30, 2022 10:54 AM
To: [log in to unmask]<mailto:[log in to unmask]> <[log in to unmask]<mailto:[log in to unmask]>>
Subject: Re: [FSL] fslpython install hangs on stage two..
* External Email - Caution *
It does not look complete. There does not appear to be an fslpython environment. the folder $FSLDIR/fslpython/envs is empty.
Aaron Tanenbaum
________________________________
From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Tanenbaum, Aaron <[log in to unmask]<mailto:[log in to unmask]>>
Sent: Tuesday, August 30, 2022 10:37 AM
To: [log in to unmask]<mailto:[log in to unmask]> <[log in to unmask]<mailto:[log in to unmask]>>
Subject: Re: [FSL] fslpython install hangs on stage two..
* External Email - Caution *
I let this one run for several hours.
Aaron Tanenbaum
________________________________
From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of paul mccarthy <[log in to unmask]<mailto:[log in to unmask]>>
Sent: Tuesday, August 30, 2022 4:17 AM
To: [log in to unmask]<mailto:[log in to unmask]> <[log in to unmask]<mailto:[log in to unmask]>>
Subject: Re: [FSL] fslpython install hangs on stage two..
* External Email - Caution *
Hi Aaron,
How long have you left it running for? The log file suggests that the installation is proceeding normally - the conda command is "resolving" the fslpython environment specification, which can take some time and RAM. I would suggest letting it run for longer.
Paul
On Mon, 29 Aug 2022 at 21:42, Tanenbaum, Aaron <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Matt,
Disk activity does stop at some point. May be 10 min after I start running the set up. The startup script is using a CPU core at 100% constantly. Attached is the fslpython_miniconda_installer.log file
Aaron Tanenbaum
________________________________
From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Matthew Webster <[log in to unmask]<mailto:[log in to unmask]>>
Sent: Thursday, August 25, 2022 3:10 PM
To: [log in to unmask]<mailto:[log in to unmask]> <[log in to unmask]<mailto:[log in to unmask]>>
Subject: Re: [FSL] fslpython install hangs on stage two..
* External Email - Caution *
Hi Aaron,
Is the CPU busy with any python-related task ( check with top ) or is there any disk activity in the $FSLDIR/fslpython folder ( most recent timestamp etc )?
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 25 Aug 2022, at 19:37, Tanenbaum, Aaron <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>
> I am setting up fsl on a system with ubuntu 20.04. The installation hangs at stage two with "0%" done.
>
> I just run the command $FSLDIR/etc/fslconf/fslpython_install.sh -f $FSLDIR
>
> Does anyone have a solution to this problem?
>
> Aaron Tanenbaum
>
>
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