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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]> 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]> on behalf of > Tanenbaum, Aaron <[log in to unmask]> > *Sent:* Wednesday, August 31, 2022 5:53 AM > *To:* [log in to unmask] <[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]> on behalf of > paul mccarthy <[log in to unmask]> > *Sent:* Wednesday, August 31, 2022 3:08 AM > *To:* [log in to unmask] <[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]> > 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]> on behalf of > Tanenbaum, Aaron <[log in to unmask]> > *Sent:* Tuesday, August 30, 2022 10:54 AM > *To:* [log in to unmask] <[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]> on behalf of > Tanenbaum, Aaron <[log in to unmask]> > *Sent:* Tuesday, August 30, 2022 10:37 AM > *To:* [log in to unmask] <[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]> on behalf of > paul mccarthy <[log in to unmask]> > *Sent:* Tuesday, August 30, 2022 4:17 AM > *To:* [log in to unmask] <[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]> > 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]> on behalf of > Matthew Webster <[log in to unmask]> > *Sent:* Thursday, August 25, 2022 3:10 PM > *To:* [log in to unmask] <[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]> > 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 > > > > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. 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