#199 Computational neuroscience labs image
Closed: Fixed 5 years ago by ankursinha. Opened 6 years ago by ankursinha.

This can be based on the comps group. It would be nice to have this ready for F30. That way, we can also market it at CNS.


Metadata Update from @ankursinha:
- Issue marked as depending on: #198

6 years ago

@acaldwell : I've assigned this to you. Let's discuss progress on this ticket so it's easy for everyone to find---does that sound OK?

Metadata Update from @ankursinha:
- Issue assigned to acaldwell

6 years ago

Metadata Update from @ankursinha:
- Issue tagged with: S: WIP

6 years ago

hi thanks for letting me know. sorry about the long wait on the response, i had an issue with my workstation and had to get a brand new computer, so i'm up and running. i will be looking through the information regarding the spin and how to get started.

hi thanks for letting me know. sorry about the long wait on the response, i had an issue with my workstation and had to get a brand new computer, so i'm up and running. i will be looking through the information regarding the spin and how to get started.

heya, are you still interested in this @acaldwell ?

Metadata Update from @ankursinha:
- Issue set to the milestone: F31 GA (was: F30 beta)

5 years ago

No response, unassigning. I'll mail the -devel list to see if we can find folks to help here.

Metadata Update from @ankursinha:
- Assignee reset

5 years ago

Metadata Update from @ankursinha:
- Issue set to the milestone: F31 GA 2019-10-29 (was: F31 GA)

5 years ago

@ankursinha hello!

I'd be glad to help out with building an ISO if you guys need one.

@ankursinha hello!
I'd be glad to help out with building an ISO if you guys need one.

thanks very much @tjzabel ! We've got a few more folks interested in helping with this ( @dan1mal , @snavin, @bt0dotninja , @major ) so I thought we'd wait a few days while they settle in and then have a meeting to kick start things. I'll send out a whenisgood thingy in a day or two :clock3:

Hey all,
I've got some experience with *nixes and am good at troubleshooting/problem-solving, but I'm definitely new at a lot of this too (fedora, neuro computational science, spins/rpms)!

So after I got some links from @ankursinha I played around and couldn't figure out how to make a spin work. So, far these are the collected links to possible resources:

https://fedoraproject.org/wiki/Spins_Process
https://fedoraproject.org/wiki/Remix
Mailing list -
https://lists.fedoraproject.org/admin/lists/spins@lists.fedoraproject.org/
https://www.youtube.com/watch?v=pHa1YHxc_bY
https://github.com/livecd-tools/livecd-tools/
https://fedoraproject.org/wiki/FedoraLiveCD
https://fedoraproject.org/wiki/Livemedia-creator-_How_to_create_and_use_a_Live_CD
https://docs.pagure.org/koji/image_build/#

I'm not really sure what part goes exactly where yet, but so far ive installed:
- fedora-packager
- livecd-tools
- fedora kickstarts
- custom kickstarts
- mock
- git-all

If anyone can add anything please do! Any advice, insights and even guesses 😄 are welcome!

I didn't take many notes or logs the last time I was playing around, but when I get a chance tomorrow, I will try and copy the messages and put them in a pastebin (https://paste.fedoraproject.org/)

@dan1mal hello!

I will be updating the Remix documentation in the coming weeks on specifically how to create ISOS from kickstart files. The fedora docs has a page on building ISOS from ks files as well. There are actually a few outstanding bugs I'm currently working through that is preventing kickstarts from building properly.

For a quick guide on building images, the livemedia-creator wiki should be enough to get you started with what packages, etc are needed.

Without using things like mock (if you're on a Fedora 30 system), this script is good to look at as well in terms of what packages are needed and what the build steps look like (Lines 30 and 34).


With that being said, the first step is creating a kickstart file with the wanted packages, which is probably going to be the hardest part. Here is an example of a standalone kickstart file based off the fedora workstation and workstation-common kickstarts. The fedora-kickstarts pagure is great to look at for a ton of examples.

Just a note: the first image we are working on is for software related to computational neuroscience because we've packaged a lot of this software that was on our list. So, once we have a functional kickstart, the list of packages can be looked into.

Unlike other images, we don't need to worry too much about the size of the image. I would propose it be based on the workstation image since the workstation is our primary edition and provides a pretty good integrated experience for users.

Hi Folks,

What's the desktop environment we gonna use?
Are we gonna use LXDE? or something else?

It would be great if we can have list of software.
I can build offline and share the kickstart files with you guys.

Unlike other images, we don't need to worry too much about the size of the image.

Once I have released an ISO and there were several complains on "Could not download". Finally found the issue was the release image was over 4GB and Windows users who were on FAT file system could not download it due to the limitation in the file system.
So, I always try to keep 3.9GB as the ceiling value.

Hi Folks,
What's the desktop environment we gonna use?
Are we gonna use LXDE? or something else?

Gnome/Workstation for a start please

It would be great if we can have list of software.

Here's what I see so far from https://src.fedoraproject.org/group/neuro-sig:

  • nest, python3-nest
  • neuron, python3-neuron
  • auryn
  • calcium-calculator
  • COPASI
  • bionetgen
  • neurord
  • python-brian2
  • python-libNeuroML
  • python-neo
  • python-nineml
  • python-PyLEMS
  • smoldyn

@zbyszek @sagitter - have I missed anything?

I can build offline and share the kickstart files with you guys.

That would be a great start---it'll also help the rest of us learn how to go about it :)

Unlike other images, we don't need to worry too much about the size of the image.

Once I have released an ISO and there were several complains on "Could not download". Finally found the issue was the release image was over 4GB and Windows users who were on FAT file system could not download it due to the limitation in the file system.
So, I always try to keep 3.9GB as the ceiling value.

Ah, that's good to note! I don't think/hope that we won't get to 3.9GB. Most of these tools, once built, are quite small. (I've not suggested we include LaTeX, for example---folks can install that if they need to).

We could drop some of the default workstation tools too tbh. Our target audience is mainly composed of users who while techie, are not exactly developers.

Hi Folks,
What's the desktop environment we gonna use?
Are we gonna use LXDE? or something else?

Gnome/Workstation for a start please

It would be great if we can have list of software.

Here's what I see so far from https://src.fedoraproject.org/group/neuro-sig:

nest, python3-nest
neuron, python3-neuron
auryn
calcium-calculator
COPASI
bionetgen
neurord
python-brian2
python-libNeuroML
python-neo
python-nineml
python-PyLEMS
smoldyn

@zbyszek @sagitter - have I missed anything?

I can build offline and share the kickstart files with you guys.

That would be a great start---it'll also help the rest of us learn how to go about it :)

Thanks for the list.

I am building an ISO with the following list of software. But not sure if I should add auryn-mpich, auryn-mpich, auryn-openmpi.

bionetgen
calcium-calculator
COPASI
getdp
nest
neuron
neurord
python3-brian2
python-brian2-doc
python3-nest
python3-neuron
python3-libNeuroML
python3-neo
python3-nineml
python-nineml-doc
python3-PyLEMS
python-PyLEMS-doc
smoldyn

I will document all steps and share with the rest of the team.

Aweseome,
What is the problem auryn-*mpi* packages?

Ah, I've just remembered---auryn does not provide a serial build. It can only be used with MPI. Let's drop it for the moment. We don't want to pull in both mpich and openmpi packages.

Use of MPI is an advanced case, and users can install the packages themselves if they wish. This is also documented in the neurofedora docs:

https://docs.fedoraproject.org/en-US/neurofedora/mpi/

Aweseome,
What is the problem auryn-mpi packages?

I just asked as I am not familiar with these packages and there is no enough information available if you do dnf info against each of these packages.
I will add all of them before sending kickstart files.

I will document all steps and share with the rest of the team.

Thanks for that. It'll really help us learn the process. If we have time, we can also help @tjzabel update the docs and so on.

Right, I think in some kind of dependency problem. You know many mpi different implementations.

Folks,

I have published initial scripts in the repo and documented steps to build an ISO locally.
https://pagure.io/neuro-sig/neuro-scripts

I hope you guys can build your first FedoraNeuro ISO. :)

Thanks @snavin, i was finally able to get livecd-creator to up and running. I did run into some errors, which I am not sure due to dependencies or my system setup.

I pasted the process on pastebin. I dont have an .ISO file but I do have everything cached.

Im busy mid-day here, so I'll get back and examine it later. If anyone has guesses what went wrong, feel free to share them.

Thank you.

Thanks @snavin, i was finally able to get livecd-creator to up and running. I did run into some errors, which I am not sure due to dependencies or my system setup.
I pasted the process on pastebin. I dont have an .ISO file but I do have everything cached.
Im busy mid-day here, so I'll get back and examine it later. If anyone has guesses what went wrong, feel free to share them.
Thank you.

@dan1mal
Can you add following entry in to fedora-live-neuro.ks and re-run the livecd-tools?
Make sure you add it after %include but before %post.

selinux --disabled

Can you add following entry in to fedora-live-neuro.ks and re-run the livecd-tools?
Make sure you add it after %include but before %post.
selinux --disabled

@snavin - that seems to have worked. The process completed.
https://paste.fedoraproject.org/paste/MKQM7BMoWiU2P1z3k14-ZQ.

I have an .ISO which I am going to try and install to VM. I just need to figure out how to transfer the ISO from the virtual box vm I created it in, onto the host computer...I'll let you know what happens! 😀

I have 1.60 (1,721,303,030) GB ISO file named F30-Neuro-0.1.0.iso that I used to create a Oracle VirtualBox machine. The live instance started right up and installation went smoothly. After installing and rebooting the system seemed to be working fine.

The software loaded onto the machine:
Accessories:
--ClipIt
--Elementary Test
--Galculator
--Leafpad
--Xarchiver
--Xpad
Graphics:
--Image Viewer
Internet:
--Midori
--Pidgin Internet Messenger
--Sylpheed
--Transmission
Office:
--AbiWord
--Gnumeric
--Osmo
Programming
--Elementary Test
Sound & Video
--Asunder CD Ripper
--GnomeBaker CD/DVD Writer
--LXMusic simple music player
--PulseAudio Volume Control
System Tools
--Fedora Release Notes
--File Manager PCManFM
--Gigolo
--LXTerminal
--Task Manager

I wonder if there is a place I could upload the ISO in case anyone wanted to try it.

@snavin thanks very much, you're instructions were perfect, and after the addition of the selinux command everything worked great.

Ah, that's quite good! GIves us quite a bit of place for software.

Now, we need to tweak it for our targeted userbase, which is science hobbyists/researchers. So, I propose:

===== Base desktop environment

GNOME. The workstation provides a great integrated experience, especially for folks just moving over from other operating systems/distributions. Given that it is our primary community edition, this also means that it is always well maintained.

More information on the package set:

sudo dnf groupinfo "Fedora Workstation"

and:

$ sudo dnf groupinfo "GNOME Desktop Environment"
Last metadata expiration check: 0:01:29 ago on Fri 16 Aug 2019 10:29:23 BST.

Group: GNOME
 Description: GNOME is a highly intuitive and user friendly desktop environment.
 Mandatory Packages:
   dconf
   gdm
   gedit
   gnome-boxes
   gnome-control-center
   gnome-initial-setup
   gnome-session-wayland-session
   gnome-session-xsession
   gnome-settings-daemon
   gnome-shell
   gnome-software
   gnome-terminal
   nautilus
   polkit
   yelp
 Default Packages:
   ModemManager
   NetworkManager-adsl
   NetworkManager-openconnect-gnome
   NetworkManager-openvpn-gnome
   NetworkManager-ppp
   NetworkManager-pptp-gnome
   NetworkManager-ssh-gnome
   NetworkManager-vpnc-gnome
   NetworkManager-wwan
   PackageKit-command-not-found
   PackageKit-gtk3-module
   adobe-source-code-pro-fonts
   at-spi2-atk
   at-spi2-core
   avahi
   baobab
   cheese
   chrome-gnome-shell
   eog
   evince
   evince-djvu
   evince-nautilus
   file-roller
   file-roller-nautilus
   fprintd-pam
   glib-networking
   gnome-backgrounds
   gnome-bluetooth
   gnome-calculator
   gnome-calendar
   gnome-characters
   gnome-classic-session
   gnome-clocks
   gnome-color-manager
   gnome-contacts
   gnome-disk-utility
   gnome-font-viewer
   gnome-getting-started-docs
   gnome-logs
   gnome-maps
   gnome-photos
   gnome-remote-desktop
   gnome-screenshot
   gnome-system-monitor
   gnome-terminal-nautilus
   gnome-themes-extra
   gnome-user-docs
   gnome-user-share
   gnome-weather
   gvfs-afc
   gvfs-afp
   gvfs-archive
   gvfs-fuse
   gvfs-goa
   gvfs-gphoto2
   gvfs-mtp
   gvfs-smb
   libcanberra-gtk2
   libcanberra-gtk3
   libproxy-mozjs
   librsvg2
   libsane-hpaio
   mesa-libEGL
   mousetweaks
   nautilus-sendto
   orca
   rygel
   sane-backends-drivers-scanners
   simple-scan
   sushi
   totem
   totem-nautilus
   tracker
   tracker-miners
   xdg-desktop-portal
   xdg-desktop-portal-gtk
   xdg-user-dirs-gtk
 Optional Packages:
   gstreamer-plugins-bad
   vlc

===== Accessories

Use what GNOME provides.

===== Image viewer

Gnome includes one. We use that.

===== Office/productivity

The workstation install includes Libreoffice. We use that instead of Abiword/Gnumeric/Osmo.

===== Sound and video

Use GNOME default. They also include tools and the required gstreamer
libraries.

===== System tools

Use Gnome default.

===== Programming and scientific tools

Gedit is included, and is now much improved.
I don't want to push users to particular IDEs etc., so we could probably let
them choose and install what they want for themselves.

Now, the science software:

  • nest, python3-nest
  • neuron, python3-neuron
  • calcium-calculator
  • COPASI
  • bionetgen
  • neurord
  • python-brian2
  • python-libNeuroML
  • python-neo
  • python-nineml
  • python-PyLEMS
  • smoldyn
  • python3-matplotlib python3-numpy python3-scipy
  • gnuplot
  • octave

I can't think of anything else at the moment.

@dan1mal---do you think us creating a "comps" group for the computational
neuroscience tools would make this easier (#198)?

I'd add various python packages. After all, the strength of Fedora is in the rich ecosystem of surrounding tools, for scripting, postprocessing, visualization, etc. I see that there's already @python-science group in comps. I'd just include that.

Also: qalculate, paraview, gnuplot.

I think we should pull in the R stack. R is the metapackage for that.

+1

Let's add all of this in and see how large the ISO is. If it gets too large, we can trim things out and prioritise.

(For example, if we pull in qualculate, we can drop gnome-calculator. )

Possible brain fart:

  • I think we should at least create a comps group for computational-modelling: this includes nest and all that

  • If needed, we could create a "meta" comps group for data-analysis too: this includes python-science, qalculate, R, gnuplot and all that (if a data science SIG is formed in the future, they can manage this, for example)?

That way, the comp-neuro image only needs to include these two comps groups instead of listing individual packages? It also makes it easier for users to install this stuff later if they didn't use the ISO image.

Thoughts?

Yes, a comps groups sounds like a good approach. This allows us to reuse the definition on non-spin installations by doing dnf install @computational-modelling or so.

Let's discuss the comps group in #198. @dan1mal --- assigning this one to you as our lab/spin lead :fireworks:

If anyone is interested in the comps bit, please assign #198 to yourself and get started too :clap:

Metadata Update from @ankursinha:
- Issue assigned to ankursinha

5 years ago

Metadata Update from @ankursinha:
- Issue assigned to dan1mal (was: ankursinha)

5 years ago

@ankursinha
Ugh, sorry, I updated your comment rather than replying to it. It was the one where you asked if I thought add a comp groups was wise. Is there a way to undo changes to comments? Ironically I cant seem to find a way.

Ill try to be more careful next time, pagure-git may need a git-comments command.

@ankursinha
Whew! I cut and paste it from the email notification from this issue. I believe I fixed it in its entirety.

In regards to your question:

@dan1mal---do you think us creating a "comps" group for the computational
neuroscience tools would make this easier (#198)?

To be frank, I have no idea of the benefits or the costs of doing that are so I couldn't say if we should or shouldn't. I tend towards being a "build it crudely and without plan, then improve with iterations/time", but I am also very happy with "aim for a structured future by building the framework, before starting to see results". So I'll defer to your judgement.

My short-term plan is to continue cobbling together the ISOs, once they are configured properly, pulling the lists to make the comps. In the meanwhile we can start working on the text/names for the comps.

Here's what I've gathered from previous posts:

Base: Gnome/Workstation

This is the Original list:

bionetgen
calcium-calculator
COPASI
getdp
nest
neuron
neurord
python3-brian2
python-brian2-doc
python3-nest
python3-neuron
python3-libNeuroML
python3-neo
python3-nineml
python-nineml-doc
python3-PyLEMS
python-PyLEMS-doc
smoldyn

Updated list
nest, python3-nest
neuron, python3-neuron
calcium-calculator
COPASI
bionetgen
neurord
python-brian2
python-libNeuroML
python-neo
python-nineml
python-PyLEMS
smoldyn
python3-matplotlib python3-numpy python3-scipy
gnuplot
octave

plus
qcalculate
paraview
gnuplot
@python-science

Update:

I generated a ks file from the fedora-live-workstation.ks and added the above files to a fedora-neuro.ks.

Two packages were not recognized: qcalculate and calcium-calculator. I believe calcium-calculator had been recognized the first time I attempted an ISO. Not sure what changed. Also #auryn was commented since the last kickstart. The neuro list looked like this:

#auryn
auryn-mpich
auryn-mpich
auryn-openmpi
bionetgen
#calcium-calculator
COPASI
#qcalculate
getdp
gnuplot
nest
neuron
neurord
octave
paraview
python3-brian2
python-brian2-doc
python3-nest
python3-neuron
python3-libNeuroML
python3-neo
python3-nineml
python-nineml-doc
python3-PyLEMS
python-PyLEMS-doc
python3-matplotlib
python3-numpy
python3-scipy
smoldyn

@python-science

Attempt 1: build workstation and neuro list together, without disabled selinux. Some errors during creation, but the ISO was generated. However it would not load.
Attempt 2: build workstation alone (original ks), without disabled selinux. Also would not load, but i managed to figure out that by removing rhgb and quiet I could see the errors. If you know any other useful switches, please let me know. Errors were regarding dbus. Lots of them.
Attempt 3: build workstation and neuro list together, with disabled selinux. some minor errors during creation. booted fine. installed fine.

I will test software another day and check the installation logs which I pulled before rebooting. If you know an easy way to confirm that the packages are intact and installed, please let me know. Otherwise, ill try and run them (the neuro list) one by one on the command line.

Size of ISO (w/o those 2 packages) is 2.40 GB (2,583,691,264 bytes).

I did not push the changes yet, but will do so if somebody confirms that we can revert back to the current state if needed.

qcalculate → qalculate
calcium-calculator → gnome-calculator (it should be pulled in by the desktop anyway)

Thanks @zbyszek I made the qalculate change and that worked.

I tried using selinux=permissive and the ISO was generated and installed, but after the welcome login screen where I made a user, there was no menu. Using ctrl-alt-f2 i tried to login as the newly created user, but that did not work.

I realized that it may be that I am running the command with sudo as a user. I will try root next with selinux set to enforcing (since that is where we want to get to, correct?)

Also I have replaced the advertisement banners that should show up in the installer, so this will be a test to see if that works too.

Probably will start this up tomorrow morning.

Did not work. I did a lot of searching for an answer to the selinux/login problem and it appears its been a long standing issue that hasn't been resolved. Even running the spin-kickstart KS files without modifications runs into this same issue. Either the ISO needs to be generated with selinux disabled to install properly. If it is set in permissive mode the ISO will install and boot, but will not autologin (https://bugzilla.redhat.com/show_bug.cgi?id=1071548) after entering use information and password. If set to enforcing mode, the ISO will create, but will not boot - failing with dbus-daemon.service errors (not sure what that is yet).

Some errors coming up are:

Mounting /dev/loop0 at /usr/share/spin-kickstarts/tmp/imgcreate-5bgs_qdm/install_root
Unknown configuration option: failovermethod = priority in /usr/share/spin-kickstarts/tmp/imgcreate-5bgs_qdm/dnf.conf-g898belc


No match for group package "reiserfs-utils"
No match for group package "xorg-x11-drv-omap"
No match for group package "totem-nautilus"
No match for group package "xorg-x11-drv-armsoc"
No match for group package "powerpc-utils"
No match for group package "gfs2-utils"
No match for group package "lsvpd"


Running scriptlet: dbus-broker-21-3.fc30.x86_64                                                                                                            628/1634 
Failed to get unit file state for dbus-daemon.service: No such file or directory
Failed to get unit file state for dbus-daemon.service: No such file or directory
Failed to disable unit, unit dbus-daemon.service does not exist.
Failed to disable unit, unit dbus-daemon.service does not exist.


Running scriptlet: kernel-core-5.2.8-200.fc30.x86_64                                                                                                      1634/1634 
dracut: No '/dev/log' or 'logger' included for syslog logging
dracut-install: ERROR: installing 'sr_mod'
dracut: FAILED:  /usr/lib/dracut/dracut-install -D /var/tmp/dracut.XYpzcN/initramfs --kerneldir /lib/modules/5.2.8-200.fc30.x86_64/ -m sr_mod sd_mod ide_cd cdrom =ata sym53c8xx aic7xxx ehci_hcd uhci_hcd ohci_hcd usb_storage usbhid uas firewire-sbp2 firewire-ohci sbp2 ohci1394 ieee1394 mmc_block sdhci sdhci-pci pata_pcmcia mptsas virtio_blk virtio_pci virtio_scsi virtio_net virtio_mmio virtio_balloon virtio-rng
dracut-install: ERROR: installing 'ext4'
dracut: FAILED:  /usr/lib/dracut/dracut-install -D /var/tmp/dracut.XYpzcN/initramfs --kerneldir /lib/modules/5.2.8-200.fc30.x86_64/ -m vfat msdos isofs ext4 xfs btrfs squashfs



Running authconfig compatibility tool.
The purpose of this tool is to enable authentication against chosen services with authselect and minimum configuration. It does not provide all capabilities of authconfig.

IMPORTANT: authconfig is replaced by authselect, please update your scripts.
See Fedora 28 Change Page: https://fedoraproject.org/wiki/Changes/AuthselectAsDefault
See man authselect-migration(7) to help you with migration to authselect
Warning: These options are not supported anymore and have no effect:
  --enableshadow
  --useshadow
  --passalgo



pdating index cache for path `/usr/share/man/man7'. Wait.../usr/bin/mandb: warning: /usr/share/man/man7/virkeycode-atset2.7.gz: whatis parse for virkeycode-atset2(7) failed
/usr/bin/mandb: warning: /usr/share/man/man7/virkeycode-atset1.7.gz: whatis parse for virkeycode-atset1(7) failed
/usr/bin/mandb: warning: /usr/share/man/man7/virkeycode-atset3.7.gz: whatis parse for virkeycode-atset3(7) failed
/usr/bin/mandb: warning: /usr/share/man/man7/virkeycode-osx.7.gz: whatis parse for virkeycode-osx(7) failed
/usr/bin/mandb: warning: /usr/share/man/man7/virkeycode-linux.7.gz: whatis parse for virkeycode-linux(7) failed
/usr/bin/mandb: warning: /usr/share/man/man7/virkeycode-qnum.7.gz: whatis parse for virkeycode-qnum(7) failed
/usr/bin/mandb: warning: /usr/share/man/man7/virkeycode-usb.7.gz: whatis parse for virkeycode-usb(7) failed
/usr/bin/mandb: warning: /usr/share/man/man7/virkeycode-win32.7.gz: whatis parse for virkeycode-win32(7) failed
/usr/bin/mandb: warning: /usr/share/man/man7/virkeycode-xtkbd.7.gz: whatis parse for virkeycode-xtkbd(7) failed
/usr/bin/mandb: warning: /usr/share/man/man7/virkeyname-linux.7.gz: whatis parse for virkeyname-linux(7) failed
/usr/bin/mandb: warning: /usr/share/man/man7/virkeyname-osx.7.gz: whatis parse for virkeyname-osx(7) failed
/usr/bin/mandb: warning: /usr/share/man/man7/virkeyname-win32.7.gz: whatis parse for virkeyname-win32(7) failed
/usr/bin/mandb: warning: /usr/share/man/man7/gnupg2.7.gz is a dangling symlink
Updating index cache for path `/usr/share/man/man1'. Wait.../usr/bin/mandb: warning: /usr/share/man/man1/ex.1.gz is a dangling symlink
/usr/bin/mandb: warning: /usr/share/man/man1/rview.1.gz is a dangling symlink
/usr/bin/mandb: warning: /usr/share/man/man1/view.1.gz is a dangling symlink
Updating index cache for path `/usr/share/man/man3'. Wait.../usr/bin/mandb: warning: /usr/share/man/man3/Net::libnetFAQ.3pm.gz: whatis parse for Net::libnetFAQ(3pm) failed
Updating index cache for path `/usr/share/man/man2'. Wait...done.
Checking for stray cats under /usr/share/man...


Updating index cache for path `/usr/share/man/uk/man1'. Wait.../usr/bin/mandb: warning: /usr/share/man/uk/man1/dos2unix.1.gz: whatis parse for unix2dos(1) failed
/usr/bin/mandb: warning: /usr/share/man/uk/man1/dos2unix.1.gz: whatis parse for mac2unix(1) failed
/usr/bin/mandb: warning: /usr/share/man/uk/man1/dos2unix.1.gz: whatis parse for dos2unix(1) failed
/usr/bin/mandb: warning: /usr/share/man/uk/man1/dos2unix.1.gz: whatis parse for unix2mac(1) failed

Checking for stray cats under /usr/local/share/man...
Checking for stray cats under /var/cache/man/local...
114 man subdirectories contained newer manual pages.
7548 manual pages were added.
0 stray cats were added.
0 old database entries were purged.
error reading information on service network: No such file or directory
cp: cannot stat '/usr/share/spin-kickstarts/tmp/imgcreate-5bgs_qdm/install_root/usr/share/licenses/*-release/*': No such file or directory
/ 100.0%

I also propose the tag easy be removed from this issue. 😐

Did not work. I did a lot of searching for an answer to the selinux/login problem and it appears its been a long standing issue that hasn't been resolved. Even running the spin-kickstart KS files without modifications runs into this same issue. Either the ISO needs to be generated with selinux disabled to install properly. If it is set in permissive mode the ISO will install and boot, but will not autologin (https://bugzilla.redhat.com/show_bug.cgi?id=1071548) after entering use information and password. If set to enforcing mode, the ISO will create, but will not boot - failing with dbus-daemon.service errors (not sure what that is yet).

We haven't spoken to the Spins SIG, have we? Given that the Fedora spins/labs were released on time, either this is a known issue with a fix or a workaround. I cannot imagine the final images to be released without seiinux.

Some errors coming up are:
Mounting /dev/loop0 at /usr/share/spin-kickstarts/tmp/imgcreate-5bgs_qdm/install_root
Unknown configuration option: failovermethod = priority in /usr/share/spin-kickstarts/tmp/imgcreate-5bgs_qdm/dnf.conf-g898belc

Looks like an option for dnf.conf, but since I can't find it in man dnf.conf, it may have been obsoleted.

No match for group package "reiserfs-utils"
No match for group package "xorg-x11-drv-omap"
No match for group package "totem-nautilus"
No match for group package "xorg-x11-drv-armsoc"
No match for group package "powerpc-utils"
No match for group package "gfs2-utils"
No match for group package "lsvpd"

Obsolete groups, OK to ignore these warnings.

Running scriptlet: dbus-broker-21-3.fc30.x86_64 628/1634
Failed to get unit file state for dbus-daemon.service: No such file or directory
Failed to get unit file state for dbus-daemon.service: No such file or directory
Failed to disable unit, unit dbus-daemon.service does not exist.
Failed to disable unit, unit dbus-daemon.service does not exist.

I seem to remember this bug in F30, but I've not experienced it myself. We'll have to ask the Spins SIG about this.

Running scriptlet: kernel-core-5.2.8-200.fc30.x86_64 1634/1634
dracut: No '/dev/log' or 'logger' included for syslog logging
dracut-install: ERROR: installing 'sr_mod'
dracut: FAILED: /usr/lib/dracut/dracut-install -D /var/tmp/dracut.XYpzcN/initramfs --kerneldir /lib/modules/5.2.8-200.fc30.x86_64/ -m sr_mod sd_mod ide_cd cdrom =ata sym53c8xx aic7xxx ehci_hcd uhci_hcd ohci_hcd usb_storage usbhid uas firewire-sbp2 firewire-ohci sbp2 ohci1394 ieee1394 mmc_block sdhci sdhci-pci pata_pcmcia mptsas virtio_blk virtio_pci virtio_scsi virtio_net virtio_mmio virtio_balloon virtio-rng
dracut-install: ERROR: installing 'ext4'
dracut: FAILED: /usr/lib/dracut/dracut-install -D /var/tmp/dracut.XYpzcN/initramfs --kerneldir /lib/modules/5.2.8-200.fc30.x86_64/ -m vfat msdos isofs ext4 xfs btrfs squashfs

Not sure about this either. Another issue to discuss with the Spins SIG.

Running authconfig compatibility tool.
The purpose of this tool is to enable authentication against chosen services with authselect and minimum configuration. It does not provide all capabilities of authconfig.

IMPORTANT: authconfig is replaced by authselect, please update your scripts.
See Fedora 28 Change Page: https://fedoraproject.org/wiki/Changes/AuthselectAsDefault
See man authselect-migration(7) to help you with migration to authselect
Warning: These options are not supported anymore and have no effect:
--enableshadow
--useshadow
--passalgo

Is the kickstart using authconfig anywhere? If this is coming from one of the scripts that we're simply using, all we can do is report it and wait for it to be fixed.

<snip>

I'd ignore the man page errors.

cp: cannot stat '/usr/share/spin-kickstarts/tmp/imgcreate-5bgs_qdm/install_root/usr/share/licenses/-release/': No such file or directory
/ 100.0%

Not a clue about this one, unfortunately.

Let's give everyone a day or two to look at the kickstart and then I suggest we submit it as a formal Fedora lab?

This is the process:

https://fedoraproject.org/wiki/Spins_Process

The page, however, has been marked as "old", so it may be worth joining the Spins mailing list to confirm if it still applies?

I also propose the tag easy be removed from this issue. 😐

It's assigned to you. Please feel free to change the metadata as you wish :clap:

calcium-calculator → gnome-calculator (it should be pulled in by the desktop anyway)

Just saw this: calcium-calculator is a package. Not sure why it isn't found. It went stable a while back:

https://src.fedoraproject.org/rpms/calcium-calculator

@dan1mal : when the images are built, what repositories are they using? Are they using the fedora release repository, and is the updates repo enabled?

calcium-calculator → gnome-calculator (it should be pulled in by the desktop anyway)

Just saw this: calcium-calculator is a package. Not sure why it isn't found. It went stable a while back:
https://src.fedoraproject.org/rpms/calcium-calculator
@dan1mal : when the images are built, what repositories are they using? Are they using the fedora release repository, and is the updates repo enabled?

I used the same fedora-repo-not-rawhide.ks in the test run that @snavin built. I'm 99% sure that calcium-calculator was found at that time.

The file looks like this:

repo --name=fedora --mirrorlist=https://mirrors.fedoraproject.org/mirrorlist?repo=fedora-$releasever&arch=$basearch
repo --name=updates --mirrorlist=https://mirrors.fedoraproject.org/mirrorlist?repo=updates-released-f$releasever&arch=$basearch

Looks OK. We can figure out the details later---one can always tweak the package set etc. Let's try to get it added to the Fedora labs first? What do you think @dan1mal ?

So this looks like the process for submitting a spin. I'm not sure how active SPINS sig is, maybe it just turns on and off when needed.

It looks like the SPINS deadline for F31 was somewhere in January

  • Created a new Spin page, as per the instructions in the Spins process - https://fedoraproject.org/wiki/Neuro_Spin#Spin_Name

  • I filled out what I could, @ankursinha / team: please edit/change/update as appropriate.

  • I updated the kickstart files and pushed the change to the live workstation (gnome) version of kickstart.

From what I read in the spins process, we should be ready to submit.

So this looks like the process for submitting a spin. I'm not sure how active SPINS sig is, maybe it just turns on and off when needed.

Yes, I'm a bit worried about this. Lots of outdated references on the spin page too :disappointed:
There are spins/labs every release, though, so even if not documented, there is something in place.

It looks like the SPINS deadline for F31 was somewhere in January

Yeh, no worries. This applies to the release process. We'll just have an "unofficial" image till F32.

Created a new Spin page, as per the instructions in the Spins process - https://fedoraproject.org/wiki/Neuro_Spin#Spin_Name

I filled out what I could, @ankursinha / team: please edit/change/update as appropriate.

I moved it to https://fedoraproject.org/wiki/Comp-Neuro_Spin and made some changes.

I updated the kickstart files and pushed the change to the live workstation (gnome) version of kickstart.

Great! I'll try and build it here and test it out sometime this week!

From what I read in the spins process, we should be ready to submit.

Sounds good. Should we get in touch with them on the mailing list and get the ball rolling on this?

I've posted to the spins mailing list asking what the current process is:

https://lists.fedoraproject.org/archives/list/spins@lists.fedoraproject.org/thread/CIGYMZTXAAOQU2DE2GQ2JENOC6SVDBTN/

It'd be quite good of more of us subscribed to the spins mailing list and kept up with it now, given that we have spin as an important deliverable :balloon:

So, turns out the wiki page for the new spin proposal was completely irrelevant. Now, we just follow the standard change process:

https://fedoraproject.org/wiki/Changes/Policy

So, the spin becomes a new "self-contained change".

Lesson learned here: if a page looks outdated, first confirm its relevance before following its steps :laughing:

It mentions a new "spin" there not a "lab" but i guess it'd be better to
file a ticket and let the Council tell us if it isnt needed.

I'll go file a ticket for this in a bit.

Metadata Update from @ankursinha:
- Issue tagged with: S: Next meeting

5 years ago

Trademark approval request has been approved

https://pagure.io/Fedora-Council/tickets/issue/269#comment-593811

We can now proceed with the change process.

Metadata Update from @ankursinha:
- Issue untagged with: S: Next meeting

5 years ago

Metadata Update from @dan1mal:
- Issue untagged with: D: Easy
- Issue tagged with: S: Next meeting

5 years ago

I can't reproduce the SELinux Disabled on the final image. I set my system as permissive looking for some Selinux messages but nothing. the build success and the result iso comes with SeLinux enforcing enabled. My setup Fedora 30 workstation without third-party repos. (see the picture)

I change the structure to be compliant with
https://pagure.io/fedora-kickstarts (our final objective)

fedora-live-neuro.ks is the main file
fedora-neuro-gnome-common.ks is used for gnome customization included by fedora-live-neuro.ks
fedora-neuro-common.ks is the specific package selection

2019-09-04-130320_1920x1080_scrot.png

Here's the Change page. Let's tweak it and then submit it to the wrangler:

https://fedoraproject.org/wiki/Changes/Comp_Neuro_Lab

Submitted to wrangler now:

https://fedoraproject.org/wiki/Changes/Comp_Neuro_Lab

Please "watch" the wiki page, and keep an eye on the -devel mailing list where it will be announced and discussed.

Should I close this ticket or leave it open for us to further discuss things?

Oh, in the meantime, can we generate an image based on F30 and put it up somewhere? I can ask infra for more space on Fedora people? That way we can start spreading the word and getting feedback on it? @bt0dotninja what do you think?

Should I close this ticket or leave it open for us to further discuss things?

I'd prefer to close it to keep the issues tidy, but perhaps we can wait for a response from the wrangler (https://fedoraproject.org/wiki/Change_Wrangler)

That way we can start spreading the word and getting feedback on it?

Once the groups are in and the F30 version is up, perhaps we can work on a brochure/pdf info sheet like the Fedora Loves Python flyer? https://pagure.io/fedora-design/fedora-loves-python-brochure

Something that can be printed for events and forwarded to interested groups.

The change proposal e-mail went out:

https://lists.fedoraproject.org/archives/list/devel-announce@lists.fedoraproject.org/thread/Z4NKZUX3SJXOC6QAC72AOEYECSS4JSKT/

Yes, +1, we can work on more swag. Let's get the image up and work on those next. Closing this now. We'll open new tickets for related tasks as we go through the process.

Metadata Update from @ankursinha:
- Issue close_status updated to: Fixed
- Issue status updated to: Closed (was: Open)

5 years ago

FESCo ticket here now. Please subscribe to it for updates, everyone: https://pagure.io/fesco/issue/2237

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