#editorial | Logs for 2021-06-13
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[00:27:15] <Bytram> =asub https://royalsocietypublishing.org
[00:27:17] <systemd> ✓ Sub-ccess! "03Brain and Testis: More Alike Than Previously Thought?" (1p) -> https://soylentnews.org
[00:27:31] <Bytram> =cite https://royalsocietypublishing.org
[00:27:32] <systemd> <p><b>Journal Reference</b>:<br/><b>Brain and testis: more alike than previously thought?</b>, <cite>Open Biology</cite> (DOI: <a href="https://doi.org/https://royalsocietypublishing.org/doi/10.1098/rsob.200322">https://royalsocietypublishing.org/doi/10.1098/rsob.200322</a>)</p>
[00:47:28] <Bytram> =notes
[00:47:28] <systemd> ♩ (♩) ♪ (♪) ♫ (♫) ♬ (♬) 🎜 (🎜) 🎝 (🎝) 🎵 (🎵) 🎶 (🎶)
[01:21:06] <Bytram> have a great night everybody!
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[14:57:51] <Bytram> =g Father's Day
[14:57:52] <systemd> https://en.wikipedia.org - Father's Day - Wikipedia
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[15:37:09] <Bytram> Davis's Dictum: Problems that go away by themselves, come back by themselves.
[16:00:54] <Bytram> =g Let's Encrypt
[16:00:55] <systemd> https://letsencrypt.org - Let's Encrypt
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[18:06:38] <Bytram> =g "Inseminator's Day"
[18:06:39] <systemd> https://tags.literotica.com - male ejaculation - Literotica.com
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[18:50:10] <Bytram> =w roller derby
[18:50:11] <systemd> Roller derby is a roller skating contact sport played by two teams of fifteen members. Roller derby is played by approximately 1,250 amateur leagues worldwide - https://en.wikipedia.org
[18:50:43] <janrinok> Bytram!!!
[18:51:29] <Bytram> janrinok: !!
[18:51:37] <janrinok> how's things?
[18:51:52] <Bytram> good! quick question?
[18:51:57] <janrinok> go
[18:52:09] <Bytram> how do you spell "oficianados"?
[18:52:59] <janrinok> aficionado
[18:53:04] <Bytram> FF suggests: aficionados but it does not look right
[18:53:20] <Bytram> good enough for me!
[18:53:26] <janrinok> well it's about as right as I know it
[18:53:47] * Bytram is almost done with writing a story sub =)
[18:54:09] <janrinok> en_GB might make the plural aficionadoes but probably not
[18:54:33] <janrinok> its a foreign word so doesn't normally follow en grammar rules
[18:55:43] <Bytram> st\ory submitted!
[18:55:48] <Bytram> story submitted!
[18:56:30] <janrinok> that's not our usual sort of sub - is it a 'random'
[18:56:48] <Bytram> good point, I do not think it is critical at thispoint
[18:57:04] <Bytram> that's what I thought I picked for the dept
[18:57:41] <Bytram> could also add "Hardware" and "Software"
[18:57:59] <janrinok> ah, it is more on-topic than the title suggests. hackaday do cover some bizarre but interesting tech items
[18:58:25] <Bytram> so true
[18:59:23] <janrinok> there is at least one spolling mistook - but we can correct that at the next stage.
[19:00:25] <Bytram> wooden't sirprize me -- arms are sore today :/
[19:01:07] <janrinok> I've now got a basic install of Gentoo up and running, and I am looking at how to install Rehash. Everything is there but I might also produce a 'Start Here' guide for dimwits such as myself.
[19:01:34] * Bytram raises hand
[19:01:50] <janrinok> There are several 'assumptions' made regarding the installation which are not evident to me, but probably are to everyone else except for you and me.
[19:02:30] * Bytram was a dimwit in a prior life, and it seems to have persisted!
[19:03:06] <janrinok> I've only ever known being a dimwit, and I only know of one life here on planet Earth.
[19:05:14] <Bytram> i'm actually somewhat curious if fluorine can shutdown and restart safely on its own, or whether staff hit have to help it get back up?
[19:05:54] <janrinok> One of the problems is that, with Gentoo, everything is compiled from source so even installing, say, mysql takes 15 minutes (so far) and still counting.
[19:06:20] * Bytram hopes there's no catastrophe to try and recover from the site reboot!
[19:06:22] <janrinok> I can see the benefits but speed of setting up a new box is not one of them
[19:06:41] <janrinok> have we got the appropriate experts standing by?
[19:07:47] <Bytram> Have tried to hail them, nothing yet... see seket channel and the story I just posted
[19:08:05] <janrinok> I've seen the story....
[19:08:14] <Bytram> nod nod
[19:08:50] <Bytram> If need be, I could txt MJ or AG
[19:10:17] <Bytram> just finished lunch -- time to do dishes -- back in a few minutes =)
[19:25:08] <janrinok> .... still compiling
[19:36:56] <janrinok> I think I'm nearly 1/3 of the way through the compilation of mysql and that has taken 45 minutes
[19:37:54] <Bytram> ugh.
[19:39:08] <Bytram> at least subsequent builds should go much quicker, IIUC.
[19:39:31] <Bytram> https://soylentnews.org
[19:39:32] <systemd> ^ 03SoylentNews Comments | Site Maintenance -- Server Migrations, Possible Storage Upgrade, Cert Updates, and More! ( https://soylentnews.org )
[19:39:44] * Bytram just replied to ^^^
[19:39:57] <Fnord666> Howdy all!
[19:40:03] <janrinok> well, only if they use some of the same precompiled libraries. But I haven't really started on Rehash yet....
[19:40:16] <Bytram> party time!
[19:40:18] <janrinok> Fnord666, hi, hope things are good with you>
[19:41:45] <Fnord666> Hi janrinok I'm doing ok. Yourself?
[19:41:45] <Bytram> and I was just thinking of lieing down^W^W lying^W taking a nap
[19:41:55] <Bytram> ;)
[19:42:11] <Fnord666> naps++
[19:42:12] <Bender> karma - naps: 15
[19:42:32] <Bytram> naps++ indeed!
[19:42:32] <Bender> karma - naps: 16
[19:43:13] * Bytram is supposed to meet a friend in ~1 hour.
[19:43:49] <Bytram> still waiting for word on the resume I submitted, and we have the site restart coming up in a few hours.
[19:44:10] <Fnord666> I've been trying to clean out the garage but it's just been too hot lately.
[19:45:14] <janrinok> Fnord666, yep, I'm getting better as each day goes by, thanks. I'm also cleaning out the garage but as that also includes taking things to the local recycling dump which isn't open on a Sunday I've been taking it easy today.
[19:45:45] <Bytram> yeaah it cooled off dramatically yesterday, very nice today, but I've spent most of the day on the site preparing for the Linode reboot.
[19:46:25] <Bytram> glad to hear you are both pacing yourself!
[19:46:39] <Fnord666> Close to 90F here (32.2C) here today.
[19:46:53] <Fnord666> edit /here//
[19:46:59] <Fnord666> s /here//
[19:47:08] <Fnord666> never mind
[19:47:19] <Bytram> here here! =)
[19:47:23] <Fnord666> That's good to hear janrinok.
[19:47:37] <janrinok> we are a bit lower than that but it is certainly good wx and quite pleasant to sit outside.
[19:48:04] <Fnord666> I'm ok with it for sitting if there's shade and a breeze.
[19:48:35] <Fnord666> I'm jsut not acclimated to doing labor in those conditions right now.
[19:49:03] <Fnord666> So it's also time to do some work on the basement when it's too hot outside.
[19:49:39] <Fnord666> Had a small water issue and the carpet in my office was ruined so I'm working on cleaning out and replacing the flooring
[19:49:49] <Bytram> got up to 83F here today and am getting frustrated with "units" in trying to get that into deg C
[19:50:20] <Bytram> that stinks! Good luck!!!
[19:50:21] <Fnord666> =g 83 fahrenheit in celsius
[19:50:21] <systemd> https://www.calculateme.com - Convert 83 Fahrenheit to Celsius
[19:50:46] <Fnord666> meh it was time for a change anyway.
[19:51:09] <Fnord666> 28.3C
[19:51:10] <Bytram> looks like it
[19:51:21] <Bytram> looks like it is 28C
[19:51:31] <Bytram> ninjad!
[19:51:37] <Fnord666> ;)
[19:51:55] <janrinok> we're about the same except it is now 21:51 so it is beginning to cool down. The nights are quite pleasant.
[19:52:21] <Bytram> that does it. I'm taking a half-hour nap. sorry guys!
[19:52:23] <Fnord666> We've had thunderstorms each evening the past week as the temp drops
[19:52:30] <Fnord666> Enjoy!
[19:52:56] <janrinok> Hopefully my compilation will have finished before your nap has - so I'll speak to you tomorrow or later in the week.
[19:53:02] <Fnord666> And we are in the middle of our 17 year cicada invasion!
[19:53:24] <janrinok> sorry can't hear you for the damned insect noises...
[19:53:38] <Fnord666> ;) Are you building the site from scratch?
[19:54:01] * Bytram is too far north, so all I can suggest is to say "bug off!"
[19:54:04] <Bytram> ;_
[19:54:05] <Fnord666> All the modules I mean?
[19:54:13] <Bytram> laters
[19:54:15] <Fnord666> Thanks Bytram
[19:54:17] <Fnord666> laters
[19:54:51] <janrinok> with Gentoo everything gets compiled from source - so even installing mysql requires 1hr+ to install!
[19:54:58] <Bytram> Fnord666: thanks for the kind words you added to the end of the site update story!
[19:55:18] <Bytram> janrinok: best of luck with your complile!
[19:55:20] <janrinok> I haven't really got started on Rehash
[19:55:31] <janrinok> Bytram, tx, have a good nap!
[19:55:52] <Fnord666> You're welcome. I know you won't add anything about yourself despite everything that you do for the site!
[19:56:36] <Fnord666> janrinok, what was behind the decision to go with gentoo if we are looking at revamping the architecture?
[19:57:59] <janrinok> Fnord666, there are lots of benefits especially control over what is and isn't installed over and above what is actually needed. And once we have 1 gentoo machine it should be relatively easy to transfer binaries to the others in turn.
[19:58:37] <Fnord666> That makes sense. I've not used gentoo before so I'm not familiar with it's nuances.
[19:58:39] <janrinok> However, for me I have to install everything (kernel onwards) from source because my architecture isn't the same as the linode servers
[19:59:29] <Fnord666> Does linode have prebuilt gentoo images that we can start from?
[20:00:26] <janrinok> I had a delay because Gentoo struggled with the UEFI boot and using GPT on my disk drives - eventually had to go back to using dos formatting. Having failed 3 installs with no obvious cause.
[20:00:28] <Fnord666> Personally I think this would be a good opportunity to refine our architecture a bit. I'm sure it has accumulated some cruft over the years.
[20:01:08] <Fnord666> Yeah I've run into UEFI boot issues with other Linux distributions as well.
[20:01:28] <janrinok> Once we have compiled one Gentoo machine - which we have already done - then quite a bit of the work is completed. But each machine will require slight differences depending on its role.
[20:02:11] <Fnord666> That makes sense.
[20:02:29] <janrinok> Ubuntu copes with UEFI no problem at all, but Gentoo doesn't. That might also be my lack of understanding of Gentoo and its nuances.
[20:04:53] <janrinok> In short, Gentoo seems a sensible choice and it doesn't impose updates upon the user - you can update whenever you wish or not, as the case may be. And if I want to replicate what we actually have - so that my installation is working the same way as everything else - then I have to install on Gentoo too.
[20:05:27] <chromas> Gentutu
[20:07:38] <janrinok> is that some kind of ballet apparel?
[20:08:05] <janrinok> I'm not putting a bloody frilly skirt on my servers!
[20:10:27] <Fnord666> Especially if you have to build it yourself!
[20:13:14] <janrinok> making a frilly skirt wouldn't take as long as this damned compilation 1hr15 and still going - and that is just the db.
[20:14:10] <Fnord666> Just add more cores!
[20:14:39] <Fnord666> oh wait, this probably isn't a mainframe.
[20:17:41] <halibut> Bytram: In units, you have tempF(83), and you want temp(C). It says 28.3333, which agrees with my manual version of 5*(83-32)/9.
[20:18:25] <halibut> Bytram: I found that by typing ``help'' at the units prompt.
[20:18:30] <janrinok> lol - to think that slashdot used to run on a 386 and my 4 core computer is taking it's time to compile the basic software requirements!
[20:18:51] <Fnord666> on google you can just search for "83 degrees fahrenheit in celsius" and it will give you the answer.
[20:19:30] <Fnord666> I bet slashdot doesn't run on that hardware any more.
[20:19:40] <Fnord666> probably can't even run their ad server on that.
[20:20:00] <halibut> janrinok: mysql is a long one for me, but I do not remember it being a multi-hour compile. Do you know what you are using for MAKEOPTS (typically set in /etc/portage/make.conf)? For a four core computer, you probably want something like -j4 or -j6.
[20:20:26] <halibut> Also, is there a binary distribution available for your test machine? You might try installing with USE=bindist.
[20:21:49] <halibut> As for UEFI, I believe Gentoo does work with that. However, you have to set up a special partition for it. See, for example: https://wiki.gentoo.org
[20:21:50] <systemd> ^ 03EFI System Partition - Gentoo Wiki
[20:22:45] <halibut> I think you only need to have the first partition be FAT. I do not think you need to put anything on it. That is the only special considerations I recall having to make for UEFI. I do not currently have access to the UEFI machine I tried that on.
[20:23:30] <janrinok> halibut: I am using the appropriate -j command for 4 cores, and I have 16Gb of RAM, and it is just over 1 1/4 hours
[20:23:48] <Fnord666> oof
[20:23:51] <janrinok> currently showing 83% through compiling
[20:23:55] <halibut> Perhaps I remember incorrectly. I never needed to wait for that one.
[20:25:15] <janrinok> it just seems longer because I am waiting to go to bed and watching the compilation is hardly exciting. Unfortunately, I've ssh'd into the machine from the computer in my bedroom so I can't shut it down without going downstairs to my server and starting it off again from there.
[20:27:11] <halibut> I strongly recommend using screen or tmux or something similar for running emerge commands. You never know when you'll want to disconnect and/or reconnect from elsewhere.
[20:29:33] <janrinok> hindsight is always 20/20, and if I had known that it would take this long I would have done just that. But me, not being as bright as I should be, thought that SSH would be sufficient.
[20:30:33] <halibut> You can try CTRL-Z, bg, and disown. That should allow it to continue running while you disconnect.
[20:30:43] <halibut> However, you will lose any output it produces.
[20:31:08] <halibut> Some of it will be stored in logs. You can also always run emerge --ask --resume later, once it finishes, to see if it was successful.
[20:31:34] <janrinok> that's a good idea, but I'm am stubbornly sticking with it as it is reaching 88% - :)
[20:32:14] <halibut> It's not entertaining, but it is strangely addictive. Perhaps this is Gentoo's equivalent of Facebook?
[20:32:21] <janrinok> lol!
[20:35:56] <Fnord666> I need to step away for a bit. Good luck on the compile janrinok
[20:36:14] <janrinok> halibut - regarding the binary distribution... The version of rehash that we have will only work with Apache 2.2 which is now fading into history. When we rewrote slash to rehash most distros had switched to Apache 2.4, which at that time was incomplete and didn't work. One of our aims is to switch over to Apache 2.4 if we can but I haven't touched Perl since 2007/2008
[20:36:28] <janrinok> Fnord666, enjoy the rest of your weekend. laters
[20:36:54] <Fnord666> Thx. Have a good evening.
[20:41:06] <halibut> I prefer compiling myself, so I have never used USE=bindist. However, unless you are building an odd version of mysql, that should not stop you from using USE=bindist for mysql by itself, while still compiling an older version of apache2 ... unless, in order to have apache-2.2, you are using an old portage tree, which forces you to use an older mysql, for which bindist is not an option ...
[20:41:39] <halibut> Anyways, I am a proponent of not using bindist, so I will not push further on that.
[20:43:51] <janrinok> as I am a Gentoo noob I am still wrestling with some the concepts that it uses. I understand the generalities but every distro is a bit different from the others and this is new to me. I welcome any advice you give me and I am taking notes of things that I have to read up on.
[20:44:41] <halibut> Are you looking to maintain a Gentoo box, or just trying to set one up for test purposes, with no intention of keeping it long term?
[20:48:03] <janrinok> I want to replicate one of our servers (create a local dev machine like the one we have on lithium) so that I can get back into the code and provide some help in maintaining it now that TMB has moved on. As we are changing all our servers to Gentoo, I must replicate what we have too.
[20:50:17] <janrinok> Yay - the compilation has finished!!! Tomorrow I move on to Apache 2.2..... But for now, it is time for my bed.
[20:50:50] <janrinok> halibut, thanks for you advice and company. Enjoy the rest of your day.
[20:51:21] <halibut> Sleep well.
[20:51:25] <janrinok> thx
[20:51:41] <halibut> I'll add some quick notes here; feel free to peruse them later.
[20:52:03] <janrinok> much obliged - I'll look at them tomorrow.
[20:52:36] <halibut> Run emerge in a screen or tmux session. Default detach for screen is ^A^D (Ctrl-A, followed by Ctrl-D). Default detach for tmux is ^B^D.
[20:52:51] <halibut> Run screen like this: screen -S Remote
[20:53:45] <halibut> This will create a screen session named Remote. It will start with one shell. Run whatever you like. Hit ^A^D at any time, and it will drop you out to your original shell, but the things you were running will still be there. Log out, log back in, or whatever; as long as the computer does not reboot, you can reconnect with: screen -r Remote
[20:56:35] <halibut> See running screen sessions with: screen -ls
[20:57:04] <halibut> For tmux, run a new session with: tmux new-session -s Remote
[20:57:23] <halibut> Disconnect with ^B^D, reconnect with: tmux attach-session -t Remote
[20:57:33] <halibut> List sessions with: tmux list-sessions
[20:58:08] <halibut> For both screen and tmux, kill the session but exiting all shells within the session. If you have not created any new shells, just exit the one shell normally.
[20:59:01] <halibut> For choosing which to use: I think screen is a little simpler, and is more commonly installed by default. tmux is a little more complicated, but has more features and flexibility. Basic usage is fairly simple for both.
[21:00:10] <halibut> For general maintenance, I would recommend making sure gentoolkit is installed (emerge -u gentoolkit).
[21:01:08] <halibut> That will provide commands like equery, for checking up on which package owns a particular file (and other stuff), and revdep-rebuild and eclean, for checking for broken executables and cleaning distfiles. More on these below.
[21:01:49] <halibut> I would also recommend installing eix (emerge -u eix), which provides a faster way of querying what is currently installed, and what installation options are available.
[21:02:02] <halibut> To update, run: emerge -auUD --with-bdeps=y @world
[21:03:27] <halibut> This will update every package to the latest version. man emerge for quick descrptions of the options. Easier to search the man page by long options. The equivalent is: emerge --ask --update --changed-use --deep --with-bdeps=y @world
[21:03:55] <halibut> To restart a failed emerge: emerge -ar
[21:04:01] <halibut> Long version: emerge --ask --resume
[21:05:29] <halibut> Sometimes emerges fail for no good reason. I think sometimes a process cleans the temp directory used for building, causing there to be missing files, or sometimes the Makefile or similar is not properly set up for parallel building, and some dependencies are not complete before another process starts. Frequently, resuming will work. Frustrating, but that seems to be the way of it (fortunately, not
[21:05:35] <halibut> nearly as common as it used to be).
[21:05:46] <halibut> After an update, run: emerge -a1 @preserved-rebuild
[21:05:58] <halibut> and: emerge -ac
[21:06:14] <halibut> Longer versions: emerge --ask --oneshot @preserved-rebuild
[21:06:16] <halibut> emerge --ask --depclean
[21:07:19] <halibut> When emerge updates a library, it will record the packages that build executables depending on the old library. The @preserved-rebuild command will rebuild those packages so the old libraries can be safely removed. The --depclean command will remove packages which were installed as dependencies, but are no longer needed.
[21:07:48] <halibut> If you want to keep something that is about to be removed, make sure it is added to the world list (the list of packages you actually want installed). A command like this will do that:
[21:08:00] <halibut> emerge --ask --noreplace <package>
[21:08:05] <halibut> To remove from the world:
[21:08:15] <halibut> emerge --ask --noreplace --deselect=y <package>
[21:08:31] <halibut> The world list is typically at: /var/lib/portage/world. It should be safe to edit it by hand, but probably better to use emerge.
[21:09:43] <halibut> The @preserved-rebuild command above has largely supplanted this, but it used to be the case that a library update would break executables depending on a library. There is a helper program to scan all installed executables and find broken ones, and rebuild there packages: revdep-rebuild -i -p
[21:11:12] <halibut> The -i forces it to start from scratch. It has multiple steps it goes through, and if you interrupt it, it can start at the step it was working on if you leave off -i. The -p tells it to only tell you what it would rebuild, not actually rebuild. Re-run without -p (or -i) to actually rebuild those packages. As I mentioned, emerge is now more careful about that sort of breakage, so it is pretty rare
[21:11:18] <halibut> that revdep-rebuild will need to rebuild anything.
[21:11:54] <halibut> This checks a few things, like notifying you about emerges that were never finished, or old logs: emaint -c all
[21:12:11] <halibut> It frequently complains about a lot of old logs. Clean them with: emaint -C logs
[21:13:08] <halibut> To update the portage tree: emaint -a sync
[21:13:35] <halibut> This is typically done before emerge -auUD --with-bdeps=y @world.
[21:14:34] <halibut> As mentioned earlier, eix is a handy program for seeing what is available. First, you need to update the database it uses with: eix-update (this needs to be run every time you update the portage tree, or eix will report out-of-date things).
[21:14:43] <halibut> To search for a particular package: eix -e mysql
[21:14:57] <halibut> To search for packages with similar names: eix mysql
[21:15:38] <halibut> To search for packages with a description matching a case-insensitive regex: eix -S my.ql
[21:17:19] <halibut> Quick overview: /usr/portage contains the portage tree. That is all files that describe what can be installed, and how to install it. Most of the directories are package categories, with a subdirectory for each package. MySQL files, for example, are in /usr/portage/dev-db/mysql/.
[21:17:54] <halibut> /usr/portage/distfiles contains the downloaded zip files and patches which which are used to extract the source code which is compiled.
[21:18:12] <halibut> Configuration of building is in /etc/portage/.
[21:19:07] <halibut> There should be a make.conf there which has overall settings. It should be well-commented. It also has a man page (man make.conf). Probably the most useful settings there to tweak are MAKEOPTS, USE, and FEATURES. Note that these are system-wide.
[21:20:13] <halibut> You can also specify per-package overrides in files like package.use (override USE flags for individual packages), and also mask packages with package.mask. man 5 portage should tell you more about those (or you could ask).
[21:20:42] <halibut> Summary of update procedure:
[21:20:53] <halibut> Update portage tree: emaint -a sync
[21:21:10] <halibut> Update installed packages: emerge -auUD --with-bdeps=y @world
[21:21:25] <halibut> If necessary, restart: emerge --ask --resume
[21:21:54] <halibut> (sometimes there is a real problem -- probably best to ask for help or search for others having similar problems, as that is a good way to learn how to debug such things).
[21:22:21] <halibut> Rebuild any executables that would be broken by library updates: emerge -a1 @preserved-rebuild
[21:22:34] <halibut> Remove no-longer necessary packages: emerge -ac
[21:23:25] <halibut> Optional extra: Check for broken executables: revdep-rebuild -i -p
[21:23:42] <halibut> If you use eix, update the eix database: eix-update
[21:24:12] <halibut> Some extra checks, and possibly cleaning old logs: emaint -c all
[21:24:20] <halibut> To clean the logs it reports: eclean -C logs
[21:26:18] <halibut> Finally, every now and then, you will want to clean old downloaded source files. Run: eclean -i packages && eclean -i distfiles
[21:27:03] <halibut> The -i makes it interactive, so it will ask you what to remove. Feel free to drop that. Alternatively, use -p instead of -i to show what would be deleted, and if all looks good, re-run without -p.
[21:27:34] <halibut> By default, this keeps anything that might be used by something in the portage tree. To really clean out anything that would not be needed for a reinstallation, use -d/--deep, but be warned that takes longer.
[21:27:47] <halibut> OK. Enough spamming the list for now. Hope that is helpful.