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#linode IRC Logs for 2006-05-02

---Logopened Tue May 02 00:00:11 2006
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00:50<interferon>i'm trying to build CLISP on my linode, but the configure hangs on "checking for working mprotect..."
00:54<interferon>does this make sense?
01:02<interferon>i'd just get the .deb, but it has a dependency on x11
01:03<Spads>google says that UML has had some patches fly by here and there to fix funny mprotect() interactions
01:03<Spads>I know little past that
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01:05<Spads>caker may know
01:05<Spads>google may be able to help you more
01:05<interferon>i guess i'll put in a support ticket
01:05<Spads>it may just be a matter of which kernel you're using
01:05<Spads>are you on latest 2.6?
01:06<Spads>have you moved /lib/tls out of the way?
01:06<interferon>strangely, i have latest 2.4 picked in the control panel, but uname reports 2.6
01:06<interferon>Spads, no i haven't
01:07<interferon>the 2.6 kernels are listed as experimental though
01:07<Spads>if you're running 2.6, you ought to move /lib/tls to like /lib/tls-old
01:07<Spads>the "latest 2.6" doesn't pick the experimental one
01:07<interferon>Spads, it sure seems like it does...
01:08<Spads>I'm on 2.6.15-linode16
01:08<Spads>via "latest 2.6"
01:08<Spads>whereas the "experimental" one is like -18
01:08<interferon>right, but every entry for 2.6 says either "experimental" or "testing" next to it
01:09<interferon>could this have something to do with our respective choices of distro?
01:09<Spads>And you don't want to test or experiment?
01:09<Spads>Doubt it.
01:09<Spads>the kernel is external to the distro
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01:10<Spads>well I have no trouble with those kernels
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01:14<interferon>well, i submitted a support ticket, maybe there's an easy workaround
01:14<interferon>Spads, thanks
01:14<gpd>only experimental due to /lib/tls issues
01:18<interferon>the only issue being that it has to be renamed?
01:19<gpd>yes - renamed|moved - if not then crashes various stuff
01:22<interferon>would anyone running 2.6 be willing to try out the ./configure and see if it works?
01:23<gpd>i can try
01:23<interferon>gpd, thanks
01:28<gpd>taking it's time - but it is progressing
01:29<interferon>it goes flawlessly on my machine ("machine") until it hits the working mprotect test
01:32<gpd>well it didn't fail
01:32<gpd>but i have no clue how to use copy/paste mode in screen
01:33<interferon>C-a C-[ will get you into it
01:33<interferon>but i don't remember how to actually select text
01:34<gpd>Spads: how do you copy text in screen?
01:34<Spads>I forget
01:34<Spads>you use spacebar or . and then arrow around
01:34<interferon>ah, Spads, you beat me to it
01:34<Spads>it is some sort of mark and point system
01:35<Spads>like emacs
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01:39<gpd>of course from putty the 'buffer' goes nowhere :(
01:40<Spads>if you're in putty
01:40<gpd>running again into a file - but it worked
01:40<Spads>just select and then right-click to paste
01:45<gpd>Spads: other way around... copy from a screen in putty --- into windows
01:45<interferon>gpd, thanks, i guess i can try uploading to 2.6 early tomorrow then
01:46<interferon>oops! upgrading
01:46<interferon>sorry, i'm barely awake
01:46<gpd>actually - spads you were right as always - new screen window, open vim, right click - job done
01:46<interferon>almost 3am my time
01:47<gpd>remind me why you need to compile?
01:47<Spads>23:02 <interferon> i'd just get the .deb, but it has a dependency on x11
01:47<Spads>I've long since given up on that
01:47<interferon>thanks, Spads :)
01:48<Spads>lisp interpreters are the one thing that drags in X libraries for me
01:48<gpd>isn't it just common x libs or something
01:48<interferon>it's bizarre that clisp has a dependency on x11
01:48<Spads>it should just be the X libs
01:48<Spads>not like x servers or anything
01:48<Spads>and that code path likely never gets traversed given what you're doing
01:48<Spads>it's just a protocol library like any other
01:49<gpd>Depends: libc6 (>= 2.3.4-1), libncurses5 (>= 5.4-5), libreadline5, libx11-6, libxext6, libxpm4, common-lisp-controller (>= 4.2)
01:49<interferon>that's a good point, i didn't realize it wasn't requiring x11 itself
01:49<interferon>in that case i guess the .deb would be fine after all
01:49<gpd>i see only xlibs coming in - which is +291kB
01:50<gpd>total disk: 11MB
01:50<gpd>xkeyboard-config - 2281 :(
01:50<interferon>i saw x-common in the dependencies and assumed it was X11 itself
01:50<Spads>base lib and extensions
01:51<interferon>well, in that case, i apologize for bothering you both
01:51<gpd>well at least i worked out how to copy and paste in screen...
01:51<gpd>[found out]
01:51<gpd>[thanks spads]
01:51<Spads>glad my memory was correct!
01:52<gpd>i find the screen help screen almost entirely unhelpful
01:53<gpd>copy ^[ [ --- err or space
01:53<interferon>i use the info node
01:53<Spads>yeah, info
01:53<Spads>great idea in the late 80s
01:53<Spads>goofy by the mid 90s
01:53<Spads>utterly useless in this day and age
01:53<interferon>not so bad from within emacs
01:54<Spads>and miserable from without
01:54<Spads>two different kinds of searching
01:55<gpd>jesus - even the info pages are total jibberish
01:55<gpd>three levels down and i still don't know how to copy
01:55<Spads>gpd: but it's hierarchically organized! JUST LIKE A REAL BOOK!
01:56<interferon>C-h i m Screen RET C-s copy
01:56<gpd>ya - which is why i can't get back up a level
01:56<gpd>without reading the info info
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02:02<interferon>thanks for the help, gpd and Spads
02:02<gpd>np - enjoy your clisp ;)
02:02<gpd>now you have me pondering why info exists and its relationship to man
02:03<interferon>mankind or /usr/bin/man?
02:03<gpd>this is why i won't find much with google?search=man info
02:03<Spads>gpd: info is an RMSism
02:04<Spads>gpd: it's an example of the sort of "hypertext systems" people used to write before the WWW became popular
02:04<gpd>why didn't it get phased into man -- or something useful
02:04<Spads>it does on debian
02:04<Spads>packages without man pages sometimes get info dumps
02:05<gpd>but the stuff in info screen is not in man screen ?
02:05<Spads>well then screen got one of each
02:05<Spads>sucks to be you
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02:51<gpd>any perl folk awake?
02:52<encode>i know perl, although not to the same calibre as some folks in here
02:52<erikh>i'm a JAPH
02:52<erikh>gpd: what is your question/
02:52<gpd>can't remember how to push an array of hashes
02:53<erikh>push, you mean to add, correct?
02:53<erikh>or do you want to dereference?
02:53<erikh>%hash = ();
02:53<erikh>$hash{mykey} = []
02:53<erikh>then to deref:
02:53<gpd>push ( @data[index], \%hash )
02:54<gpd>ie. i want to puth that hash into the array data - but at the index
02:54<gpd>but not quite got it right
02:54<erikh>push @{$hash{key}}, "foo"
02:54<gpd>so i would end up with:
02:54<encode>doesnt push only work at the end of the array, rather than an arbitary index
02:54<erikh>encode: yessir
02:54<gpd>$data[index]{key} = value
02:55<erikh>gpd: do you need an array of hashes, or a hash of arrays?
02:55<gpd>i thought i could generate an array on the fly to hold it?
02:55<erikh>what you wrote is an array of hashes.
02:55<gpd>i need an array of hashes
02:55<erikh>$data = []
02:55<erikh>push @$data, { }
02:56<erikh>$data->[0] == new hash ref you just created
02:56<erikh>$data->[0]{key} = "value"
02:56<gpd>yeah - but i want to somehow retain the index
02:56<erikh>oh... well, perl will populate the indices sparsely
02:56<gpd>push @$data[$position], \%hash ???
02:56<erikh>so you could just $data->[31337] = {}
02:56<erikh>and perl will handle it as long as t he array already exists.
02:57<erikh>I suggest you use a hash for that.
02:57<gpd>but i have multiple things with the same index :(
02:57<erikh>it will be much faster.
02:57<gpd>so i may be totally borked
02:57<erikh>use a hash of hashes
02:57<encode>does perl allocate memory for the non-existent elements of a sparse array?
02:57<erikh>save yourself some hell
02:57<erikh>encode: I believe so
02:57<erikh>but I'd have to check
02:57<encode>yes, thats what i thought too
02:57<gpd>i had hash of hash but i wanted to speed things up
02:57<erikh>what it'd allocate woul dbe very small though, as there's no data associated with it
02:58<gpd>as i was looping the whole hash and skipping most of it
02:58<encode>which has potential to suck greatly
02:58<erikh>basically, the contents of whatever undef resolves to
02:58<erikh>encode: yes....
02:58<erikh>gpd: your structure says to me that hash of hash would be best
02:58<erikh>/unless/ you can express it better as a tree, but I don't have time to get into what the best structure is :)
02:58<gpd>but i have data for variable=1-100
02:59<erikh>gpd: what are you doing, exactly?
02:59<gpd>ok - i have:
02:59<gpd>gene, position, chromosome
02:59<gpd>and data: position, value
02:59<erikh>value is the gene and chromosome?
02:59<erikh>or ...?
03:00<gpd>i want to locate the position, value data within the lookup table of gene, position, chromosoem
03:00<erikh>what does value consist of?
03:00<gpd>so i read in all the gene, position, chromosome into a hash of hashes
03:00<gpd>and then loop throught the data looking up the position
03:00<encode>gpd: or
03:00<gpd>(i'm sure there is a better way to do this)
03:01<encode>sort the keys by position
03:01<gpd>[not being a programmer!]
03:01<erikh>heh, is value something unique or does it consist of the rest of that data?
03:01<gpd>value is unique -- data from an experiment
03:01<erikh>does it relate somehow to the other data?
03:02<erikh>this is ideal for a database, which makes me think hash tables would be best.
03:02<gpd>yes, the position and chromosome correspond to the other stuff
03:02<erikh>ok, make one hash position => value
03:02<erikh>and another one position => { gene, chromosome }
03:02<erikh>then do an intersection
03:02<gpd>but the positions are not directly corresponding
03:03<gpd>i need to do a > and < to find the right bit
03:03<gpd>i wonder if mysql might work
03:03<erikh>are we talking about large sets of data or small sets?
03:03<erikh>ok, do your < and > in your intersection
03:03<erikh>saves memory
03:04<erikh>unless I'm misunderstanding you.
03:04<erikh>(which is extremely likely)
03:04<gpd>can you explain how to do an intersection?
03:04<erikh>gpd: are you familiar with set theory?
03:04<gpd>yes, but not in programming
03:04<erikh>it's the same thing
03:04<erikh>A intersect B = A + B
03:05<erikh>err, that's a wretched explanation
03:05<erikh>you have two sets with a shared key
03:05<gpd>how does it relate to hashes of hashes?
03:05<erikh>yoru key in this case is position
03:06<erikh>we want to merge the data into a single hash for position, with your value, chromosome, and gene data in the same hash
03:06<gpd>so i might have: 100 => 0.5 (position, data)
03:06<erikh>the < and > will increase the result of the return data, but it will essentially be an intersection
03:06<gpd>and 50 => start, 200 => end, name => GENE1
03:06<erikh>if that's extra data you add into it, sure.
03:07<gpd>well the positions are acutally start and ends :(
03:07<erikh>they key is position though, you can iterate through valid positions, combining the data that's prebuilt
03:07<erikh>see what I just said
03:08<erikh>I really HTH
03:08<gpd>ok -need a second for brain to digest
03:08<erikh>I feel blind working with this as I don't know enough about what you're doing to understand anything beyond the structure information that you're giving me
03:09<gpd>it is microarray data from genomic experiments
03:09<gpd>the data is for binding to a fragment
03:10<gpd>the framents are tiled across a chromosome
03:10<gpd>for chromosome 1 you have data for 1,20,30,40,50... etc
03:10<gpd>where that number is the number of bases from the left end of the chromosome
03:10<gpd>there is then a library file
03:10<gpd>this contains information about gene positions
03:10<gpd>eg. gene1 is from base 100---200
03:11<gpd>there are also genes going backwards
03:11<gpd>eg. gene2 is from 400--200
03:11<erikh>oy, now you're racking my brain :)
03:11<gpd>for data at position 140 - i want to say -- ok this in in gene1
03:11<gpd>and it is 40 bases away from the start of gene1
03:11<erikh>well, how much do you know about sql
03:11<erikh>do you know what a join is?
03:12<erikh>that's more or less what I'm describing, just in perl.
03:12<gpd>i can find out - if you think sql is the best option
03:12<gpd>the dataset is FREAKING huge
03:12<gpd>so sql might be good idea ;)
03:12<erikh>yeah. use a database.
03:13<gpd>how about if i want to do things like: what is the mean of all values in range 100-200 ?
03:13<erikh>damn, it's late
03:13<erikh>that's really easy in sql
03:13<erikh>just use an aggregate function
03:13<erikh>heck, you could do this all in excel, if you like pain.
03:14<gpd>hah - too large for excel
03:14<erikh>but you could do it! :)
03:14<erikh>anyways, I need to go, good luck on your project!
03:14<gpd>excel has 65k row limit or similar
03:14<gpd>ya - thanks -i'll go read about sql :)
03:21<encode>does open's spreadsheet also have a 65k row limit?
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03:35<jcsincla>Anyone else having trouble getting to their linode?
03:35<@mikegrb>jcsincla: hello, on it
03:35<@mikegrb>jcsincla: it's host45
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03:47<lhunath> has become unreachable, could anything be going on to cause this?
03:47<@mikegrb>yes, I'm taking care of it right now
03:47<@mikegrb>shouldn't be much longer before it is back up
03:48<lhunath>right, thanks :)
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03:53<jdub>my linode seems to keep powering off soon after boot
03:53<jdub>doesn't seem to be anything obvious spat out on the tty
03:54<@mikegrb>username jdub?
03:54<jdub>it boots successfully, and i can briefly log in via ssh, then *poof*
03:54[~]jdub has been using the 2.6.16+tls kernel with success for a while now
03:55<@mikegrb>there have been some reports of this same thing from other people
03:55<jdub>with that kernel?
03:55<jdub>hmm, should i try the new 2.6.17 one? (does that have tls love?)
03:55<jdub>or revert to 2.6.15
03:55<@mikegrb>I believe it does
03:56<@mikegrb>give the .17 a shot first, couldn't hurt, eh?
03:56<jdub>ok, worth a try
03:56<@mikegrb>but if you have the same problem, reverting to .15 should get you back in business
03:56<@mikegrb>just minus tls love
03:56<jdub>that died during boot
03:57[~]jdub tries 2.6.15
03:57<@mikegrb>I haven't talked to chris about that one so I don't know exactly what it's purpose was
03:58<jdub>what were the other reporters running?
03:58<@mikegrb>initially it only seemed like it affected red hat/fedora types
03:58<@mikegrb>but it has affected others as well
03:58<@mikegrb>more recently
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03:59<jdub>line_ioctl: tty0: unknown ioctl: 0x5603
03:59<jdub>^ interesting?
03:59<jdub>that's from 2.6.15 too though
03:59<jdub>so less immediately useful
04:00<jdub>ok - i will watch this
04:01<jdub>thanks for your help mikegrb
04:01<@mikegrb>not a problem
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04:19<linbot>New news from forums: Reboot: host45 in System and Network Status <>
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04:32<jcsincla>mikegrb: Any idea how long the linodes will take to come up?
04:35<@mikegrb>doesn't look like it should be much longer if you aren't already up
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04:42<jcsincla>mikegrb: It's starting now. Just taking a very long time to do it. Thanks for the help. I'm off to bed now.
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08:43<linbot>New news from forums: xen update in Xen Public Beta <>
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10:14<warewolf>how very strange.
10:14<warewolf>I just got spam, written arabic.
10:14<warewolf>one massive .gif
10:17<warewolf>I've never seen arabic spam before
10:17<warewolf>it's a first for me
10:23<kriby>i blame bush
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11:46<gpd>warewolf: it occurs to me that nearly all emails with gifs are spams --- therefore reject them!
11:46[~]gpd wonder how best to do this
11:47<gpd>maybe i should just bite the bullet and install SA
11:47<kriby>procmail is the easiest way
11:47<kriby># Attachments
11:47<kriby>:0 B
11:47<kriby>* ^Content-Transfer-Encoding: base64
11:47<kriby>* name="[^"]*\.(exe|bat|scr|pif|lnk|com|vs|wsf|vbe|wsh|hta|cpl|vbs|zip)"
11:48<kriby>that dumps everything with an attachment into the spam folder
11:48<kriby>well, not all attachments.. just the ones listed
11:48<gpd>certainly looks like a cunning plan
11:48<kriby>works great for me.. i haven't noticed missing any important mails as a result..
11:48[~]gpd adds to the list of things to do
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14:38<fo0bar> <-- P4 2.6GHz overclocked to 3.9GHz
14:44<linbot>New news from forums: DRDB on linode in Linux Networking <>
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15:53<iggy>caker: ping
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17:28<gpd>kriby: still there?
17:32<gpd>i found a howto for procmail/courier/postfix but the only referece is to mailbox_command=/usr/bin/procmail in
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18:09<bdragon>Did host45 just hang?
18:10<@caker>I think so .. it'll be just a minute...
18:17<fo0bar>screw your insignificant problems... livejournal is down!
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18:51<gpd>so it seems that procmail can't be used with virutal users - recommendation is to use maildrop
18:51[~]gpd continues blathering about insignificant problems
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20:21<encode>^^ interesting
20:21<encode>i cant spoof from my linode :(
20:27<npmr>slashdot still exists?
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20:29<encode>haha npmr
20:29<gpd> <-- makes /. slightly less annoying
20:30<encode>it gets rid of the flame wars?
20:30<encode>oh. no, still the same content
20:31<Spads>gpd: yeah, I used to read alterslash back in 2001
20:31<Spads>but slashdot is still too 1990s for my taste
20:32<encode>Spads: what do you read instead?
20:34<Spads>encode: all sorts of things
20:35<Spads>encode: the problem is that by 2001 the actual editors of slashdot stopped bothering to read slashdot
20:35<Spads>that's why you had all those duplicates
20:35<encode>i only started reading it in 2000
20:35<Spads>when I started reading it it still had that stupid "lined notebook paper" look
20:35<encode>yep, i'm pretty sure the editors are some eliza bot cmdrtaco hacked together
20:36<Spads>slashdot is pretty insipid
20:36<Spads>I stick to my own aggregated stuff
20:36<encode>the comements suck
20:36<Spads>everything sucks
20:36<encode>and digg has all /.'s stories anyway
20:36<Spads>get better links elsewhere
20:36<npmr>i'll drink to that
20:39<gpd>tough crowd
20:40<encode>gpd: how are you going with that programming problem you were asking about before?
20:40<gpd>all done thanks encode - had a brainwave this morning :)
20:40<gpd>realized there was a *much* simpler way to do it
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20:42<gpd>although - now it starts to get difficult - so i am in denial
20:49<warewolf>wtf happened ti livejournal
20:49<warewolf>like, their DNS broke or someshit.
20:50<warewolf>yah, broked.
20:50<warewolf>oh well, guess I don't get to reply to a friend's post.
20:50[~]warewolf -c work &
20:51<encode>what does the -c do?
20:51<encode>gpd: cool :)
20:51<encode>are you still doing it in perl?
20:55<@mikegrb>encode: not only can you not send ip packets from an ip address not assigned to your account, you can't even re3
20:56<encode>re3? what is re3?
20:56<@mikegrb>respond to arp queries and such for ips that aren't on your account
20:56<encode>yeah well
20:56<@mikegrb>re3 == my son trying to help
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22:06<sec39>anyone having problems with host45?
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23:39<fo0bar>Thanks to Finnix, I've made $17.10 in advertising. By that rate, I will have a payment check August 2007
23:40<encode>i cant see any advertising on the finnix site though
23:40<fo0bar>it blends in well
23:40<encode>maybe its getting adblocked
23:40<encode>ahh there it is
23:41<encode>the gooooooooooooooooooooooooooooooooooole ad?
23:43<encode>it makes the page layout all wonky
23:48<fo0bar>mikegrb: feel like testing a G5 build of finnix sometime in the near future?
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---Logclosed Wed May 03 00:00:59 2006