Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-06-25

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All times shown according to UTC.

Time Nick Message
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15:46 blackrim josephwb: I added some of the files for plants. going to move to fungi, they are in a new folder.
15:46 blackrim you can see from load_mls how i load them in given that they are in another folder
15:51 blackrim doing asterids now which is really large. so we will see if that hits a limit
16:21 josephwb yeah, i see
16:56 blackrim OK, died from memory on the medium memory machine (256GB). going to try 512GB next
17:02 josephwb wowzers
17:03 josephwb no way metazoa is going to work
17:03 blackrim how many trees/tips i nthat one?
17:11 josephwb re-runnning the gcmdr script now as it crashed last time
17:13 josephwb 141 trees
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17:37 blackrim how many tips (as counted by the top of the mls input)
17:39 josephwb tweaking stuff here; just a sec
17:41 josephwb 21152
17:42 josephwb getting OSError: Argument list too long
17:42 blackrim my goodness. can't imagine that will finish. i can't get on smithbigmem1 right now so have to wait until ryan can add my ip
17:42 blackrim which program is giving you that
17:42 josephwb gcmdr
17:42 blackrim hm, where
17:43 josephwb passing to extract_taxonomy_from_ids
17:43 josephwb general_tm_utils.py line 273
17:44 blackrim oh right. yeah, that is going to be a problem. if we want to send arguments that long we will have to pass a file unless you can find another solution. i can add the file option but not sure if it is worth it if it just isn't going to run. maybe we should try my smaller file on smithbigmem1 first because coding in the file
17:45 josephwb yes, smaller
17:45 josephwb i think we ran into this b4
17:45 josephwb had to write to temp file
17:45 josephwb read back in
17:46 blackrim could be . this is a problem in phyx that i solved with a file (pruning operation)
17:50 josephwb i'll break metazoa into smaller pieces
17:51 blackrim ok, working on fungi
17:52 josephwb but what about the studies that extend across groups?
17:55 josephwb seems like breaking it by the Contexts we have set up is a good place to start
17:55 blackrim yeah, your file is probably just fine to break basically as you have it
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18:19 josephwb blackrim: how big was the dataset that dies on 256 GB?
18:19 blackrim 96 trees ; > 9000 taxa
18:19 josephwb ok; communicating with berry right now
18:31 josephwb blackrim: any questions for Berry?
18:32 blackrim not really (seems like he has already answered the important things about the open source or not).
18:32 josephwb right
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18:48 blackrim █✚█
18:49 blackrim sorry about that
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19:05 josephwb blackrim: how are you running MLS remotely
19:06 blackrim well, if the remote machine has X running then you just have to export DISPLAY=WHEREthedisplay is
19:06 blackrim then you run, but you can't logout
19:06 blackrim you also have to ssh -X ip
19:07 blackrim well you don't have to if a monitor is hooked to the machine, but you have to do that if a monitor is not connected
19:16 josephwb ok, was able to get it to work with just ssh -X ip
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