| --- Log opened Mon Jul 24 00:00:08 2017 | ||
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| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/3859 synchronized by MikeLing | 04:40 |
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| olinguyen_ | wiking: do you have a moment? | 05:46 |
| @wiking | olinguyenhi | 07:13 |
| @wiking | sorry just got around | 07:13 |
| @wiking | yes | 07:13 |
| olinguyen_ | I'm starting to get involved more with the actual shogun code base. I'm having trouble compiling some stuff | 07:14 |
| olinguyen_ | i'm running a docker instance as shown in the readmes | 07:15 |
| olinguyen_ | when trying to compile 'make random_forest' i get the following error | 07:15 |
| olinguyen_ | Translation of dependencies failed! Could not translate file multiclass_classifier/multiclass_logisticregression.sg to .cpp. | 07:15 |
| olinguyen_ | Any idea what i could be doing wrong | 07:15 |
| olinguyen_ | wiking, i'm on the develop branch, fyi | 07:16 |
| @wiking | mmm | 07:17 |
| @wiking | you try to compile a meta example? | 07:17 |
| olinguyen_ | I'm trying to compile the random forest target | 07:18 |
| olinguyen_ | seems like the meta examples are part of the targets (or i might not be fully understanding whats happening) | 07:18 |
| olinguyen_ | longer error message, could helpful: [ 3%] Generating example multiclass_classifier-multiclass_logisticregression Translation of dependencies failed! Could not translate file multiclass_classifier/multiclass_logisticregression.sg to .cpp. Traceback (most recent call last): File "/home/gsoc2017-shogun-dataproject/shogun/examples/meta/generator/generate.py", line 158, in <module> generatedFilesOutputDir=args.parser_files_di | 07:20 |
| olinguyen_ | Am I doing the right thing here? Since I'll be making changes on random forest, I only want to build the random_forest target. Am I missing a step or something? | 07:24 |
| @wiking | olinguyen but that just an example | 08:02 |
| @wiking | how to use random forest | 08:02 |
| @wiking | if you do changes in random forest | 08:02 |
| @wiking | namely in the library | 08:02 |
| @wiking | you will stll need to ocmpile shogun itself | 08:02 |
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| olinguyen_ | wiking, my bad on that part | 08:11 |
| olinguyen_ | When trying to make all, I get this error however | 08:11 |
| olinguyen_ | fatal error: shogun/mathematics/JacobiEllipticFunctions.h: No such file or directory #include <shogun/mathematics/JacobiEllipticFunctions.h> | 08:11 |
| olinguyen_ | that files missing in the develop branch | 08:12 |
| @wiking | mmm | 08:13 |
| @wiking | did u do git pull and git submodule update --init ? | 08:13 |
| @wiking | as some stuff | 08:14 |
| @wiking | moved from the main repo | 08:14 |
| @wiking | to the gpl part | 08:14 |
| @wiking | inclind JacobiEllipticFunctions.h | 08:15 |
| olinguyen_ | i forgot to run the submodule update again. I think it's fine now, thanks! | 08:19 |
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| olinguyen_ | wiking, so even when compiling all i end up with the same error as before in the end | 09:51 |
| olinguyen_ | [ 91%] Generating example multiclass_classifier-multiclass_logisticregression Translation of dependencies failed! Could not translate file multiclass_classifier/multiclass_logisticregression.sg to .cpp. | 09:52 |
| olinguyen_ | should I just turn off the build w/ examples? | 09:52 |
| olinguyen_ | turned off the examples, worked. sorry for bugging you :P, it is late here and haven't had much sleep | 09:54 |
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| @sukey | [https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/3950 opened by Galaxy-Fish | 10:50 |
| Trixis | wiking: im testing the library you linked right now, fingers crossed | 12:31 |
| @wiking | fingerz x-ed | 12:32 |
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| Trixis | wiking: hm it loaded the library just fine, but then i got unsatisfied link error when init() gets called... might be just because i have an older jar in classpath, ill try rebuilding with the one you supplied. also, "ldd: warning: you do not have execution permission for `./libshogun.so'" not sure if thats an issue or not | 12:56 |
| @wiking | there's the jar | 12:56 |
| @wiking | no? | 12:56 |
| Trixis | wiking: my .jar contains the older (6.0.0 i think) shogun.jar | 12:58 |
| Trixis | wiking: ooh did modshogun get renamed? | 13:05 |
| @wiking | i did it | 13:05 |
| @wiking | manuall to shogun.so | 13:05 |
| @wiking | *manually | 13:05 |
| Trixis | wiking: no i mean in the sources, did the class get renamed | 13:06 |
| @wiking | yes | 13:06 |
| Trixis | because it's not in the jar anymore | 13:06 |
| Trixis | ahh | 13:06 |
| Trixis | what's it called now? | 13:06 |
| @wiking | shogun | 13:06 |
| Trixis | kk | 13:06 |
| Trixis | that explains the link error lol | 13:06 |
| @wiking | org/shogun/IntronList.class | 13:07 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/3942 synchronized by micmn | 13:08 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/3942 | 13:08 |
| Trixis | well, it's in the queue | 13:13 |
| Trixis | fingers crossed | 13:13 |
| Trixis | now it's running | 13:15 |
| Trixis | no crash so far | 13:15 |
| Trixis | looks promising | 13:15 |
| Trixis | wiking: thanks, it's working! | 13:23 |
| @wiking | lol cool | 13:24 |
| @wiking | :) | 13:24 |
| @wiking | it was easy | 13:24 |
| @wiking | :> | 13:24 |
| Trixis | haha | 13:24 |
| Trixis | i mean the job crashed because of a different error, but this seems to be an issue on my side... or the way you construct binary labels changed between versions, lol | 13:25 |
| Trixis | wiking: how bad are these warnings? "libgomp: Thread creation failed: Resource temporarily unavailable" ? | 13:43 |
| @wiking | oh | 13:44 |
| @wiking | wtf | 13:44 |
| Trixis | are they only going to slow performance | 13:44 |
| Trixis | or are they going to influence the integrity of the run? | 13:44 |
| Trixis | oh they crashed it | 13:45 |
| Trixis | lovely | 13:45 |
| Trixis | lo | 13:45 |
| Trixis | l | 13:45 |
| Trixis | wiking: seems to be a cluster issue i guess | 13:46 |
| @wiking | mmm | 13:49 |
| @wiking | i never ever seen these errors | 13:49 |
| @wiking | https://github.com/sequencing/isaac_aligner/issues/10 | 13:49 |
| @wiking | i guess you ahve some hard limits on the cluster | 13:49 |
| @wiking | you can play with the number of threads | 13:50 |
| @wiking | with the env var SHOGUN_NUM_THREADS=<N> | 13:50 |
| @wiking | but i think this is more about runtime speed | 13:50 |
| @wiking | nothing else | 13:50 |
| Trixis | ye apparently it happens if the machine allocated has the number of cores requested but the job gets assigned only a limited amount | 13:50 |
| Trixis | oshit segfault | 13:52 |
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| @wiking | Trixis, does it work or not really ? :) | 14:38 |
| Trixis | not really | 14:38 |
| Trixis | i fixed the segfaults due to the omp error | 14:38 |
| Trixis | by setting the number of threads to match requested cores | 14:38 |
| Trixis | but | 14:38 |
| Trixis | now im getting label errors - apparently they're invalid due to only containing one class. Except, they are initialised with two classes and this error didnt occur when i tested it locally on a small dataset :\ | 14:40 |
| @wiking | :P | 14:44 |
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| @wiking | ok but this is more like error with the logic | 14:44 |
| @wiking | but shogun itself work | 14:45 |
| @wiking | s | 14:45 |
| @wiking | so that is a great news :) | 14:45 |
| Trixis | ye | 14:46 |
| Trixis | haha | 14:46 |
| Trixis | i hope it's an error with logic, perhaps i changed something unwittingly | 14:46 |
| Trixis | ill retest it locally once shogun finishes rebuilding (snappy got updated, and shogun was linked against prev version -.-) | 14:48 |
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| geektoni | ping HeikoS | 14:55 |
| Trixis | wiking: seems to be an issue with the new version of shogun, do you know where i can find what changes have been done to labels/binary labels? | 15:10 |
| @wiking | Trixis, u can simply take that verison | 15:11 |
| @wiking | and change only 1 line in cmake | 15:11 |
| Trixis | hmm | 15:11 |
| @wiking | to generate the same thing | 15:11 |
| @wiking | that i gave you | 15:11 |
| @wiking | so then you dont have problems with the labels etc | 15:12 |
| Trixis | i also need the centos utils, though | 15:12 |
| @wiking | heheeh yeah but you can do all that | 15:12 |
| @wiking | on your machine + centos docker image | 15:12 |
| Trixis | true | 15:12 |
| @wiking | in the docker image you build the thing | 15:12 |
| @wiking | and then take it | 15:12 |
| @wiking | that's what i did | 15:13 |
| @wiking | this is the diff for the cmake https://pastebin.com/q4M2xFeK | 15:13 |
| Trixis | actually, i might run down to the IT and get them to install the devtools | 15:13 |
| @wiking | simple stuff | 15:13 |
| Trixis | yah i just request the install | 15:34 |
| Trixis | now i just have to wait a bit | 15:34 |
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| Trixis | wiking: what exactly do the devtools-2 do in the context of the static linking? | 16:38 |
| @HeikoS | wiking: you around? | 16:48 |
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| @wiking | Trixis, allows you to compile shogun on rhel6 | 20:44 |
| Trixis | wiking: ah so its not just the gcc thats important inside | 20:45 |
| @wiking | as otherwise i dont know how else u could compile c++11 in rhel | 20:45 |
| @wiking | nono it's only that | 20:45 |
| @wiking | that you have a gcc that is newer | 20:45 |
| @wiking | so u can compile | 20:45 |
| Trixis | huh. because i tried compiling it with the static flag / edited cmake, + i used module load gcc 4.9.1 | 20:45 |
| Trixis | but | 20:45 |
| Trixis | it doesnt seem to be linked correctly | 20:46 |
| Trixis | because running ldd shows a lot of libraries and its throwing an error that it cant find suitable version of libompg ... except its searching at the site of the old gcc | 20:46 |
| Trixis | not the 4.9.1 its linked against ( as confirmed by gcc) | 20:47 |
| @wiking | Trixis, you ran ldd on? | 21:48 |
| Trixis | wiking: src/interfaces/libmodshogun.so | 21:48 |
| Trixis | the one i compiled with the static flag | 21:48 |
| @wiking | what was the ldd output of that? | 21:49 |
| Trixis | wiking: https://pastebin.com/SSU5yBET | 21:50 |
| @wiking | Trixis, ok but first of all ldd will take what your ldcache gives | 21:52 |
| @wiking | ldd is looking for libgomp.so.1 | 21:52 |
| @wiking | so if /sw/opt/gcc-4.9.3/lib64/ is not in ldpath | 21:52 |
| @wiking | then it wont find it | 21:52 |
| @wiking | and will default to something else | 21:52 |
| Trixis | it was in ld_library_path | 21:52 |
| @wiking | thats why ldd uses taht | 21:53 |
| Trixis | hm | 21:54 |
| @wiking | but if you put this .so | 21:54 |
| @wiking | to a machine where tehre's no /sw/opt/gcc-4.9.3/lib6 | 21:54 |
| @wiking | then it'll use soemthing else | 21:54 |
| @wiking | if libgomp.so.1 is available | 21:54 |
| Trixis | wiking: hence it should find it when i run it, no? | 21:54 |
| @wiking | yes | 21:55 |
| @wiking | using your env setup | 21:55 |
| @wiking | those libs | 21:55 |
| @wiking | are loaded during runtime | 21:55 |
| Trixis | except it picks up the gcc in usr/lib | 21:55 |
| Trixis | "| | 21:55 |
| @wiking | if avilable | 21:55 |
| Trixis | *:| | 21:55 |
| @wiking | yeah but that's what it should do | 21:55 |
| @wiking | no? | 21:55 |
| Trixis | shouldnt it use the /sw/opt/ gcc? | 21:56 |
| @wiking | i mean it's requiring | 21:56 |
| @wiking | libgomp.so.1 | 21:56 |
| @wiking | which is a verison of libgomp | 21:56 |
| @wiking | if /usr/lib has that | 21:56 |
| @wiking | it should be fine | 21:56 |
| Trixis | yeah except the one there is outdated as fuck | 21:57 |
| Trixis | so it throws an error that minimum req. version couldnt be found | 21:57 |
| Trixis | also if i static linked it | 21:57 |
| Trixis | should it still be doing this? | 21:57 |
| @wiking | well | 21:58 |
| @wiking | but yeah | 21:59 |
| @wiking | good question | 21:59 |
| @wiking | why gomp is still .so there | 21:59 |
| Trixis | wiking: "[ 77%] Linking CXX shared module libmodshogun.so" | 22:00 |
| Trixis | compare to | 22:01 |
| @wiking | ok i guess | 22:01 |
| Trixis | [ 77%] Linking CXX static library libshogun.a | 22:01 |
| @wiking | cmake flags for static linking | 22:01 |
| @wiking | is not yet 100% | 22:01 |
| @wiking | can u run ldd on | 22:02 |
| @wiking | the so i have given u? | 22:02 |
| Trixis | cmake -DCMAKE_INSTALL_PREFIX=$HOME -DJavaModular=ON -DBUILD_META_EXAMPLES=OFF -DENABLE_HDF5=OFF -DLIBSHOGUN_BUILD_STATIC=ON .. was the cmake command | 22:02 |
| Trixis | wiking: i did that and the output was like 4 lines | 22:02 |
| Trixis | sec if i can find it in terminal history | 22:03 |
| Trixis | hm cant find it, the point is however that libompg wasnt there definitely | 22:05 |
| Trixis | in fact | 22:05 |
| Trixis | most of those werent there | 22:05 |
| @wiking | ok | 22:08 |
| @wiking | then i guess in this caeeeeee | 22:08 |
| @wiking | case | 22:08 |
| @wiking | gomp is pulled in by openmp | 22:08 |
| @wiking | i mean | 22:08 |
| @wiking | by openblass | 22:08 |
| @wiking | *openblas | 22:08 |
| @wiking | i need to sleep | 22:09 |
| @wiking | its 4am | 22:09 |
| @wiking | sorry man | 22:09 |
| @wiking | you should minimize your external dependencies in shogun | 22:09 |
| @wiking | turn off blas etc | 22:09 |
| Trixis | its ok | 22:12 |
| Trixis | kk | 22:12 |
| Trixis | i will | 22:12 |
| Trixis | thanks a lot | 22:12 |
| Trixis | sleep well | 22:13 |
| --- Log closed Tue Jul 25 00:00:10 2017 | ||
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