Hi, I am trying to use MZmine to analyze 88 samples in profile mode. I get Java timeout with java-6-openjdk, java-7-openjdk or java-7-oracle (all at the latest versions. This occurs on only some samples and appears to be consistent. I tried setting my dirty.ratio to 25 (as suggested for timeouts like these) but this does not work.
Please advise, Dougie $ dmesg tail [55542.624258] INFO: task java:24545 blocked for more than 120 seconds. [55542.624264] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [55542.624268] java D ffff88082ed13f40 0 24545 24544 0x00000000 [55542.624276] ffff8807d27cfcd8 0000000000000082 ffff8807c0e41740 ffff8807d27cffd8 [55542.624284] ffff8807d27cffd8 ffff8807d27cffd8 ffff8807db2bc5c0 ffff8807c0e41740 [55542.624291] ffff8807c0e41740 ffff8807fcbe8380 ffff880784929d48 ffff8807fcbe83e8 [55542.624298] Call Trace: [55542.624313] [<ffffffff816cb1b9>] schedule+0x29/0x70 [55542.624322] [<ffffffff8105e275>] do_exit+0x1b5/0x9d0 [55542.624330] [<ffffffff810b52dd>] ? futex_wait_queue_me+0xcd/0x100 [55542.624336] [<ffffffff810b507b>] ? __unqueue_futex+0x3b/0x70 [55542.624342] [<ffffffff810b5a40>] ? futex_wait+0x140/0x2d0 [55542.624349] [<ffffffff8105eb0f>] do_group_exit+0x3f/0xa0 [55542.624356] [<ffffffff8106e581>] get_signal_to_deliver+0x1c1/0x610 [55542.624365] [<ffffffff8101439f>] do_signal+0x3f/0x8d0 [55542.624373] [<ffffffff8108f416>] ? wake_up_new_task+0xf6/0x170 [55542.624381] [<ffffffff810579df>] ? do_fork+0xff/0x360 [55542.624388] [<ffffffff81014cb0>] do_notify_resume+0x80/0xb0 [55542.624393] [<ffffffff816d4c1a>] int_signal+0x12/0x17 [55542.624399] INFO: task java:24546 blocked for more than 120 seconds. [55542.624402] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [55542.624405] java D ffff88082ed53f40 0 24546 24544 0x00000000 [55542.624410] ffff880792d81cd8 0000000000000082 ffff8807c0e445c0 ffff880792d81fd8 [55542.624418] ffff880792d81fd8 ffff880792d81fd8 ffff8807a5b92e80 ffff8807c0e445c0 [55542.624428] ffff8807c0e445c0 ffff8807fcbe8380 ffff880784929d48 ffff8807fcbe83e8 [55542.624437] Call Trace: [55542.624447] [<ffffffff816cb1b9>] schedule+0x29/0x70 [55542.624454] [<ffffffff8105e275>] do_exit+0x1b5/0x9d0 [55542.624461] [<ffffffff810b52dd>] ? futex_wait_queue_me+0xcd/0x100 [55542.624468] [<ffffffff810b507b>] ? __unqueue_futex+0x3b/0x70 [55542.624474] [<ffffffff810b5a40>] ? futex_wait+0x140/0x2d0 [55542.624482] [<ffffffff8105eb0f>] do_group_exit+0x3f/0xa0 [55542.624490] [<ffffffff8106e581>] get_signal_to_deliver+0x1c1/0x610 [55542.624499] [<ffffffff8101439f>] do_signal+0x3f/0x8d0 [55542.624507] [<ffffffff81161227>] ? mprotect_fixup+0x157/0x280 [55542.624516] [<ffffffff81014cb0>] do_notify_resume+0x80/0xb0 [55542.624523] [<ffffffff816d4c1a>] int_signal+0x12/0x17 [55542.624530] INFO: task java:24550 blocked for more than 120 seconds. [55542.624533] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [55542.624536] java D ffff88082ec13f40 0 24550 24544 0x00000000 [55542.624543] ffff88078483dcd8 0000000000000082 ffff880802db9740 ffff88078483dfd8 [55542.624551] ffff88078483dfd8 ffff88078483dfd8 ffff8802c3fdae80 ffff880802db9740 [55542.624559] ffff880802db9740 ffff8807fcbe8380 ffff880784929d48 ffff8807fcbe83e8 [55542.624567] Call Trace: [55542.624576] [<ffffffff816cb1b9>] schedule+0x29/0x70 [55542.624582] [<ffffffff8105e275>] do_exit+0x1b5/0x9d0 [55542.624588] [<ffffffff810b52dd>] ? futex_wait_queue_me+0xcd/0x100 [55542.624593] [<ffffffff810b507b>] ? __unqueue_futex+0x3b/0x70 [55542.624599] [<ffffffff810b5a40>] ? futex_wait+0x140/0x2d0 [55542.624605] [<ffffffff8105eb0f>] do_group_exit+0x3f/0xa0 [55542.624612] [<ffffffff8106e581>] get_signal_to_deliver+0x1c1/0x610 [55542.624620] [<ffffffff8101439f>] do_signal+0x3f/0x8d0 [55542.624627] [<ffffffff810941b3>] ? pick_next_task_fair+0x63/0x180 [55542.624634] [<ffffffff81014cb0>] do_notify_resume+0x80/0xb0 [55542.624640] [<ffffffff816d4c1a>] int_signal+0x12/0x17 [55542.624645] INFO: task java:24551 blocked for more than 120 seconds. [55542.624648] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [55542.624650] java D ffff88082ec13f40 0 24551 24544 0x00000000 [55542.624655] ffff88072896fcd8 0000000000000082 ffff8802c3fdae80 ffff88072896ffd8 [55542.624662] ffff88072896ffd8 ffff88072896ffd8 ffff8802c3fddd00 ffff8802c3fdae80 [55542.624668] ffff8802c3fdae80 ffff8807fcbe8380 ffff880784929d48 ffff8807fcbe83e8 [55542.624675] Call Trace: [55542.624682] [<ffffffff816cb1b9>] schedule+0x29/0x70 [55542.624688] [<ffffffff8105e275>] do_exit+0x1b5/0x9d0 [55542.624693] [<ffffffff810b52dd>] ? futex_wait_queue_me+0xcd/0x100 [55542.624699] [<ffffffff810b507b>] ? __unqueue_futex+0x3b/0x70 [55542.624705] [<ffffffff810b5a40>] ? futex_wait+0x140/0x2d0 [55542.624711] [<ffffffff8105eb0f>] do_group_exit+0x3f/0xa0 [55542.624718] [<ffffffff8106e581>] get_signal_to_deliver+0x1c1/0x610 [55542.624725] [<ffffffff8101439f>] do_signal+0x3f/0x8d0 [55542.624733] [<ffffffff8108bbaa>] ? finish_task_switch+0x4a/0xf0 [55542.624740] [<ffffffff81014cb0>] do_notify_resume+0x80/0xb0 [55542.624745] [<ffffffff816d4c1a>] int_signal+0x12/0x17 [55542.624750] INFO: task java:24552 blocked for more than 120 seconds. [55542.624753] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [55542.624755] java D ffff88082ec13f40 0 24552 24544 0x00000000 [55542.624760] ffff880728981cd8 0000000000000082 ffff8802c3fddd00 ffff880728981fd8 [55542.624767] ffff880728981fd8 ffff880728981fd8 ffff8802c3fdc5c0 ffff8802c3fddd00 [55542.624773] ffff8802c3fddd00 ffff8807fcbe8380 ffff880784929d48 ffff8807fcbe83e8 [55542.624780] Call Trace: [55542.624787] [<ffffffff816cb1b9>] schedule+0x29/0x70 [55542.624793] [<ffffffff8105e275>] do_exit+0x1b5/0x9d0 [55542.624799] [<ffffffff810b52dd>] ? futex_wait_queue_me+0xcd/0x100 [55542.624804] [<ffffffff810b507b>] ? __unqueue_futex+0x3b/0x70 [55542.624810] [<ffffffff810b5a40>] ? futex_wait+0x140/0x2d0 [55542.624816] [<ffffffff8105eb0f>] do_group_exit+0x3f/0xa0 [55542.624823] [<ffffffff8106e581>] get_signal_to_deliver+0x1c1/0x610 [55542.624830] [<ffffffff8101439f>] do_signal+0x3f/0x8d0 [55542.624837] [<ffffffff8108bbaa>] ? finish_task_switch+0x4a/0xf0 [55542.624845] [<ffffffff81014cb0>] do_notify_resume+0x80/0xb0 [55542.624850] [<ffffffff816d4c1a>] int_signal+0x12/0x17 [55542.624855] INFO: task java:24553 blocked for more than 120 seconds. [55542.624858] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [55542.624860] java D ffff88082ec13f40 0 24553 24544 0x00000000 [55542.624865] ffff8803247b9cd8 0000000000000082 ffff8802c3fdc5c0 ffff8803247b9fd8 [55542.624872] ffff8803247b9fd8 ffff8803247b9fd8 ffff88066da35d00 ffff8802c3fdc5c0 [55542.624879] ffff8802c3fdc5c0 ffff8807fcbe8380 ffff880784929d48 ffff8807fcbe83e8 [55542.624885] Call Trace: [55542.624893] [<ffffffff816cb1b9>] schedule+0x29/0x70 [55542.624899] [<ffffffff8105e275>] do_exit+0x1b5/0x9d0 [55542.624906] [<ffffffff810b52dd>] ? futex_wait_queue_me+0xcd/0x100 [55542.624914] [<ffffffff810b507b>] ? __unqueue_futex+0x3b/0x70 [55542.624920] [<ffffffff810b5a40>] ? futex_wait+0x140/0x2d0 [55542.624927] [<ffffffff8105eb0f>] do_group_exit+0x3f/0xa0 [55542.624935] [<ffffffff8106e581>] get_signal_to_deliver+0x1c1/0x610 [55542.624944] [<ffffffff8101439f>] do_signal+0x3f/0x8d0 [55542.624951] [<ffffffff810941b3>] ? pick_next_task_fair+0x63/0x180 [55542.624960] [<ffffffff81014cb0>] do_notify_resume+0x80/0xb0 [55542.624967] [<ffffffff816d4c1a>] int_signal+0x12/0x17 [55542.624973] INFO: task java:24554 blocked for more than 120 seconds. [55542.624976] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [55542.624979] java D ffff88082ec53f40 0 24554 24544 0x00000000 [55542.624985] ffff880788671cd8 0000000000000082 ffff8802c3fd9740 ffff880788671fd8 [55542.624993] ffff880788671fd8 ffff880788671fd8 ffff880802d89740 ffff8802c3fd9740 [55542.625001] ffff8802c3fd9740 ffff8807fcbe8380 ffff880784929d48 ffff8807fcbe83e8 [55542.625009] Call Trace: [55542.625020] [<ffffffff816cb1b9>] schedule+0x29/0x70 [55542.625026] [<ffffffff8105e275>] do_exit+0x1b5/0x9d0 [55542.625032] [<ffffffff810b52dd>] ? futex_wait_queue_me+0xcd/0x100 [55542.625038] [<ffffffff810b507b>] ? __unqueue_futex+0x3b/0x70 [55542.625043] [<ffffffff810b5a40>] ? futex_wait+0x140/0x2d0 [55542.625049] [<ffffffff8105eb0f>] do_group_exit+0x3f/0xa0 [55542.625056] [<ffffffff8106e581>] get_signal_to_deliver+0x1c1/0x610 [55542.625063] [<ffffffff8101439f>] do_signal+0x3f/0x8d0 [55542.625070] [<ffffffff810135d1>] ? __switch_to+0x181/0x4a0 [55542.625075] [<ffffffff81094140>] ? set_next_entity+0x80/0x90 [55542.625081] [<ffffffff8108bbaa>] ? finish_task_switch+0x4a/0xf0 [55542.625089] [<ffffffff81014cb0>] do_notify_resume+0x80/0xb0 [55542.625094] [<ffffffff816d4c1a>] int_signal+0x12/0x17 [55542.625099] INFO: task java:24555 blocked for more than 120 seconds. [55542.625101] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [55542.625104] java D ffff88082ec13f40 0 24555 24544 0x00000000 [55542.625109] ffff8807b2dcdcd8 0000000000000082 ffff88066da35d00 ffff8807b2dcdfd8 [55542.625115] ffff8807b2dcdfd8 ffff8807b2dcdfd8 ffff880759d45d00 ffff88066da35d00 [55542.625121] ffff88066da35d00 ffff8807fcbe8380 ffff880784929d48 ffff8807fcbe83e8 [55542.625127] Call Trace: [55542.625135] [<ffffffff816cb1b9>] schedule+0x29/0x70 [55542.625141] [<ffffffff8105e275>] do_exit+0x1b5/0x9d0 [55542.625146] [<ffffffff810b52dd>] ? futex_wait_queue_me+0xcd/0x100 [55542.625152] [<ffffffff810b507b>] ? __unqueue_futex+0x3b/0x70 [55542.625157] [<ffffffff810b5a40>] ? futex_wait+0x140/0x2d0 [55542.625163] [<ffffffff8105eb0f>] do_group_exit+0x3f/0xa0 [55542.625170] [<ffffffff8106e581>] get_signal_to_deliver+0x1c1/0x610 [55542.625178] [<ffffffff8101439f>] do_signal+0x3f/0x8d0 [55542.625184] [<ffffffff810135d1>] ? __switch_to+0x181/0x4a0 [55542.625190] [<ffffffff81094140>] ? set_next_entity+0x80/0x90 [55542.625196] [<ffffffff8108bbaa>] ? finish_task_switch+0x4a/0xf0 [55542.625203] [<ffffffff81014cb0>] do_notify_resume+0x80/0xb0 [55542.625208] [<ffffffff816d4c1a>] int_signal+0x12/0x17 [55542.625213] INFO: task java:24556 blocked for more than 120 seconds. [55542.625215] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [55542.625218] java D ffff88082ed53f40 0 24556 24544 0x00000000 [55542.625223] ffff88079caafcd8 0000000000000082 ffff8807a5b92e80 ffff88079caaffd8 [55542.625230] ffff88079caaffd8 ffff88079caaffd8 ffff880366cfc5c0 ffff8807a5b92e80 [55542.625236] ffff8807a5b92e80 ffff8807fcbe8380 ffff880784929d48 ffff8807fcbe83e8 [55542.625242] Call Trace: [55542.625250] [<ffffffff816cb1b9>] schedule+0x29/0x70 [55542.625255] [<ffffffff8105e275>] do_exit+0x1b5/0x9d0 [55542.625261] [<ffffffff810b52dd>] ? futex_wait_queue_me+0xcd/0x100 [55542.625266] [<ffffffff810b507b>] ? __unqueue_futex+0x3b/0x70 [55542.625272] [<ffffffff810b5a40>] ? futex_wait+0x140/0x2d0 [55542.625278] [<ffffffff8105eb0f>] do_group_exit+0x3f/0xa0 [55542.625285] [<ffffffff8106e581>] get_signal_to_deliver+0x1c1/0x610 [55542.625293] [<ffffffff8101439f>] do_signal+0x3f/0x8d0 [55542.625299] [<ffffffff810941b3>] ? pick_next_task_fair+0x63/0x180 [55542.625307] [<ffffffff81014cb0>] do_notify_resume+0x80/0xb0 [55542.625312] [<ffffffff816d4c1a>] int_signal+0x12/0x17 [55542.625317] INFO: task java:24557 blocked for more than 120 seconds. [55542.625319] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [55542.625322] java D ffff88082ec13f40 0 24557 24544 0x00000000 [55542.625327] ffff880784907cd8 0000000000000082 ffff880759d45d00 ffff880784907fd8 [55542.625333] ffff880784907fd8 ffff880784907fd8 ffff880759d42e80 ffff880759d45d00 [55542.625339] ffff880759d45d00 ffff8807fcbe8380 ffff880784929d48 ffff8807fcbe83e8 [55542.625346] Call Trace: [55542.625353] [<ffffffff816cb1b9>] schedule+0x29/0x70 [55542.625359] [<ffffffff8105e275>] do_exit+0x1b5/0x9d0 [55542.625364] [<ffffffff810b52dd>] ? futex_wait_queue_me+0xcd/0x100 [55542.625370] [<ffffffff810b507b>] ? __unqueue_futex+0x3b/0x70 [55542.625376] [<ffffffff810b5a40>] ? futex_wait+0x140/0x2d0 [55542.625382] [<ffffffff8105eb0f>] do_group_exit+0x3f/0xa0 [55542.625389] [<ffffffff8106e581>] get_signal_to_deliver+0x1c1/0x610 [55542.625396] [<ffffffff8101439f>] do_signal+0x3f/0x8d0 [55542.625403] [<ffffffff8108bbaa>] ? finish_task_switch+0x4a/0xf0 [55542.625411] [<ffffffff81014cb0>] do_notify_resume+0x80/0xb0 [55542.625416] [<ffffffff816d4c1a>] int_signal+0x12/0x17 ------------------------------------------------------------------------------ This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
