-
-
Save rtnh/e2eab6afa7c0a37dbc96578d0f73c540 to your computer and use it in GitHub Desktop.
sambamba markdup trace
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| === kernel ring buffer === | |
| [Thu May 19 21:30:30 2016] ------------[ cut here ]------------ | |
| [Thu May 19 21:30:30 2016] WARNING: at /home/builder/builds/kernel/3.10.0-327.18.2.el7/20160512110105/BUILD/kernel-3.10.0-327.18.2.el7/linux-3.10.0-327.18.2.el7.x86_64/arch/x86/include/asm/thread_info.h:249 sigsuspend+0x6d/0x70() | |
| [Thu May 19 21:30:30 2016] Modules linked in: binfmt_misc rpcsec_gss_krb5 nfsv4 dns_resolver nfs fscache dm_mod kvm_intel kvm ppdev crc32_pclmul ghash_clmulni_intel aesni_intel lrw gf128mul glue_helper ablk_helper cryptd sg parport_pc parport i2c_piix4 pcspkr nfsd auth_rpcgss nfs_acl lockd grace sunrpc ip_tables ext4 mbcache jbd2 sr_mod cdrom ata_generic pata_acpi virtio_console virtio_net virtio_blk cirrus syscopyarea sysfillrect sysimgblt drm_kms_helper ttm crct10dif_pclmul crct10dif_common crc32c_intel ata_piix drm virtio_pci libata virtio_ring i2c_core serio_raw virtio floppy | |
| [Thu May 19 21:30:30 2016] CPU: 6 PID: 27988 Comm: sambamba Not tainted 3.10.0-327.18.2.el7.x86_64 #1 | |
| [Thu May 19 21:30:30 2016] Hardware name: Mission Critical Cloud Cosmic KVM Hypervisor, BIOS seabios-1.7.5-11.el7 04/01/2014 | |
| [Thu May 19 21:30:30 2016] 0000000000000000 000000006917ea9a ffff8817b4f1fef8 ffffffff81635a0c | |
| [Thu May 19 21:30:30 2016] ffff8817b4f1ff30 ffffffff8107b200 ffff8817b6cd1700 0000000000000000 | |
| [Thu May 19 21:30:30 2016] 00002aed9c8049c0 00002aed9c802ab8 00002aed71846700 ffff8817b4f1ff40 | |
| [Thu May 19 21:30:30 2016] Call Trace: | |
| [Thu May 19 21:30:30 2016] [<ffffffff81635a0c>] dump_stack+0x19/0x1b | |
| [Thu May 19 21:30:30 2016] [<ffffffff8107b200>] warn_slowpath_common+0x70/0xb0 | |
| [Thu May 19 21:30:30 2016] [<ffffffff8107b34a>] warn_slowpath_null+0x1a/0x20 | |
| [Thu May 19 21:30:30 2016] [<ffffffff81094a6d>] sigsuspend+0x6d/0x70 | |
| [Thu May 19 21:30:30 2016] [<ffffffff81094abf>] SyS_rt_sigsuspend+0x4f/0x70 | |
| [Thu May 19 21:30:30 2016] [<ffffffff816461c9>] system_call_fastpath+0x16/0x1b | |
| [Thu May 19 21:30:30 2016] ---[ end trace 2cc1c91b6249668a ]--- | |
| ======= | |
| === strace frozen sambamba process === | |
| [pid 27990] rt_sigsuspend(~[USR2 RTMIN RT_1] <unfinished ...> | |
| [pid 27989] rt_sigsuspend(~[USR2 RTMIN RT_1] <unfinished ...> | |
| [pid 27988] futex(0x2aed9a3efd1c, FUTEX_WAIT_PRIVATE, 82721, NULL <unfinished ...> | |
| [pid 27987] futex(0x2aed9a3efd1c, FUTEX_WAIT_PRIVATE, 82721, NULL <unfinished ...> | |
| [pid 27986] futex(0x8371f0, FUTEX_WAIT_PRIVATE, 0, NULL <unfinished ...> | |
| [pid 27985] futex(0x8374a0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> | |
| [pid 27984] futex(0x8374a0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...> | |
| [pid 27980] futex(0x2aed7182741c, FUTEX_WAIT_PRIVATE, 98226, NULL <unfinished ...> | |
| [pid 27979] futex(0x2aed7182741c, FUTEX_WAIT_PRIVATE, 98226, NULL <unfinished ...> | |
| [pid 27978] futex(0x2aed7182741c, FUTEX_WAIT_PRIVATE, 98226, NULL <unfinished ...> | |
| [pid 27977] futex(0x2aed7182741c, FUTEX_WAIT_PRIVATE, 98226, NULL <unfinished ...> | |
| [pid 27976] futex(0x2aed7182741c, FUTEX_WAIT_PRIVATE, 98226, NULL <unfinished ...> | |
| [pid 27975] futex(0x2aed7182741c, FUTEX_WAIT_PRIVATE, 98226, NULL <unfinished ...> | |
| [pid 27974] futex(0x2aed7182741c, FUTEX_WAIT_PRIVATE, 98226, NULL <unfinished ...> | |
| [pid 27973] futex(0x2aed7182741c, FUTEX_WAIT_PRIVATE, 98226, NULL <unfinished ...> | |
| [pid 27972] futex(0x8374a0, FUTEX_WAIT_PRIVATE, 2, NULL | |
| ======= | |
| ==== backtrace thread frozen sambamba process === | |
| Id Target Id Frame | |
| 16 Thread 0x2aed72915700 (LWP 27973) "sambamba" 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| 15 Thread 0x2aed72b16700 (LWP 27974) "sambamba" 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| 14 Thread 0x2aed72d17700 (LWP 27975) "sambamba" 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| 13 Thread 0x2aed72f18700 (LWP 27976) "sambamba" 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| 12 Thread 0x2aed73119700 (LWP 27977) "sambamba" 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| 11 Thread 0x2aed7331a700 (LWP 27978) "sambamba" 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| 10 Thread 0x2aed7351b700 (LWP 27979) "sambamba" 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| 9 Thread 0x2aed7371c700 (LWP 27980) "sambamba" 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| 8 Thread 0x2aed9c000700 (LWP 27984) "sambamba" 0x00002aed71c2cf4d in __lll_lock_wait () from /lib64/libpthread.so.0 | |
| 7 Thread 0x2aed9c201700 (LWP 27985) "sambamba" 0x00002aed71c2cf4d in __lll_lock_wait () from /lib64/libpthread.so.0 | |
| 6 Thread 0x2aed9c402700 (LWP 27986) "sambamba" 0x00002aed71c2c790 in sem_wait () from /lib64/libpthread.so.0 | |
| 5 Thread 0x2aed9c603700 (LWP 27987) "sambamba" 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| 4 Thread 0x2aed9c804700 (LWP 27988) "sambamba" 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| 3 Thread 0x2aed9ca05700 (LWP 27989) "sambamba" 0x00002aed72388972 in sigsuspend () from /lib64/libc.so.6 | |
| 2 Thread 0x2aed9cc06700 (LWP 27990) "sambamba" 0x00002aed72388972 in sigsuspend () from /lib64/libc.so.6 | |
| * 1 Thread 0x2aed71823600 (LWP 27972) "sambamba" 0x00002aed71c2cf4d in __lll_lock_wait () from /lib64/libpthread.so.0 | |
| Thread 16 (Thread 0x2aed72915700 (LWP 27973)): | |
| #0 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| #1 0x00000000005608e0 in core.sync.condition.Condition.wait() () | |
| #2 0x000000000054754a in std.parallelism.TaskPool.pop() () | |
| #3 0x000000000054747a in std.parallelism.TaskPool.startWorkLoop() () | |
| #4 0x000000000055e7fe in thread_entryPoint () | |
| #5 0x00002aed71c26dc5 in start_thread () from /lib64/libpthread.so.0 | |
| #6 0x00002aed72449ced in clone () from /lib64/libc.so.6 | |
| Thread 15 (Thread 0x2aed72b16700 (LWP 27974)): | |
| #0 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| #1 0x00000000005608e0 in core.sync.condition.Condition.wait() () | |
| #2 0x000000000054754a in std.parallelism.TaskPool.pop() () | |
| #3 0x000000000054747a in std.parallelism.TaskPool.startWorkLoop() () | |
| #4 0x000000000055e7fe in thread_entryPoint () | |
| #5 0x00002aed71c26dc5 in start_thread () from /lib64/libpthread.so.0 | |
| #6 0x00002aed72449ced in clone () from /lib64/libc.so.6 | |
| Thread 14 (Thread 0x2aed72d17700 (LWP 27975)): | |
| #0 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| #1 0x00000000005608e0 in core.sync.condition.Condition.wait() () | |
| #2 0x000000000054754a in std.parallelism.TaskPool.pop() () | |
| #3 0x000000000054747a in std.parallelism.TaskPool.startWorkLoop() () | |
| #4 0x000000000055e7fe in thread_entryPoint () | |
| #5 0x00002aed71c26dc5 in start_thread () from /lib64/libpthread.so.0 | |
| #6 0x00002aed72449ced in clone () from /lib64/libc.so.6 | |
| Thread 13 (Thread 0x2aed72f18700 (LWP 27976)): | |
| #0 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| #1 0x00000000005608e0 in core.sync.condition.Condition.wait() () | |
| #2 0x000000000054754a in std.parallelism.TaskPool.pop() () | |
| #3 0x000000000054747a in std.parallelism.TaskPool.startWorkLoop() () | |
| #4 0x000000000055e7fe in thread_entryPoint () | |
| #5 0x00002aed71c26dc5 in start_thread () from /lib64/libpthread.so.0 | |
| #6 0x00002aed72449ced in clone () from /lib64/libc.so.6 | |
| Thread 12 (Thread 0x2aed73119700 (LWP 27977)): | |
| #0 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| #1 0x00000000005608e0 in core.sync.condition.Condition.wait() () | |
| #2 0x000000000054754a in std.parallelism.TaskPool.pop() () | |
| #3 0x000000000054747a in std.parallelism.TaskPool.startWorkLoop() () | |
| #4 0x000000000055e7fe in thread_entryPoint () | |
| #5 0x00002aed71c26dc5 in start_thread () from /lib64/libpthread.so.0 | |
| #6 0x00002aed72449ced in clone () from /lib64/libc.so.6 | |
| Thread 11 (Thread 0x2aed7331a700 (LWP 27978)): | |
| #0 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| #1 0x00000000005608e0 in core.sync.condition.Condition.wait() () | |
| #2 0x000000000054754a in std.parallelism.TaskPool.pop() () | |
| #3 0x000000000054747a in std.parallelism.TaskPool.startWorkLoop() () | |
| #4 0x000000000055e7fe in thread_entryPoint () | |
| #5 0x00002aed71c26dc5 in start_thread () from /lib64/libpthread.so.0 | |
| #6 0x00002aed72449ced in clone () from /lib64/libc.so.6 | |
| Thread 10 (Thread 0x2aed7351b700 (LWP 27979)): | |
| #0 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| #1 0x00000000005608e0 in core.sync.condition.Condition.wait() () | |
| #2 0x000000000054754a in std.parallelism.TaskPool.pop() () | |
| #3 0x000000000054747a in std.parallelism.TaskPool.startWorkLoop() () | |
| #4 0x000000000055e7fe in thread_entryPoint () | |
| #5 0x00002aed71c26dc5 in start_thread () from /lib64/libpthread.so.0 | |
| #6 0x00002aed72449ced in clone () from /lib64/libc.so.6 | |
| Thread 9 (Thread 0x2aed7371c700 (LWP 27980)): | |
| #0 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| #1 0x00000000005608e0 in core.sync.condition.Condition.wait() () | |
| #2 0x000000000054754a in std.parallelism.TaskPool.pop() () | |
| #3 0x000000000054747a in std.parallelism.TaskPool.startWorkLoop() () | |
| #4 0x000000000055e7fe in thread_entryPoint () | |
| #5 0x00002aed71c26dc5 in start_thread () from /lib64/libpthread.so.0 | |
| #6 0x00002aed72449ced in clone () from /lib64/libc.so.6 | |
| Thread 8 (Thread 0x2aed9c000700 (LWP 27984)): | |
| #0 0x00002aed71c2cf4d in __lll_lock_wait () from /lib64/libpthread.so.0 | |
| #1 0x00002aed71c28d1d in _L_lock_840 () from /lib64/libpthread.so.0 | |
| #2 0x00002aed71c28c3a in pthread_mutex_lock () from /lib64/libpthread.so.0 | |
| #3 0x0000000000560f7a in core.sync.mutex.Mutex.lock() () | |
| #4 0x000000000056f66d in gc.gc.GC.malloc() () | |
| #5 0x0000000000411d34 in bio.bam.readrange.__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ.BamReadRange.readNext() () | |
| #6 0x0000000000442e49 in std.parallelism.TaskPool.__T3mapS403bio3bam11multireader17adjustTagsInRangeZ.__T3mapTS3std5range575__T3ZipTS3std9algorithm422__T9MapResultS2523bio3bam11multireader110__T13multiBamReadsTS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangeZ13multiBamReadsFS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangemZ9__lambda3TS3std5range133__T3ZipTS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangeTS3std5range13__T6RepeatTmZ6RepeatZ3ZipZ9MapResultTS3std5range61__T6RepeatTC3bio3bam5utils15samheadermerger15SamHeaderMergerZ6RepeatTS3std5range13__T6RepeatTmZ6RepeatZ3ZipZ.map() () | |
| #7 0x0000000000442eaf in std.parallelism.TaskPool.__T3mapS403bio3bam11multireader17adjustTagsInRangeZ.__T3mapTS3std5range575__T3ZipTS3std9algorithm422__T9MapResultS2523bio3bam11multireader110__T13multiBamReadsTS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangeZ13multiBamReadsFS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangemZ9__lambda3TS3std5range133__T3ZipTS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangeTS3std5range13__T6RepeatTmZ6RepeatZ3ZipZ9MapResultTS3std5range61__T6RepeatTC3bio3bam5utils15samheadermerger15SamHeaderMergerZ6RepeatTS3std5range13__T6RepeatTmZ6RepeatZ3ZipZ.map() () | |
| ---Type <return> to continue, or q <return> to quit--- | |
| #8 0x0000000000442993 in std.parallelism.__T4TaskS213std11parallelism3runTDFAS3std8typecons140__T5TupleTS3bio3bam11multireader41__T12MultiBamReadTS3bio3bam4read7BamReadZ12MultiBamReadTC3bio3bam5utils15samheadermerger15SamHeaderMergerZ5TupleZAS3std8typecons140__T5TupleTS3bio3bam11multireader41__T12MultiBamReadTS3bio3bam4read7BamReadZ12MultiBamReadTC3bio3bam5utils15samheadermerger15SamHeaderMergerZ5TupleTAS3std8typecons140__T5TupleTS3bio3bam11multireader41__T12MultiBamReadTS3bio3bam4read7BamReadZ12MultiBamReadTC3bio3bam5utils15samheadermerger15SamHeaderMergerZ5TupleZ.Task.impl() () | |
| #9 0x00000000005472c4 in std.parallelism.TaskPool.doJob() () | |
| #10 0x000000000054746b in std.parallelism.TaskPool.startWorkLoop() () | |
| #11 0x000000000055e7fe in thread_entryPoint () | |
| #12 0x00002aed71c26dc5 in start_thread () from /lib64/libpthread.so.0 | |
| #13 0x00002aed72449ced in clone () from /lib64/libc.so.6 | |
| Thread 7 (Thread 0x2aed9c201700 (LWP 27985)): | |
| #0 0x00002aed71c2cf4d in __lll_lock_wait () from /lib64/libpthread.so.0 | |
| #1 0x00002aed71c28d1d in _L_lock_840 () from /lib64/libpthread.so.0 | |
| #2 0x00002aed71c28c3a in pthread_mutex_lock () from /lib64/libpthread.so.0 | |
| #3 0x0000000000560f7a in core.sync.mutex.Mutex.lock() () | |
| #4 0x000000000056f66d in gc.gc.GC.malloc() () | |
| #5 0x0000000000411d34 in bio.bam.readrange.__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ.BamReadRange.readNext() () | |
| #6 0x0000000000442e49 in std.parallelism.TaskPool.__T3mapS403bio3bam11multireader17adjustTagsInRangeZ.__T3mapTS3std5range575__T3ZipTS3std9algorithm422__T9MapResultS2523bio3bam11multireader110__T13multiBamReadsTS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangeZ13multiBamReadsFS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangemZ9__lambda3TS3std5range133__T3ZipTS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangeTS3std5range13__T6RepeatTmZ6RepeatZ3ZipZ9MapResultTS3std5range61__T6RepeatTC3bio3bam5utils15samheadermerger15SamHeaderMergerZ6RepeatTS3std5range13__T6RepeatTmZ6RepeatZ3ZipZ.map() () | |
| #7 0x0000000000442eaf in std.parallelism.TaskPool.__T3mapS403bio3bam11multireader17adjustTagsInRangeZ.__T3mapTS3std5range575__T3ZipTS3std9algorithm422__T9MapResultS2523bio3bam11multireader110__T13multiBamReadsTS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangeZ13multiBamReadsFS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangemZ9__lambda3TS3std5range133__T3ZipTS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangeTS3std5range13__T6RepeatTmZ6RepeatZ3ZipZ9MapResultTS3std5range61__T6RepeatTC3bio3bam5utils15samheadermerger15SamHeaderMergerZ6RepeatTS3std5range13__T6RepeatTmZ6RepeatZ3ZipZ.map() () | |
| #8 0x0000000000442993 in std.parallelism.__T4TaskS213std11parallelism3runTDFAS3std8typecons140__T5TupleTS3bio3bam11multireader41__T12MultiBamReadTS3bio3bam4read7BamReadZ12MultiBamReadTC3bio3bam5utils15samheadermerger15SamHeaderMergerZ5TupleZAS3std8typecons140__T5TupleTS3bio3bam11multireader41__T12MultiBamReadTS3bio3bam4read7BamReadZ12MultiBamReadTC3bio3bam5utils15samheadermerger15SamHeaderMergerZ5TupleTAS3std8typecons140__T5TupleTS3bio3bam11multireader41__T12MultiBamReadTS3bio3bam4read7BamReadZ12MultiBamReadTC3bio3bam5utils15samheadermerger15SamHeaderMergerZ5TupleZ.Task.impl() () | |
| #9 0x00000000005472c4 in std.parallelism.TaskPool.doJob() () | |
| #10 0x000000000054746b in std.parallelism.TaskPool.startWorkLoop() () | |
| #11 0x000000000055e7fe in thread_entryPoint () | |
| #12 0x00002aed71c26dc5 in start_thread () from /lib64/libpthread.so.0 | |
| #13 0x00002aed72449ced in clone () from /lib64/libc.so.6 | |
| Thread 6 (Thread 0x2aed9c402700 (LWP 27986)): | |
| #0 0x00002aed71c2c790 in sem_wait () from /lib64/libpthread.so.0 | |
| #1 0x000000000055f931 in core.thread.suspend() () | |
| #2 0x000000000055fad4 in thread_suspendAll () | |
| #3 0x000000000056faac in gc.gc.Gcx.fullcollect() () | |
| #4 0x0000000000570791 in gc.gc.Gcx.bigAlloc() () | |
| #5 0x000000000056f8c2 in gc.gc.GC.mallocNoSync() () | |
| #6 0x000000000056f67e in gc.gc.GC.malloc() () | |
| #7 0x0000000000411d34 in bio.bam.readrange.__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ.BamReadRange.readNext() () | |
| #8 0x0000000000442e49 in std.parallelism.TaskPool.__T3mapS403bio3bam11multireader17adjustTagsInRangeZ.__T3mapTS3std5range575__T3ZipTS3std9algorithm422__T9MapResultS2523bio3bam11multireader110__T13multiBamReadsTS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangeZ13multiBamReadsFS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangemZ9__lambda3TS3std5range133__T3ZipTS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangeTS3std5range13__T6RepeatTmZ6RepeatZ3ZipZ9MapResultTS3std5range61__T6RepeatTC3bio3bam5utils15samheadermerger15SamHeaderMergerZ6RepeatTS3std5range13__T6RepeatTmZ6RepeatZ3ZipZ.map() () | |
| #9 0x0000000000442eaf in std.parallelism.TaskPool.__T3mapS403bio3bam11multireader17adjustTagsInRangeZ.__T3mapTS3std5range575__T3ZipTS3std9algorithm422__T9MapResultS2523bio3bam11multireader110__T13multiBamReadsTS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangeZ13multiBamReadsFS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangemZ9__lambda3TS3std5range133__T3ZipTS3bio3bam9readrange55__T12BamReadRangeS343bio3bam9readrange14withoutOffsetsZ12BamReadRangeTS3std5range13__T6RepeatTmZ6RepeatZ3ZipZ9MapResultTS3std5range61__T6RepeatTC3bio3bam5utils15samheadermerger15SamHeaderMergerZ6RepeatTS3std5range13__T6RepeatTmZ6RepeatZ3ZipZ.map() () | |
| #10 0x0000000000442993 in std.parallelism.__T4TaskS213std11parallelism3runTDFAS3std8typecons140__T5TupleTS3bio3bam11multireader41__T12MultiBamReadTS3bio3bam4read7BamReadZ12MultiBamReadTC3bio3bam5utils15samheadermerger15SamHeaderMergerZ5TupleZAS3std8typecons140__T5TupleTS3bio3bam11multireader41__T12MultiBamReadTS3bio3bam4read7BamReadZ12MultiBamReadTC3bio3bam5utils15samheadermerger15SamHeaderMergerZ5TupleTAS3std8typecons140__T5TupleTS3bio3bam11multireader41__T12MultiBamReadTS3bio3bam4read7BamReadZ12MultiBamReadTC3bio3bam5utils15samheadermerger15SamHeaderMergerZ5TupleZ.Task.impl() () | |
| #11 0x00000000005472c4 in std.parallelism.TaskPool.doJob() () | |
| #12 0x000000000054746b in std.parallelism.TaskPool.startWorkLoop() () | |
| #13 0x000000000055e7fe in thread_entryPoint () | |
| #14 0x00002aed71c26dc5 in start_thread () from /lib64/libpthread.so.0 | |
| #15 0x00002aed72449ced in clone () from /lib64/libc.so.6 | |
| Thread 5 (Thread 0x2aed9c603700 (LWP 27987)): | |
| #0 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| #1 0x00000000005608e0 in core.sync.condition.Condition.wait() () | |
| #2 0x000000000054754a in std.parallelism.TaskPool.pop() () | |
| #3 0x000000000054747a in std.parallelism.TaskPool.startWorkLoop() () | |
| #4 0x000000000055e7fe in thread_entryPoint () | |
| #5 0x00002aed71c26dc5 in start_thread () from /lib64/libpthread.so.0 | |
| #6 0x00002aed72449ced in clone () from /lib64/libc.so.6 | |
| Thread 4 (Thread 0x2aed9c804700 (LWP 27988)): | |
| #0 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| #1 0x00000000005608e0 in core.sync.condition.Condition.wait() () | |
| #2 0x000000000054754a in std.parallelism.TaskPool.pop() () | |
| #3 0x000000000054747a in std.parallelism.TaskPool.startWorkLoop() () | |
| #4 0x000000000055e7fe in thread_entryPoint () | |
| #5 0x00002aed71c26dc5 in start_thread () from /lib64/libpthread.so.0 | |
| #6 0x00002aed72449ced in clone () from /lib64/libc.so.6 | |
| Thread 3 (Thread 0x2aed9ca05700 (LWP 27989)): | |
| #0 0x00002aed72388972 in sigsuspend () from /lib64/libc.so.6 | |
| #1 0x000000000055eaf0 in core.thread.thread_suspendHandler() () | |
| #2 0x000000000055eb82 in core.thread.callWithStackShell() () | |
| #3 <signal handler called> | |
| #4 0x00002aed71c2a6d3 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| ---Type <return> to continue, or q <return> to quit--- | |
| #5 0x00000000005608e0 in core.sync.condition.Condition.wait() () | |
| #6 0x000000000054754a in std.parallelism.TaskPool.pop() () | |
| #7 0x000000000054747a in std.parallelism.TaskPool.startWorkLoop() () | |
| #8 0x000000000055e7fe in thread_entryPoint () | |
| #9 0x00002aed71c26dc5 in start_thread () from /lib64/libpthread.so.0 | |
| #10 0x00002aed72449ced in clone () from /lib64/libc.so.6 | |
| Thread 2 (Thread 0x2aed9cc06700 (LWP 27990)): | |
| #0 0x00002aed72388972 in sigsuspend () from /lib64/libc.so.6 | |
| #1 0x000000000055eaf0 in core.thread.thread_suspendHandler() () | |
| #2 0x000000000055eb82 in core.thread.callWithStackShell() () | |
| #3 <signal handler called> | |
| #4 0x00002aed71c2a6d5 in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0 | |
| #5 0x00000000005608e0 in core.sync.condition.Condition.wait() () | |
| #6 0x000000000054754a in std.parallelism.TaskPool.pop() () | |
| #7 0x000000000054747a in std.parallelism.TaskPool.startWorkLoop() () | |
| #8 0x000000000055e7fe in thread_entryPoint () | |
| #9 0x00002aed71c26dc5 in start_thread () from /lib64/libpthread.so.0 | |
| #10 0x00002aed72449ced in clone () from /lib64/libc.so.6 | |
| Thread 1 (Thread 0x2aed71823600 (LWP 27972)): | |
| #0 0x00002aed71c2cf4d in __lll_lock_wait () from /lib64/libpthread.so.0 | |
| #1 0x00002aed71c28d1d in _L_lock_840 () from /lib64/libpthread.so.0 | |
| #2 0x00002aed71c28c3a in pthread_mutex_lock () from /lib64/libpthread.so.0 | |
| #3 0x0000000000560f7a in core.sync.mutex.Mutex.lock() () | |
| #4 0x000000000056f66d in gc.gc.GC.malloc() () | |
| #5 0x0000000000564acf in gc_qalloc () | |
| #6 0x000000000056acc1 in _adDupT () | |
| #7 0x000000000044b65a in sambamba.markdup.__T20CollateReadPairRangeTC3std5range51__T10InputRangeTS8sambamba7markdup14IndexedBamReadZ10InputRangeVb1S298sambamba7markdup10simpleHashZ.CollateReadPairRange.copyToOverflowList() () | |
| #8 0x000000000044a928 in sambamba.markdup.__T20CollateReadPairRangeTC3std5range51__T10InputRangeTS8sambamba7markdup14IndexedBamReadZ10InputRangeVb1S298sambamba7markdup10simpleHashZ.CollateReadPairRange.popFrontHashTable() () | |
| #9 0x00000000004493a1 in sambamba.markdup.__T19getDuplicateOffsetsTC3std5range51__T10InputRangeTS8sambamba7markdup14IndexedBamReadZ10InputRangeZ.getDuplicateOffsets() () | |
| #10 0x0000000000447615 in sambamba.markdup.markdup_main() () | |
| #11 0x000000000056684c in _d_run_main () | |
| #12 0x00002aed72374b15 in __libc_start_main () from /lib64/libc.so.6 | |
| #13 0x0000000000404e19 in _start () | |
| ======== |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment