Hi Sébastien, nope, that doesn't seem to be the problem. Just removed all the line breaks (besides before/after headers), and run it again, still get the same error. Funnily this actually produces a result, but I think it aborts prematurely....let's say it has to. If I only throw in my 7 scaffolds (with 13 single Ns), then ray claims right now to produce 193 contigs in 136 scaffolds, and I think all the result files are present. Doesn't seem to make too much sense for me at the moment.
Any other idea :/? Bastian ________________________________________ From: Sébastien Boisvert [sebastien.boisver...@ulaval.ca] Sent: Monday, September 16, 2013 3:29 PM To: denovoassembler-users@lists.sourceforge.net Subject: Re: [Denovoassembler-users] *** glibc detected *** Ray: free(): invalid next size (normal): 0x00000000029887d0 *** On 16/09/13 08:48 AM, Hornung, Bastian wrote: > Hi @ all, > > sorry, it's me again. > Seems I try to many dumb things, or so. > > Currently my problem is that I try to load > - a set of scaffolds (7, ranging from 1.1 mb to 200 bp; yes, I know, the last > one is probably trash; only single Ns in the scaffolds) in fasta format > - a set of 454 reads (length ~420 bp) as fastq > - with a kmer size of 35. Hi, The problem is likely due to a lack of support for multi-line fasta files. https://github.com/sebhtml/ray/issues/163 > > After some time (don't know, around 30 minutes, with 18 cores), I get > (attention, very long): > > *** glibc detected *** Ray: free(): invalid next size (normal): > 0x00000000029887d0 *** > [ssb3:16233] *** Process received signal *** > [ssb3:16233] Signal: Aborted (6) > [ssb3:16233] Signal code: (-6) > [ssb3:16223] *** Process received signal *** > [ssb3:16223] Signal: Aborted (6) > [ssb3:16223] Signal code: (-6) > *** glibc detected *** Ray: free(): invalid next size (normal): > 0x00000000028587d0Ray(_ZN13RingAllocator5clearEv+0x15)[0x567e65] > [ssb3:16230] *** Process received signal *** > [ssb3:16230] Signal: Aborted (6) > [ssb3:16230] Signal code: (-6) > Ray(_ZN7Machine5startEv+0x1304)[0x46cc84] > Ray(_ZN11RankProcessI7MachineE3runEv+0x9f)[0x46a87f] > [ssb3:16233] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f53e4de7cb0] > [ssb3:16233] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) > [0x7f53e4a4e425] > [ssb3:16233] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) > [0x7f53e4a51b8b] > [ssb3:16233] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x7439e) [0x7f53e4a8c39e] > [ssb3:16233] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96) [0x7f53e4a96b96] > [ssb3:16233] [ 5] Ray(_ZN13RingAllocator5clearEv+0x15) [0x567e65] > [ssb3:16233] [ 6] Ray(_ZN11ComputeCore10destructorEv+0x20) [0x587e90] > [ssb3:16233] [ 7] Ray(_ZN7Machine5startEv+0x1304) [0x46cc84] > [ssb3:16233] [ 8] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a87f] > [ssb3:16233] [ 9] Ray(main+0xc7) [0x465617] > [ssb3:16233] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f53e4a3976d] > [ssb3:16233] [11] Ray() [0x466c21] > [ssb3:16233] *** End of error message *** > 00400000-005f0000 r-xp 00000000 fc:00 20715372 > /home/bastian/tools/Ray-v2.2.0/Ray > 007ef000-007f0000 r--p 001ef000 fc:00 20715372 > /home/bastian/tools/Ray-v2.2.0/Ray > 007f0000-007f1000 rw-p 001f0000 fc:00 20715372 > /home/bastian/tools/Ray-v2.2.0/Ray > 007f1000-007ff000 rw-p 00000000 00:00 0 > 02273000-052df000 rw-p 00000000 00:00 0 > [heap] > 7f0d56bc8000-7f0d5b7cf000 rw-p 00000000 00:00 0 > 7f0d5c7d0000-7f0d607d2000 rw-s 00000000 fc:00 35784771 > /tmp/openmpi-sessions-bastian@ssb3_0/33278/1/shared_mem_pool.ssb3 > 7f0d607d8000-7f0d607e5000 r-xp 00000000 fc:00 39715023 > /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so > 7f0d607e5000-7f0d609e4000 ---p 0000d000 fc:00 39715023 > /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so > 7f0d609e4000-7f0d609e5000 r--p 0000c000 fc:00 39715023 > /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so > 7f0d609e5000-7f0d609e6000 rw-p 0000d0[ssb3:16223] [ 0] > /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) [0x7fb3f0927cb0] > [ssb3:16223] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) > [0x7fb3f058e425] > [ssb3:16223] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) > [0x7fb3f0591b8b] > [ssb3:16223] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x7439e) [0x7fb3f05cc39e] > [ssb3:16223] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96) [0x7fb3f05d6b96] > [ssb3:16223] [ 5] Ray(_ZN13RingAllocator5clearEv+0x15) [0x567e65] > [ssb3:16223] [ 6] Ray(_ZN11ComputeCore10destructorEv+0x20) [0x587e90] > [ssb3:16223] [ 7] Ray(_ZN7Machine5startEv+0x1304) [0x46cc84] > [ssb3:16223] [ 8] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a87f] > [ssb3:16223] [ 9] Ray(main+0xc7) [0x465617] > [ssb3:16223] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7fb3f057976d] > [ssb3:16223] [11] Ray() [0x466c21] > [ssb3:16223] *** End of error message *** > [ssb3:16230] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7fdf70b8fcb0] > [ssb3:16230] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) > [0x7fdf707f6425] > [ssb3:16230] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) > [0x7fdf707f9b8b] > [ssb3:16230] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x7439e) [0x7fdf7083439e] > [ssb3:16230] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96) [0x7fdf7083eb96] > [ssb3:16230] [ 5] Ray(_ZN13RingAllocator5clearEv+0x15) [0x567e65] > [ssb3:16230] [ 6] Ray(_ZN11ComputeCore10destructorEv+0x20) [0x587e90] > [ssb3:16230] [ 7] Ray(_ZN7Machine5startEv+0x1304) [0x46cc84] > [ssb3:16230] [ 8] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a87f] > [ssb3:16230] [ 9] Ray(main+0xc7) [0x465617] > [ssb3:16230] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7fdf707e176d] > [ssb3:16230] [11] Ray() [0x466c21] > [ssb3:16230] *** End of error message *** > [ssb3:16225] *** Process received signal *** > [ssb3:16225] Signal: Aborted (6) > [ssb3:16225] Signal code: (-6) > *** glibc detected *** Ray: free(): invalid next size (normal): > 0x000000000274a7d0 *** > ======= Backtrace: ========= > /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7f2c1c36eb96] > [ssb3:16225] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f0d666ffcb0] > [ssb3:16225] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) > [0x7f0d66366425] > [ssb3:16225] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) > [0x7f0d66369b8b] > [ssb3:16225] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x7439e) [0x7f0d663a439e] > [ssb3:16225] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96) [0x7f0d663aeb96] > [ssb3:16225] [ 5] Ray(_ZN13RingAllocator5clearEv+0x15) [0x567e65] > [ssb3:16225] [ 6] Ray(_ZN11ComputeCore10destructorEv+0x20) [0x587e90] > [ssb3:16225] [ 7] Ray(_ZN7Machine5startEv+0x1304) [0x46cc84] > [ssb3:16225] [ 8] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a87f] > [ssb3:16225] [ 9] Ray(main+0xc7) [0x465617] > [ssb3:16225] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f0d6635176d] > [ssb3:16225] [11] Ray() [0x466c21] > [ssb3:16225] *** End of error message *** > Ray(_ZN11ComputeCore10destructorEv+0x20)[0x587e90] > Ray(_ZN7Machine5startEv+0x1304)[0x46cc84] > [ssb3:16214] *** Process received signal *** > [ssb3:16214] Signal: Aborted (6) > [ssb3:16214] Signal code: (-6) > Ray(_ZN11RankProcessI7MachineE3runEv+0x9f)[0x46a87f] > Ray(main+0xc7)[0x465617] > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f2c1c31176d] > Ray[0x466c21] > ======= Memory map: ======== > 00400000-005f0000 r-xp 00000000 fc:00 20715372 > /home/bastian/tools/Ray-v2.2.0/Ray > 007ef000-007f0000 r--p 001ef000 fc:00 20715372 > /home/bastian/tools/Ray-v2.2.0/Ray > 007f0000-007f1000 rw-p 001f0000 fc:00 20715372 > /home/bastian/tools/Ray-v2.2.0/Ray > 007f1000-007ff000 rw-p 00000000 00:00 0 > 02035000-04be4000 rw-p 00000000 00:00 0 > [heap] > 7f2c0cb88000-7f2c1178f000 rw-p 00000000 00:00 0 > 7f2c12790000-7f2c16792000 rw-s 00000000 fc:00 35784771 > /tmp/openmpi-sessions-bastian@ssb3_0/33278/1/shared_mem_pool.ssb3 > 7f2c16798000-7f2c167a5000 r-xp 00000000 fc:00 39715023 > /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so > 7f2c167a5000-7f2c169a4000 ---p 0000d000 fc:00 39715023 > /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so > 7f2c169a4000-7f2c169a5000 r--p 0000c000 fc:00 39715023 > /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so > 7f2c169a5000-7f2c169a6000 rw-p 0000d000 fc:00 39715023 > /usr/lib/openmpi/lib/openmpi/mca_osc_rdma.so > 7f2c169a8000-7f2c169b2000 r-xp 00000000 fc:00 39715022 > /usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so > 7f2c169b2000-7f2c16bb1000 ---p 0000a000 fc:00 39715022 > /usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so > 7f2c16bb1000-7f2c16bb2000 r--p 00009000 fc:00 39715022 > /usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so > 7f2c16bb2000-7f2c16bb3000 rw-p 0000a000 fc:00 39715022 > /usr/lib/openmpi/lib/openmpi/mca_osc_pt2pt.so > 7f2c16bb8000-7f2c16bcf000 r-xp 00000000 fc:00 39714996 > /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so > 7f2c16bcf000-7f2c16dce000 ---p 00017000 fc:00 39714996 > /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so > 7f2c16dce000-7f2c16dcf000 r--p 00016000 fc:00 39714996 > /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so > 7f2c16dcf000-7f2c16dd0000 rw-p 00017000 fc:00 39714996 > /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so > 7f2c16dd0000-7f2c16dd3000 r-xp 00000000 fc:00 39714995 > /usr/lib/openmpi/lib/openmpi/mca_coll_sync.so > 7f2c16dd3000-7f2c16fd2000 ---p 00003000 fc:00 39714995 > /usr/lib/openmpi/lib/openmpi/mca_coll_sync.so > 7f2c16fd2000-7f2c16fd3000 r--p 00002000 fc:00 39714995 > /usr/lib/openmpi/lib/openmpi/mca_coll_sync.so > 7f2c16fd3000-7f2c16fd4000 rw-p 00003000 fc:00 39714995 > /usr/lib/openmpi/lib/openmpi/mca_coll_sync.so > 7f2c16fd8000-7f2c16fdd000 r-xp 00000000 fc:00 39714994 > /usr/lib/openmpi/lib/openmpi/mca_coll_sm.so > 7f2c16fdd000-7f2c171dc000 ---p 00005000 fc:00 39714994 > /usr/lib/openmpi/lib/openmpi/mca_coll_sm.so > 7f2c171dc000-7f2c171dd000 r--p 00004000 fc:00 39714994 > /usr/lib/openmpi/lib/openmpi/mca_coll_sm.so > 7f2c171dd000-7f2c171de000 rw-p 00005000 fc:00 39714994 > /usr/lib/openmpi/lib/openmpi/mca_coll_sm.so > 7f2c171e0000-7f2c171e2000 r-xp 00000000 fc:00 39714993 > [ssb3:16214] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7fab2f6d7cb0] > [ssb3:16214] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) > [0x7fab2f33e425] > [ssb3:16214] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) > [0x7fab2f341b8b] > [ssb3:16214] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x7439e) [0x7fab2f37c39e] > [ssb3:16214] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96) [0x7fab2f386b96] > [ssb3:16214] [ 5] Ray(_ZN13RingAllocator5clearEv+0x15) [0x567e65] > [ssb3:16214] [ 6] Ray(_ZN11ComputeCore10destructorEv+0x20) [0x587e90] > [ssb3:16214] [ 7] Ray(_ZN7Machine5startEv+0x1304) [0x46cc84] > [ssb3:16214] [ 8] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a87f] > [ssb3:16214] [ 9] Ray(main+0xc7) [0x465617] > [ssb3:16214] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7fab2f32976d] > [ssb3:16214] [11] Ray() [0x466c21] > [ssb3:16214] *** End of error message *** > [ssb3:16224] *** Process received signal *** > [ssb3:16224] Signal: Aborted (6) > [ssb3:16224] Signal code: (-6) > [ssb3:16224] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f2c1c6bfcb0] > [ssb3:16224] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) > [0x7f2c1c326425] > [ssb3:16224] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) > [0x7f2c1c329b8b] > [ssb3:16224] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x7439e) [0x7f2c1c36439e] > [ssb3:16224] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96) [0x7f2c1c36eb96] > [ssb3:16224] [ 5] Ray(_ZN13RingAllocator5clearEv+0x15) [0x567e65] > [ssb3:16224] [ 6] Ray(_ZN11ComputeCore10destructorEv+0x20) [0x587e90] > [ssb3:16224] [ 7] Ray(_ZN7Machine5startEv+0x1304) [0x46cc84] > [ssb3:16224] [ 8] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a87f] > [ssb3:16224] [ 9] Ray(main+0xc7) [0x465617] > [ssb3:16224] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f2c1c31176d] > [ssb3:16224] [11] Ray() [0x466c21] > [ssb3:16224] *** End of error message *** > [ssb3:16215] *** Process received signal *** > [ssb3:16215] Signal: Aborted (6) > [ssb3:16215] Signal code: (-6) > [ssb3:16218] *** Process received signal *** > [ssb3:16218] Signal: Segmentation fault (11) > [ssb3:16218] Signal code: Address not mapped (1) > [ssb3:16218] Failing at address: 0x60 > [ssb3:16229] *** Process received signal *** > [ssb3:16229] Signal: Aborted (6) > [ssb3:16229] Signal code: (-6) > *** glibc detected *** Ray: double free or corruption (!prev): > 0x00000000017fd7d0 *** > ======= Backtrace: ========= > [ssb3:16219] *** Process received signal *** > [ssb3:16219] Signal: Aborted (6) > [ssb3:16219] Signal code: (-6) > Ray([ssb3:16215] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7fdfad0ffcb0] > [ssb3:16215] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) > [0x7fdfacd66425] > [ssb3:16215] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) > [0x7fdfacd69b8b] > [ssb3:16215] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x7439e) [0x7fdfacda439e] > [ssb3:16215] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96) [0x7fdfacdaeb96] > [ssb3:16215] [ 5] Ray(_ZN13RingAllocator5clearEv+0x15) [0x567e65] > [ssb3:16215] [ 6] Ray(_ZN11ComputeCore10destructorEv+0x20) [0x587e90] > [ssb3:16215] [ 7] Ray(_ZN7Machine5startEv+0x1304) [0x46cc84] > [ssb3:16215] [ 8] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a87f] > [ssb3:16215] [ 9] Ray(main+0xc7) [0x465617] > [ssb3:16215] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7fdfacd5176d] > [ssb3:16215] [11] Ray() [0x466c21] > [ssb3:16215] *** End of error message *** > [ssb3:16232] *** Process received signal *** > [ssb3:16232] Signal: Aborted (6) > [ssb3:16232] Signal code: (-6) > Ray[ssb3:16229] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f9f89b3fcb0] > [ssb3:16229] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) > [0x7f9f897a6425] > [ssb3:16229] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) > [0x7f9f897a9b8b] > [ssb3:16229] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x7439e) [0x7f9f897e439e] > [ssb3:16229] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96) [0x7f9f897eeb96] > [ssb3:16229] [ 5] Ray(_ZN13RingAllocator5clearEv+0x15) [0x567e65] > [ssb3:16229] [ 6] Ray(_ZN11ComputeCore10destructorEv+0x20) [0x587e90] > [ssb3:16229] [ 7] Ray(_ZN7Machine5startEv+0x1304) [0x46cc84] > [ssb3:16229] [ 8] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a87f] > [ssb3:16229] [ 9] Ray(main+0xc7) [0x465617] > [ssb3:16229] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f9f8979176d] > [ssb3:16229] [11] Ray() [0x466c21] > [ssb3:16229] *** End of error message *** > [ssb3:16222] *** Process received signal *** > [ssb3:16222] Signal: Aborted (6) > [ssb3:16222] Signal code: (-6) > *** glibc detected *** Ray: free(): invalid next size (normal): > 0x0000000001f4f7d0 *** > [ssb3:16216] *** Process received signal *** > [ssb3:16216] Signal: Aborted (6) > [ssb3:16216] Signal code: (-6) > Ray(_ZN13RingAllocator5clearEv+0x15)[0x567e65] > [ssb3:16219] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f2b1f337cb0] > [ssb3:16219] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) > [0x7f2b1ef9e425] > [ssb3:16219] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) > [0x7f2b1efa1b8b] > [ssb3:16219] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x7439e) [0x7f2b1efdc39e] > [ssb3:16219] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96) [0x7f2b1efe6b96] > [ssb3:16219] [ 5] Ray(_ZN13RingAllocator5clearEv+0x15) [0x567e65] > [ssb3:16219] [ 6] Ray(_ZN11ComputeCore10destructorEv+0x20) [0x587e90] > [ssb3:16219] [ 7] Ray(_ZN7Machine5startEv+0x1304) [0x46cc84] > [ssb3:16219] [ 8] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a87f] > [ssb3:16219] [ 9] Ray(main+0xc7) [0x465617] > [ssb3:16219] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f2b1ef8976d] > [ssb3:16219] [11] Ray() [0x466c21] > [ssb3:16219] *** End of error message *** > [ssb3:16232] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f6111fdfcb0] > [ssb3:16232] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) > [0x7f6111c46425] > [ssb3:16232] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) > [0x7f6111c49b8b] > [ssb3:16232] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x7439e) [0x7f6111c8439e] > [ssb3:16232] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96) [0x7f6111c8eb96] > [ssb3:16232] [ 5] Ray(_ZN13RingAllocator5clearEv+0x15) [0x567e65] > [ssb3:16232] [ 6] Ray(_ZN11ComputeCore10destructorEv+0x20) [0x587e90] > [ssb3:16232] [ 7] Ray(_ZN7Machine5startEv+0x1304) [0x46cc84] > [ssb3:16232] [ 8] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a87f] > [ssb3:16232] [ 9] Ray(main+0xc7) [0x465617] > [ssb3:16232] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f6111c3176d] > [ssb3:16232] [11] Ray() [0x466c21] > [ssb3:16232] *** End of error message *** > *** glibc detected *** Ray: free(): invalid next size (normal): > 0x00000000023227d0 *** > [ssb3:16222] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f3aab52fcb0] > [ssb3:16222] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) > [0x7f3aab196425] > [ssb3:16222] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) > [0x7f3aab199b8b] > [ssb3:16222] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x7439e) [0x7f3aab1d439e] > [ssb3:16222] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96) [0x7f3aab1deb96] > [ssb3:16222] [ 5] Ray(_ZN13RingAllocator5clearEv+0x15) [0x567e65] > [ssb3:16222] [ 6] Ray(_ZN11ComputeCore10destructorEv+0x20) [0x587e90] > [ssb3:16222] [ 7] Ray(_ZN7Machine5startEv+0x1304) [0x46cc84] > [ssb3:16222] [ 8] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a87f] > [ssb3:16222] [ 9] Ray(main+0xc7) [0x465617] > [ssb3:16222] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f3aab18176d] > [ssb3:16222] [11] Ray() [0x466c21] > [ssb3:16222] *** End of error message *** > [ssb3:16216] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f42b3f7fcb0] > [ssb3:16216] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) > [0x7f42b3be6425] > [ssb3:16216] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) > [0x7f42b3be9b8b] > [ssb3:16216] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x7439e) [0x7f42b3c2439e] > [ssb3:16216] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96) [0x7f42b3c2eb96] > [ssb3:16216] [ 5] Ray(_ZN13RingAllocator5clearEv+0x15) [0x567e65] > [ssb3:16216] [ 6] Ray(_ZN11ComputeCore10destructorEv+0x20) [0x587e90] > [ssb3:16216] [ 7] Ray(_ZN7Machine5startEv+0x1304) [0x46cc84] > [ssb3:16216] [ 8] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a87f] > [ssb3:16216] [ 9] Ray(main+0xc7) [0x465617] > [ssb3:16216] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f42b3bd176d] > [ssb3:16216] [11] Ray() [0x466c21] > [ssb3:16216] *** End of error message *** > Ray[ssb3:16227] *** Process received signal *** > [ssb3:16227] Signal: Aborted (6) > [ssb3:16227] Signal code: (-6) > Ray(_ZN7Machine5startEv+0x1304)[0x46cc84] > Ray(_ZN11RankProcessI7MachineE3runEv+0x9f)[0x46a87f] > Ray(main+0xc7)[0x465617] > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f90edd5176d] > Ray[0x466c21] > ======= Memory map: ======== > *** glibc detected *** Ray: free(): invalid next size (normal): > 0x0000000001ef87d0 *** > ======= Backtrace: ========= > /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7f56f3feeb96] > Ray(_ZN13RingAllocator5clearEv+0x15)[0x567e65] > Ray(_ZN11ComputeCore10destructorEv+0x20)[0x587e90] > Ray(_ZN7Machine5startEv+0x1304)[0x46cc84] > Ray(_ZN11RankProcessI7MachineE3runEv+0x9f)[0x46a87f] > [ssb3:16228] *** Process received signal *** > [ssb3:16228] Signal: Aborted (6) > [ssb3:16228] Signal code: (-6) > [ssb3:16228] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f90ee0ffcb0] > [ssb3:16228] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) > [0x7f90edd66425] > [ssb3:16228] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) > [0x7f90edd69b8b] > [ssb3:16228] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x7439e) [0x7f90edda439e] > [ssb3:16228] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96) [0x7f90eddaeb96] > [ssb3:16228] [ 5] Ray(_ZN13RingAllocator5clearEv+0x15) [0x567e65] > [ssb3:16228] [ 6] Ray(_ZN11ComputeCore10destructorEv+0x20) [0x587e90] > [ssb3:16228] [ 7] Ray(_ZN7Machine5startEv+0x1304) [0x46cc84] > [ssb3:16228] [ 8] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a87f] > [ssb3:16228] [ 9] Ray(main+0xc7) [0x465617] > [ssb3:16228] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f90edd5176d] > [ssb3:16228] [11] Ray() [0x466c21] > [ssb3:16228] *** End of error message *** > [ssb3:16231] *** Process received signal *** > [ssb3:16231] Signal: Aborted (6) > [ssb3:16231] Signal code: (-6) > [ssb3:16231] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f56f433fcb0] > [ssb3:16231] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) > [0x7f56f3fa6425] > [ssb3:16231] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) > [0x7f56f3fa9b8b] > [ssb3:16231] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x7439e) [0x7f56f3fe439e] > [ssb3:16231] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96) [0x7f56f3feeb96] > [ssb3:16231] [ 5] Ray(_ZN13RingAllocator5clearEv+0x15) [0x567e65] > [ssb3:16231] [ 6] Ray(_ZN11ComputeCore10destructorEv+0x20) [0x587e90] > [ssb3:16231] [ 7] Ray(_ZN7Machine5startEv+0x1304) [0x46cc84] > [ssb3:16231] [ 8] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a87f] > [ssb3:16231] [ 9] Ray(main+0xc7) [0x465617] > [ssb3:16231] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f56f3f9176d] > [ssb3:16231] [11] Ray() [0x466c21] > [ssb3:16231] *** End of error message *** > [ssb3:16227] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f6855ac7cb0] > [ssb3:16227] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) > [0x7f685572e425] > [ssb3:16227] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x17b) > [0x7f6855731b8b] > [ssb3:16227] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x7439e) [0x7f685576c39e] > [ssb3:16227] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96) [0x7f6855776b96] > [ssb3:16227] [ 5] Ray(_ZN13RingAllocator5clearEv+0x15) [0x567e65] > [ssb3:16227] [ 6] Ray(_ZN11ComputeCore10destructorEv+0x20) [0x587e90] > [ssb3:16227] [ 7] Ray(_ZN7Machine5startEv+0x1304) [0x46cc84] > [ssb3:16227] [ 8] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a87f] > [ssb3:16227] [ 9] Ray(main+0xc7) [0x465617] > [ssb3:16227] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f685571976d] > [ssb3:16227] [11] Ray() [0x466c21] > [ssb3:16227] *** End of error message *** > -------------------------------------------------------------------------- > mpiexec noticed that process rank 2 with PID 16216 on node ssb3 exited on > signal 6 (Aborted). > -------------------------------------------------------------------------- > > That also happens when I only load the scaffolds in. > I also get that it seems to be...er...somehow a problem with the memory > allocation, but have no real idea how. > Does anyone have a clue? > > Already thanks in advance, > > Bastian > > > ------------------------------------------------------------------------------ > LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! > 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, 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BEST VALUE: New Multi-Library Power Pack includes > Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. > http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk > _______________________________________________ > Denovoassembler-users mailing list > Denovoassembler-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > ------------------------------------------------------------------------------ LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users ------------------------------------------------------------------------------ LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
