dstreett
commented
7 years ago Hi @cogillsb, Thank you for using my software. :)
SD has been reprogrammed and is bundled into a suite of software here - https://github.com/ibest/HTStream. Would you mind re-running it with this up to date software? It is the same algorithm, however, it is a lot faster, has unit test, and cleaner overall code.
Currently, I'm working on documentation to help users but that isn't quite ready yet. So, if you have any questions, please feel free to submit an issue and I can help with installation.
Again, thanks for your interest in the software! Let me know how if you run into any issues getting HTStream and SD working.
Hi David,
I am trying to implement super_deduper in a microbial pipeline, but I keep getting intermittent errors. The most recent one I have posted in the title. The full trace is shown below. Any help you could provide would be greatly appreciated!
glibc detected super_deduper: realloc(): invalid next size: 0x0000000000cb6890 *** ======= Backtrace: ========= /lib64/libc.so.6[0x3c1b275f3e] /lib64/libc.so.6[0x3c1b27be1a] /lib64/libc.so.6(realloc+0x158)[0x3c1b27c058] super_deduper[0x401f85] super_deduper[0x40254e] super_deduper[0x402406] super_deduper[0x402668] super_deduper[0x404aec] super_deduper[0x404f4d] /lib64/libc.so.6(__libc_start_main+0xfd)[0x3c1b21ed1d] super_deduper[0x401019] ======= Memory map: ======== 00400000-00408000 r-xp 00000000 00:15 75956256 /srv/gsfs0/software/super-deduper/1.4/super_deduper 00607000-00608000 rw-p 00007000 00:15 75956256 /srv/gsfs0/software/super-deduper/1.4/super_deduper 00ca4000-00cd6000 rw-p 00000000 00:00 0 [heap] 3c1ae00000-3c1ae20000 r-xp 00000000 08:01 8781848 /lib64/ld-2.12.so 3c1b01f000-3c1b020000 r--p 0001f000 08:01 8781848 /lib64/ld-2.12.so 3c1b020000-3c1b021000 rw-p 00020000 08:01 8781848 /lib64/ld-2.12.so 3c1b021000-3c1b022000 rw-p 00000000 00:00 0 3c1b200000-3c1b38a000 r-xp 00000000 08:01 8781850 /lib64/libc-2.12.so 3c1b38a000-3c1b58a000 ---p 0018a000 08:01 8781850 /lib64/libc-2.12.so 3c1b58a000-3c1b58e000 r--p 0018a000 08:01 8781850 /lib64/libc-2.12.so 3c1b58e000-3c1b590000 rw-p 0018e000 08:01 8781850 /lib64/libc-2.12.so 3c1b590000-3c1b594000 rw-p 00000000 00:00 0 3c1be00000-3c1be83000 r-xp 00000000 08:01 8781864 /lib64/libm-2.12.so 3c1be83000-3c1c082000 ---p 00083000 08:01 8781864 /lib64/libm-2.12.so 3c1c082000-3c1c083000 r--p 00082000 08:01 8781864 /lib64/libm-2.12.so 3c1c083000-3c1c084000 rw-p 00083000 08:01 8781864 /lib64/libm-2.12.so 3c1c600000-3c1c615000 r-xp 00000000 08:01 8781966 /lib64/libz.so.1.2.3 3c1c615000-3c1c814000 ---p 00015000 08:01 8781966 /lib64/libz.so.1.2.3 3c1c814000-3c1c815000 r--p 00014000 08:01 8781966 /lib64/libz.so.1.2.3 3c1c815000-3c1c816000 rw-p 00015000 08:01 8781966 /lib64/libz.so.1.2.3 2b0b64cf0000-2b0b64cf1000 rw-p 00000000 00:00 0 2b0b64cfe000-2b0b64cff000 rw-p 00000000 00:00 0 2b0b64cff000-2b0b64e7c000 r-xp 00000000 00:15 73079182 /srv/gsfs0/software/gnu/gcc/5.2.0/lib64/libstdc++.so.6.0.21 2b0b64e7c000-2b0b6507c000 ---p 0017d000 00:15 73079182 /srv/gsfs0/software/gnu/gcc/5.2.0/lib64/libstdc++.so.6.0.21 2b0b6507c000-2b0b65086000 r--p 0017d000 00:15 73079182 /srv/gsfs0/software/gnu/gcc/5.2.0/lib64/libstdc++.so.6.0.21 2b0b65086000-2b0b65088000 rw-p 00187000 00:15 73079182 /srv/gsfs0/software/gnu/gcc/5.2.0/lib64/libstdc++.so.6.0.21 2b0b65088000-2b0b6508c000 rw-p 00000000 00:00 0 2b0b6508c000-2b0b650a2000 r-xp 00000000 00:15 72592589 /srv/gsfs0/software/gnu/gcc/5.2.0/lib64/libgcc_s.so.1 2b0b650a2000-2b0b652a1000 ---p 00016000 00:15 72592589 /srv/gsfs0/software/gnu/gcc/5.2.0/lib64/libgcc_s.so.1 2b0b652a1000-2b0b652a2000 rw-p 00015000 00:15 72592589 /srv/gsfs0/software/gnu/gcc/5.2.0/lib64/libgcc_s.so.1 2b0b652a2000-2b0b653a8000 rw-p 00000000 00:00 0 2b0b68000000-2b0b68021000 rw-p 00000000 00:00 0 2b0b68021000-2b0b6c000000 ---p 00000000 00:00 0 7fff6eea8000-7fff6eebe000 rw-p 00000000 00:00 0 [stack] 7fff6eed2000-7fff6eed3000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]