DASedit segfault
diriano opened this issue · 1 comments
diriano commented
Dear Dr. Myers,
I have run the scrubber pipeline (DASqv -v -c80; DAStrim -v -g22 -b28; DASpatch -v ; DASedit -v), on data that was previously processed with DAMAPPER as per the instructions in your blog.
DASedit is dying as reported in this post (issue #4 ). I have run lldb and below you find the backtrace (bt command). I am using the latest code from github.
I have run, to the same exact results, on two different servers with linux: CenOS 7.4.1708 and Red Hat 6.5. The RH server is a SGI machine with 1.7TB RAM and 280 cores.
Any hints on what could be happening?
Thanks a lot in advance.
$ lldb
(lldb) file /data/SCRUBBING_Software/bin/DASedit
(lldb) run -v reads/Vintermedia_DB scrubbed_reads/Vintermedia_CleanDBb
Process 14562 launched: '/data/SCRUBBING_Software/bin/DASedit' (x86_64)
Process 14562 stopped
* thread #1: tid = 14562, 0x00007fb100a399c3 libc.so.6`__GI___mempcpy + 147, name = 'DASedit', stop reason = invalid address (fault address: 0x0)
frame #0: 0x00007fb100a399c3 libc.so.6`__GI___mempcpy + 147
libc.so.6`__GI___mempcpy + 147:
-> 0x7fb100a399c3: movb %al, (%rdi)
0x7fb100a399c5: incl %ecx
0x7fb100a399c7: leaq 0x1(%rsi), %rsi
0x7fb100a399cb: leaq 0x1(%rdi), %rdi
(lldb) bt
* thread #1: tid = 14562, 0x00007fb100a399c3 libc.so.6`__GI___mempcpy + 147, name = 'DASedit', stop reason = invalid address (fault address: 0x0)
* frame #0: 0x00007fb100a399c3 libc.so.6`__GI___mempcpy + 147
frame #1: 0x00007fb100a2642e libc.so.6`_IO_file_xsgetn + 382
frame #2: 0x00007fb100a1ba7f libc.so.6`__GI__IO_fread + 143
frame #3: 0x00000000004194ec DASedit`Load_Subread(db=<unavailable>, i=<unavailable>, beg=3941, end=<unavailable>, read=0x0038efd800487b7c, ascii=0) + 172 at DB.c:1721
frame #4: 0x0000000000402775 DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb1012661a4, depth=<unavailable>) + 101 at DASedit.c:133
frame #5: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb1012653b0, depth=<unavailable>) + 282 at DASedit.c:146
frame #6: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb101264575, depth=<unavailable>) + 282 at DASedit.c:146
frame #7: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb101263781, depth=<unavailable>) + 282 at DASedit.c:146
frame #8: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb101262946, depth=<unavailable>) + 282 at DASedit.c:146
frame #9: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb101261b52, depth=<unavailable>) + 282 at DASedit.c:146
frame #10: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb101260d17, depth=<unavailable>) + 282 at DASedit.c:146
frame #11: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb10125ff23, depth=<unavailable>) + 282 at DASedit.c:146
frame #12: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb10125f0e8, depth=<unavailable>) + 282 at DASedit.c:146
frame #13: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb10125e2f4, depth=<unavailable>) + 282 at DASedit.c:146
frame #14: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb10125d4b9, depth=<unavailable>) + 282 at DASedit.c:146
frame #15: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb10125c6c5, depth=<unavailable>) + 282 at DASedit.c:146
frame #16: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb10125b88a, depth=<unavailable>) + 282 at DASedit.c:146
frame #17: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb10125aa96, depth=<unavailable>) + 282 at DASedit.c:146
frame #18: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb101259c5b, depth=<unavailable>) + 282 at DASedit.c:146
frame #19: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb101258e67, depth=<unavailable>) + 282 at DASedit.c:146
frame #20: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb10125802c, depth=<unavailable>) + 282 at DASedit.c:146
frame #21: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb101257238, depth=<unavailable>) + 282 at DASedit.c:146
frame #22: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb1012563fd, depth=<unavailable>) + 282 at DASedit.c:146
frame #23: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb101255609, depth=<unavailable>) + 282 at DASedit.c:146
frame #24: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb1012547ce, depth=<unavailable>) + 282 at DASedit.c:146
frame #25: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb1012539da, depth=<unavailable>) + 282 at DASedit.c:146
frame #26: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb101252b9f, depth=<unavailable>) + 282 at DASedit.c:146
frame #27: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb101251dab, depth=<unavailable>) + 282 at DASedit.c:146
frame #28: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb101250f70, depth=<unavailable>) + 282 at DASedit.c:146
frame #29: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb10125017c, depth=<unavailable>) + 282 at DASedit.c:146
frame #30: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb10124f341, depth=<unavailable>) + 282 at DASedit.c:146
frame #31: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb10124e54d, depth=<unavailable>) + 282 at DASedit.c:146
frame #32: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb10124d712, depth=<unavailable>) + 282 at DASedit.c:146
frame #33: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb10124c91e, depth=<unavailable>) + 282 at DASedit.c:146
frame #34: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb10124bae3, depth=<unavailable>) + 282 at DASedit.c:146
frame #35: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb10124acef, depth=<unavailable>) + 282 at DASedit.c:146
frame #36: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb101249eb4, depth=<unavailable>) + 282 at DASedit.c:146
frame #37: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb1012490c0, depth=<unavailable>) + 282 at DASedit.c:146
frame #38: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb101248285, depth=<unavailable>) + 282 at DASedit.c:146
frame #39: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb101247491, depth=<unavailable>) + 282 at DASedit.c:146
frame #40: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb101246656, depth=<unavailable>) + 282 at DASedit.c:146
frame #41: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb101245862, depth=<unavailable>) + 282 at DASedit.c:146
frame #42: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb101244a27, depth=<unavailable>) + 282 at DASedit.c:146
frame #43: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb101243c33, depth=<unavailable>) + 282 at DASedit.c:146
frame #44: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb101242df8, depth=<unavailable>) + 282 at DASedit.c:146
frame #45: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb101242004, depth=<unavailable>) + 282 at DASedit.c:146
frame #46: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb1012411c9, depth=<unavailable>) + 282 at DASedit.c:146
frame #47: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb1012403d5, depth=<unavailable>) + 282 at DASedit.c:146
frame #48: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb10123f59a, depth=<unavailable>) + 282 at DASedit.c:146
frame #49: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb10123e7a6, depth=<unavailable>) + 282 at DASedit.c:146
frame #50: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb10123d96b, depth=<unavailable>) + 282 at DASedit.c:146
frame #51: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb10123cb77, depth=<unavailable>) + 282 at DASedit.c:146
frame #52: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb10123bd3c, depth=<unavailable>) + 282 at DASedit.c:146
frame #53: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb10123af48, depth=<unavailable>) + 282 at DASedit.c:146
frame #54: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb10123a10d, depth=<unavailable>) + 282 at DASedit.c:146
frame #55: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb101239319, depth=<unavailable>) + 282 at DASedit.c:146
frame #56: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb1012384de, depth=<unavailable>) + 282 at DASedit.c:146
frame #57: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb1012376ea, depth=<unavailable>) + 282 at DASedit.c:146
frame #58: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb1012368af, depth=<unavailable>) + 282 at DASedit.c:146
frame #59: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb101235abb, depth=<unavailable>) + 282 at DASedit.c:146
frame #60: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb101234c80, depth=<unavailable>) + 282 at DASedit.c:146
frame #61: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb101233e8c, depth=<unavailable>) + 282 at DASedit.c:146
frame #62: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0ec0034b0, target=0x00007fb101233051, depth=<unavailable>) + 282 at DASedit.c:146
frame #63: 0x000000000040282a DASedit`Load_Model(patch=0x00007fb0e6e4e9dc, target=0x00007fb10123225d, depth=<unavailable>) + 282 at DASedit.c:146
frame #64: 0x0000000000401f01 DASedit`main(argc=<unavailable>, argv=<unavailable>) + 3745 at DASedit.c:570
frame #65: 0x00007fb1009d1c05 libc.so.6`__libc_start_main + 245
diriano commented
I am closing the issue. It appears that it happened due to a hardware problem. I replaced two memory slots and now the pipeline runs to completion.