mothur

dist.shared on linux subsystem and windows 10 seg fault


#1

Hi Pat and Sarah

everyone on windows is getting seg fault when running dist.shared

 dist.shared(shared=dec17ws.trim.contigs.good.unique.good.filter.precluster.pick.pick.opti_mcc.shared, calc = braycurtis-jest-thetayc, subsample = 5000)

The computers running mothur 1.39.5 for linux on the linux subsystem for windows 10

Using 1 processors.
deep.water.wm2.BlitzH2O51 contains 10. Eliminating.
0.03
Segmentation fault (core dumped)

The windows executable just crashed with no error.

People on Macs using the same files had no problem.

thanks
Kendra


#2

Actually a couple students on linux subsystem got this type of error

mothur > dist.shared(shared=dec17ws.trim.contigs.good.unique.good.filter.precluster.pick.pick.opti_mcc.shared, calc = braycurtis - jest - thetayc, subsample = 5000, iters = 100)

Using 1 processors.
deep.water.wm2.BlitzH2O51 contains 10. Eliminating.
0.03
*** Error in `../mothur/mothur': free(): invalid next size (normal): 0x000000000210fc20 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fe3881977e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7fe3881a037a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7fe3881a453c]
../mothur/mothur[0x1159d43]
../mothur/mothur[0x11986ec]
../mothur/mothur[0x508f3e]
../mothur/mothur[0xbd8e08]
../mothur/mothur[0xbdc3f9]
../mothur/mothur[0x44f479]
../mothur/mothur[0x409b69]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fe388140830]
../mothur/mothur[0x40f4f1]
======= Memory map: ========
00400000-01446000 r-xp 00000000 00:00 120120                     /mnt/c/Users/Mark/Documents/UCONN/Microbiome/mothur/mothur
01645000-01648000 rw-p 01045000 00:00 120120                     /mnt/c/Users/Mark/Documents/UCONN/Microbiome/mothur/mothur
01648000-0164a000 rw-p 00000000 00:00 0
01f6e000-029d9000 rw-p 00000000 00:00 0                          [heap]
7fe380000000-7fe380021000 rw-p 00000000 00:00 0
7fe380021000-7fe384000000 ---p 00000000 00:00 0
7fe387530000-7fe3875b1000 rw-p 00000000 00:00 0
7fe3875c0000-7fe387641000 rw-p 00000000 00:00 0
7fe387650000-7fe3876d1000 rw-p 00000000 00:00 0
7fe3876e0000-7fe387761000 rw-p 00000000 00:00 0
7fe387770000-7fe3877f1000 rw-p 00000000 00:00 0
7fe387800000-7fe387881000 rw-p 00000000 00:00 0
7fe387890000-7fe387911000 rw-p 00000000 00:00 0
7fe387920000-7fe3879a1000 rw-p 00000000 00:00 0
7fe3879b0000-7fe387a31000 rw-p 00000000 00:00 0
7fe387a40000-7fe387ac1000 rw-p 00000000 00:00 0
7fe387b60000-7fe387be1000 rw-p 00000000 00:00 0
7fe387bf0000-7fe387c71000 rw-p 00000000 00:00 0
7fe387c80000-7fe387d01000 rw-p 00000000 00:00 0
7fe387d10000-7fe387d91000 rw-p 00000000 00:00 0
7fe387da0000-7fe387e21000 rw-p 00000000 00:00 0
7fe387e30000-7fe387e71000 rw-p 00000000 00:00 0
7fe387ef0000-7fe387f15000 r-xp 00000000 00:00 59474              /lib/x86_64-linux-gnu/libtinfo.so.5.9
7fe387f15000-7fe387f19000 ---p 00025000 00:00 59474              /lib/x86_64-linux-gnu/libtinfo.so.5.9
7fe387f19000-7fe388114000 ---p 00029000 00:00 59474              /lib/x86_64-linux-gnu/libtinfo.so.5.9
7fe388114000-7fe388118000 r--p 00024000 00:00 59474              /lib/x86_64-linux-gnu/libtinfo.so.5.9
7fe388118000-7fe388119000 rw-p 00028000 00:00 59474              /lib/x86_64-linux-gnu/libtinfo.so.5.9
7fe388120000-7fe3882e0000 r-xp 00000000 00:00 59436              /lib/x86_64-linux-gnu/libc-2.23.so
7fe3882e0000-7fe3882e9000 ---p 001c0000 00:00 59436              /lib/x86_64-linux-gnu/libc-2.23.so
7fe3882e9000-7fe3884e0000 ---p 001c9000 00:00 59436              /lib/x86_64-linux-gnu/libc-2.23.so
7fe3884e0000-7fe3884e4000 r--p 001c0000 00:00 59436              /lib/x86_64-linux-gnu/libc-2.23.so
7fe3884e4000-7fe3884e6000 rw-p 001c4000 00:00 59436              /lib/x86_64-linux-gnu/libc-2.23.so
7fe3884e6000-7fe3884ea000 rw-p 00000000 00:00 0
7fe3884f0000-7fe388506000 r-xp 00000000 00:00 59547              /lib/x86_64-linux-gnu/libgcc_s.so.1
7fe388506000-7fe388705000 ---p 00016000 00:00 59547              /lib/x86_64-linux-gnu/libgcc_s.so.1
7fe388705000-7fe388706000 rw-p 00015000 00:00 59547              /lib/x86_64-linux-gnu/libgcc_s.so.1
7fe388710000-7fe388818000 r-xp 00000000 00:00 59604              /lib/x86_64-linux-gnu/libm-2.23.so
7fe388818000-7fe38881a000 ---p 00108000 00:00 59604              /lib/x86_64-linux-gnu/libm-2.23.so
7fe38881a000-7fe388a17000 ---p 0010a000 00:00 59604              /lib/x86_64-linux-gnu/libm-2.23.so
7fe388a17000-7fe388a18000 r--p 00107000 00:00 59604              /lib/x86_64-linux-gnu/libm-2.23.so
7fe388a18000-7fe388a19000 rw-p 00108000 00:00 59604              /lib/x86_64-linux-gnu/libm-2.23.so
7fe388a20000-7fe388b92000 r-xp 00000000 00:00 86585              /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fe388b92000-7fe388b9f000 ---p 00172000 00:00 86585              /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fe388b9f000-7fe388d92000 ---p 0017f000 00:00 86585              /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fe388d92000-7fe388d9c000 r--p 00172000 00:00 86585              /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fe388d9c000-7fe388d9e000 rw-p 0017c000 00:00 86585              /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fe388d9e000-7fe388da2000 rw-p 00000000 00:00 0
7fe388db0000-7fe388ded000 r-xp 00000000 00:00 59438              /lib/x86_64-linux-gnu/libreadline.so.6.3
7fe388ded000-7fe388df5000 ---p 0003d000 00:00 59438              /lib/x86_64-linux-gnu/libreadline.so.6.3
7fe388df5000-7fe388fed000 ---p 00045000 00:00 59438              /lib/x86_64-linux-gnu/libreadline.so.6.3
7fe388fed000-7fe388fef000 r--p 0003d000 00:00 59438              /lib/x86_64-linux-gnu/libreadline.so.6.3
7fe388fef000-7fe388ff5000 rw-p 0003f000 00:00 59438              /lib/x86_64-linux-gnu/libreadline.so.6.3
7fe388ff5000-7fe388ff6000 rw-p 00000000 00:00 0
7fe389000000-7fe389026000 r-xp 00000000 00:00 59421              /lib/x86_64-linux-gnu/ld-2.23.so
7fe389040000-7fe389081000 rw-p 00000000 00:00 0
7fe389088000-7fe389220000 r--p 00000000 00:00 89881              /usr/lib/locale/locale-archive
7fe389220000-7fe389221000 rw-p 00000000 00:00 0
7fe389225000-7fe389226000 r--p 00025000 00:00 59421              /lib/x86_64-linux-gnu/ld-2.23.so
7fe389226000-7fe389227000 rw-p 00026000 00:00 59421              /lib/x86_64-linux-gnu/ld-2.23.so
7fe389227000-7fe389228000 rw-p 00000000 00:00 0
7fe389230000-7fe389232000 rw-p 00000000 00:00 0
7fe389240000-7fe389241000 rw-p 00000000 00:00 0
7fe389250000-7fe389251000 rw-p 00000000 00:00 0
7fe389260000-7fe389261000 rw-p 00000000 00:00 0
7fe389270000-7fe389272000 rw-p 00000000 00:00 0
7fe389277000-7fe38927e000 r--s 00000000 00:00 87567              /usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache
7fffda3c5000-7fffdabc5000 rw-p 00000000 00:00 0                  [stack]
7fffdb286000-7fffdb287000 r-xp 00000000 00:00 0                  [vdso]
Aborted (core dumped)

#3

Thanks for reporting this bug. In version 1.39, we compiled using c++11 features. The change effected how some systems handle mothur’s threading functions, causing unexpected behavior. The 1.40.0 release has been delayed so we can correct this issue.