augustus - aborted (core dumped)

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psb21
Posts: 2
Joined: Thu Dec 01, 2016 2:25 am

augustus - aborted (core dumped)

Post by psb21 »

Hello,

I start running several augustus v3.2.2 processes (testing different parameters) providing an additional hintsfile from several sources. After ~4 days running, all of them stop with the same problem (std error log file didn't capture this, as i was running in screen i can only see the information below). Did this ever happened to someone ?

My linux server version is Ubuntu 12.04 LTS and kernel version 3.11.0-26-generic.
Thanks,
Pedro Barbosa

7fcf9bcc6000-7fcf9bec5000 ---p 00016000 08:02 666911 /usr/local/lib/libz.so.1.2.8
7fcf9bec5000-7fcf9bec6000 r--p 00015000 08:02 666911 /usr/local/lib/libz.so.1.2.8
7fcf9bec6000-7fcf9bec7000 rw-p 00016000 08:02 666911 /usr/local/lib/libz.so.1.2.8
7fcf9bec8000-7fcf9bed7000 r-xp 00000000 08:02 2097157 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7fcf9bed7000-7fcf9c0d6000 ---p 0000f000 08:02 2097157 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7fcf9c0d6000-7fcf9c0d7000 r--p 0000e000 08:02 2097157 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7fcf9c0d7000-7fcf9c0d8000 rw-p 0000f000 08:02 2097157 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7fcf9c0d8000-7fcf9c0f0000 r-xp 00000000 08:02 2110523 /lib/x86_64-linux-gnu/libpthread-2.21.so
7fcf9c0f0000-7fcf9c2f0000 ---p 00018000 08:02 2110523 /lib/x86_64-linux-gnu/libpthread-2.21.so
7fcf9c2f0000-7fcf9c2f1000 r--p 00018000 08:02 2110523 /lib/x86_64-linux-gnu/libpthread-2.21.so
7fcf9c2f1000-7fcf9c2f2000 rw-p 00019000 08:02 2110523 /lib/x86_64-linux-gnu/libpthread-2.21.so
7fcf9c2f2000-7fcf9c2f6000 rw-p 00000000 00:00 0
7fcf9c2f8000-7fcf9c4b8000 r-xp 00000000 08:02 2110536 /lib/x86_64-linux-gnu/libc-2.21.so
7fcf9c4b8000-7fcf9c6b8000 ---p 001c0000 08:02 2110536 /lib/x86_64-linux-gnu/libc-2.21.so
7fcf9c6b8000-7fcf9c6bc000 r--p 001c0000 08:02 2110536 /lib/x86_64-linux-gnu/libc-2.21.so
7fcf9c6bc000-7fcf9c6be000 rw-p 001c4000 08:02 2110536 /lib/x86_64-linux-gnu/libc-2.21.so
7fcf9c6be000-7fcf9c6c2000 rw-p 00000000 00:00 0
7fcf9c6c8000-7fcf9c6de000 r-xp 00000000 08:02 2097561 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fcf9c6de000-7fcf9c8dd000 ---p 00016000 08:02 2097561 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fcf9c8dd000-7fcf9c8de000 r--p 00015000 08:02 2097561 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fcf9c8de000-7fcf9c8df000 rw-p 00016000 08:02 2097561 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fcf9c8e0000-7fcf9c9e7000 r-xp 00000000 08:02 2110531 /lib/x86_64-linux-gnu/libm-2.21.so
7fcf9c9e7000-7fcf9cbe6000 ---p 00107000 08:02 2110531 /lib/x86_64-linux-gnu/libm-2.21.so
7fcf9cbe6000-7fcf9cbe7000 r--p 00106000 08:02 2110531 /lib/x86_64-linux-gnu/libm-2.21.so
7fcf9cbe7000-7fcf9cbe8000 rw-p 00107000 08:02 2110531 /lib/x86_64-linux-gnu/libm-2.21.so
7fcf9cbe8000-7fcf9cd55000 r-xp 00000000 08:02 525573 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fcf9cd55000-7fcf9cf55000 ---p 0016d000 08:02 525573 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fcf9cf55000-7fcf9cf5f000 r--p 0016d000 08:02 525573 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fcf9cf5f000-7fcf9cf61000 rw-p 00177000 08:02 525573 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fcf9cf61000-7fcf9cf65000 rw-p 00000000 00:00 0
7fcf9cf68000-7fcf9cf7e000 r-xp 00000000 08:02 681944 /usr/local/lib/libboost_iostreams.so.1.58.0
7fcf9cf7e000-7fcf9d17e000 ---p 00016000 08:02 681944 /usr/local/lib/libboost_iostreams.so.1.58.0
7fcf9d17e000-7fcf9d17f000 r--p 00016000 08:02 681944 /usr/local/lib/libboost_iostreams.so.1.58.0
7fcf9d17f000-7fcf9d180000 rw-p 00017000 08:02 681944 /usr/local/lib/libboost_iostreams.so.1.58.0
7fcf9d180000-7fcf9d1a4000 r-xp 00000000 08:02 2110522 /lib/x86_64-linux-gnu/ld-2.21.so
7fcf9d37d000-7fcf9d380000 rw-p 00000000 00:00 0
7fcf9d3a1000-7fcf9d3a3000 rw-p 00000000 00:00 0
7fcf9d3a3000-7fcf9d3a4000 r--p 00023000 08:02 2110522 /lib/x86_64-linux-gnu/ld-2.21.so
7fcf9d3a4000-7fcf9d3a5000 rw-p 00024000 08:02 2110522 /lib/x86_64-linux-gnu/ld-2.21.so
7fcf9d3a5000-7fcf9d3a7000 rw-p 00000000 00:00 0
7fcf9d3a7000-7fcf9d3ac000 rw-p 00000000 00:00 0
7fffdab0a000-7fffdab2c000 rw-p 00000000 00:00 0 [stack]
7fffdac00000-7fffdac02000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)

real 5111m47.010s
user 5040m4.028s
sys 69m17.702s
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katharina
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Re: augustus - aborted (core dumped)

Post by katharina »

Maybe it has happened, before.

The best thing in such cases is to try to narrow down the problem to a tiny example to give us something to work with. E.g. try to reproduce the error on a single scaffold with a small hints file and a particular extrinsic.cfg file, a particular species parameter set... pack these files, accompanied by the command that causes the crash, reproducibly, and we will try to track the problem.
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