[Debian-med-packaging] Bug#951280: [duroux.patrice at orange.fr: Bug#951280: ncbi-blast+: runtime trap with at least blastn and makeblastdb]
Aaron M. Ucko
ucko at debian.org
Thu Feb 13 18:45:46 GMT 2020
Hi, Andreas (and Olivier).
I saw this latest report, thanks, just wasn't able to comment
immediately. Configuring ncbi-blast+ with the additional flag
--without-sse42 should address Patrice's error.
The other report (which I'd missed earlier, sorry) comes down to a
discrepancy between where different NCBI source bases look for
systemwide configuration files. ncbi-data, which ships .ncbirc, places
it in /etc/ncbi per the expectations of the C Toolkit from which it
originates (ncbi-tools6), whereas C++ code (namely ncbi-blast+) looks
directly in /etc. I suppose ncbi-data can and should gain /etc/.ncbirc
as a symlink to /etc/ncbi/.ncbirc.
I should be able to take care of both tweaks over the weekend.
-- Aaron
Andreas Tille <tille at debian.org> writes:
> Hi Aaron & Olivier,
>
> could you please have a look into this as well as
>
> https://lists.debian.org/debian-med/2020/01/msg00095.html
>
> (which probably should also be reported as bug).
>
> Both should be probably of higher severity since it affects usability
> of the program.
>
> Kind regards
>
> Andreas.
>
> From: Patrice DUROUX <duroux.patrice at orange.fr>
> Subject: Bug#951280: ncbi-blast+: runtime trap with at least blastn and makeblastdb
> To: Debian Bug Tracking System <submit at bugs.debian.org>
> Date: Thu, 13 Feb 2020 18:42:20 +0100 (55 minutes, 37 seconds ago)
> X-Debian-PR-Message: report 951280
> X-Debian-PR-Package: ncbi-blast+
> X-Debian-PR-Keywords:
> X-Debian-PR-Source: ncbi-blast+
>
> Package: ncbi-blast+
> Version: 2.8.1-1
> Severity: important
>
> Dear Maintainer,
>
> * What led up to the situation?
>
> Running commands like one of the following:
>
> blastn -query test.fasta -subject test.fasta
>
> makeblastdb -dbtype nucl -in test.fasta
>
> * What was the outcome of this action?
>
> A runtime trap with a message 'Instruction non permise'
> (sorry for the french message, got the same in a LANG=C env)
>
> Here are extracts from dmesg:
>
> [16975777.040241] traps: blastn[16028] trap invalid opcode ip:7f5c96a4598c sp:7ffece18a380 error:0 in libblast.so[7f5c96a04000+66000]
> [16976213.970602] traps: makeblastdb[17484] trap invalid opcode ip:7fca6c0bfb02 sp:7ffe3fae78a0 error:0 in libxutil.so[7fca6c08c000+83000]
>
> and here is the output got using gdb and ncbi-blast+-dbgsym:
>
> gdb --args blastn -query test.fasta -subject test.fasta
> GNU gdb (Debian 8.2.1-2+b3) 8.2.1
> Copyright (C) 2018 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law.
> Type "show copying" and "show warranty" for details.
> This GDB was configured as "x86_64-linux-gnu".
> Type "show configuration" for configuration details.
> For bug reporting instructions, please see:
> <http://www.gnu.org/software/gdb/bugs/>.
> Find the GDB manual and other documentation resources online at:
> <http://www.gnu.org/software/gdb/documentation/>.
>
> For help, type "help".
> Type "apropos word" to search for commands related to "word"...
> Reading symbols from blastn...Reading symbols from /usr/lib/debug/.build-id/00/382f3290f9ed8c1cace9c6e03d714c031cbd3d.debug...done.
> done.
> (gdb) go
> Command requires an argument.
> (gdb) run
> Starting program: /usr/bin/blastn -query test.fasta -subject test.fasta
>
> [Thread debugging using libthread_db enabled]
> Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
> BLASTN 2.8.1+
>
> Program received signal SIGILL, Illegal instruction.
> 0x00007ffff7afe98c in BLAST_ComputeLengthAdjustment (K=<optimized out>, logK=-0.77652878949899629, alpha_d_lambda=1.171875, beta=-2,
> query_length=query_length at entry=86, db_length=db_length at entry=86, db_num_seqs=db_num_seqs at entry=1, length_adjustment=length_adjustment at entry=0x7fffffffcf84)
> at ./c++/src/algo/blast/core/blast_stat.c:5093
> 5093 ./c++/src/algo/blast/core/blast_stat.c: No such file or directory.
> (gdb)
>
> The CPU info of the hardware used to run the commands is:
>
> # lscpu
> Architecture: x86_64
> CPU op-mode(s): 32-bit, 64-bit
> Byte Order: Little Endian
> Address sizes: 40 bits physical, 48 bits virtual
> CPU(s): 16
> On-line CPU(s) list: 0-15
> Thread(s) per core: 2
> Core(s) per socket: 2
> Socket(s): 4
> NUMA node(s): 1
> Vendor ID: GenuineIntel
> CPU family: 15
> Model: 6
> Model name: Intel(R) Xeon(TM) CPU 3.40GHz
> Stepping: 8
> CPU MHz: 3391.598
> BogoMIPS: 6783.19
> Virtualization: VT-x
> L1d cache: 16K
> L2 cache: 1024K
> L3 cache: 16384K
> NUMA node0 CPU(s): 0-15
> Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc pebs bts nopl cpuid pni dtes64 monitor ds_cpl vmx est tm2 cid cx16 xtpr pdcm lahf_lm pti tpr_shadow vnmi
>
> I hope that is enough information to be helpful.
>
> Thanks,
> Patrice
>
> -- System Information:
> Debian Release: 10.3
> APT prefers stable-updates
> APT policy: (500, 'stable-updates'), (500, 'stable-debug'), (500, 'stable')
> Architecture: amd64 (x86_64)
>
> Kernel: Linux 4.19.0-5-amd64 (SMP w/16 CPU cores)
> Locale: LANG=C, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE=C (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> Init: systemd (via /run/systemd/system)
> LSM: AppArmor: enabled
>
> Versions of packages ncbi-blast+ depends on:
> ii libbz2-1.0 1.0.6-9.2~deb10u1
> ii libc6 2.28-10
> ii libgcc1 1:8.3.0-6
> ii libgomp1 8.3.0-6
> ii liblmdb0 0.9.22-1
> ii libmbedcrypto3 2.16.0-1
> ii libmbedtls12 2.16.0-1
> ii libpcre3 2:8.39-12
> ii libstdc++6 8.3.0-6
> ii ncbi-data 6.1.20170106+dfsg1-0+deb10u2
> ii perl 5.28.1-6
> ii python 2.7.16-1
> ii zlib1g 1:1.2.11.dfsg-1
>
> ncbi-blast+ recommends no packages.
>
> ncbi-blast+ suggests no packages.
>
> -- no debconf information
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