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 <ti...@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.patr...@orange.fr> > Subject: Bug#951280: ncbi-blast+: runtime trap with at least blastn and > makeblastdb > To: Debian Bug Tracking System <sub...@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@entry=86, db_length=db_length@entry=86, > db_num_seqs=db_num_seqs@entry=1, > length_adjustment=length_adjustment@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
