Re: Urgent: Spades Update before freeze

[Juhani Numminen <juhaninumminen0@gmail.com>]

Andreas Tille kirjoitti 26.2.2021 klo 17.14:
> Hi,
>
> there was an answer to the opened issue here:
>
>     https://github.com/ablab/spades/issues/671#issuecomment-786692020
>
> I'm not really sure how this relates to the problem Juhani has
> described and unfortunately I'm currently lacking the time to
> work on this (due to real life things that weekend).

Thanks for opening the issue. With the info given in that comment,
the previous problem is fixed by using spades's local boost.

Now when I run the self-tests, I get an Illegal Instruction error.

> $ metaspades --test
>
...
>
> == Error ==  system call for: "['/usr/libexec/spades/spades-hammer', '/home/juhani/Projektit/deb/spades/spades/spades_test/corrected/configs/config.info']" finished abnormally, OS return value: -4
>
> In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru
> or report an issue on our GitHub repository github.com/ablab/spades
> Please provide us with params.txt and spades.log files from the output directory.
>
> SPAdes log can be found here: /home/juhani/Projektit/deb/spades/spades/spades_test/spades.log

Here's a GDB session.

> $ gdb /usr/libexec/spades/spades-hammer
...
> (gdb) r /home/juhani/Projektit/deb/spades/spades/spades_test/corrected/configs/config.info
...

  0:00:00.333     1M / 83M   INFO   K-mer Counting           (kmer_data.cpp             : 309)   Filtering singleton k-mers
  0:00:00.336     1M / 83M   INFO   K-mer Counting           (kmer_data.cpp             : 315)   Processing /usr/share/spades/test_dataset/ecoli_1K_1.fq.gz
Thread 3 "spades-hammer" received signal SIGILL, Illegal instruction.
[Switching to Thread 0x7ffff7221700 (LWP 17206)]
offset_lower_bound (qf=0x7fffffffb760, qf=0x7fffffffb760, slot_index=2699) at ./assembler/ext/src/gqf/gqf.c:496
warning: Source file is more recent than executable.
496			return popcnt(occupieds) - popcnt(runends);
(gdb) bt
#0  offset_lower_bound (qf=0x7fffffffb760, qf=0x7fffffffb760, slot_index=2699) at ./assembler/ext/src/gqf/gqf.c:496
#1  is_empty (slot_index=2699, qf=0x7fffffffb760) at ./assembler/ext/src/gqf/gqf.c:503
#2  insert1 (qf=0x7fffffffb760, hash=<optimized out>, lock=lock@entry=true, spin=<optimized out>) at ./assembler/ext/src/gqf/gqf.c:1032
#3  0x00005555555ec218 in qf_insert (qf=qf@entry=0x7fffffffb760, key=<optimized out>, value=value@entry=0, count=count@entry=1, lock=lock@entry=true, spin=spin@entry=true) at ./assembler/ext/src/gqf/gqf.c:1629
#4  0x00005555555a6f7f in qf::cqf::add (spin=true, lock=true, count=1, d=<optimized out>, this=0x7fffffffb760) at ./assembler/src/common/adt/cqf.hpp:44
#5  qf::cqf_with_hasher<Seq<21ul, unsigned long> >::add (spin=true, lock=true, count=1, o=..., this=0x7fffffffb760) at ./assembler/src/common/adt/cqf.hpp:131
#6  KMerMultiplicityCounter::operator() (this=0x7fffffffb760, r=std::unique_ptr<Read> = {...}) at ./assembler/src/projects/hammer/kmer_data.cpp:215
#7  0x000055555559c397 in hammer::ReadProcessor::_ZN6hammer13ReadProcessor3RunI11ireadstream23KMerMultiplicityCounterEEbRT_RT0_._omp_fn.0(void) () at /usr/include/c++/10/bits/unique_ptr.h:172
#8  0x00007ffff7c27de6 in ?? () from /usr/lib/x86_64-linux-gnu/libgomp.so.1
#9  0x00007ffff7f67ea7 in start_thread (arg=<optimized out>) at pthread_create.c:477
#10 0x00007ffff7b2adef in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:95
(gdb)