On Fri, Feb 26, 2021 at 09:58:11PM +0200, Juhani Numminen wrote: > > 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.
Hmmm, its a schame that we need a boost code copy - but well, if this is the only solution that is possible for now we should go that route. > 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 > > [email protected] > > 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) > I'd recommend forwarding this in another issue. Spades upstream is very quick in responding and supportive as we have seen. Kind regards Andreas. -- http://fam-tille.de
