Re: Kmc might cause iva autopkgtest fail on arm64 (possibly memory issue?)
Hi Sascha,
On Mon, Nov 16, 2020 at 04:19:23PM +0100, Sascha Steinbiss wrote:
> Hi,
>
> > run_kmc.sh: line 2: 5046 Segmentation fault kmc -fa -m4 -k95 -sf1 -ci25 -cs1000000 -cx1000000 /tmp/tmp.GkQzyocbDU/test/iva.out/tmp.common_kmers.8oo5afnl/reads.fa kmc_out $PWD > /dev/null
> [...]
> > There are more Segmentation faults in connection with kmc later.
> > I think a Segmentation fault is just not good. Is anybody up for
> > this issue?
>
> This is on ARM, and tests on amd64 are OK... could this just be a RAM
> issue on the test box? I very vaguely remember that kmc needs quite a
> bit of RAM, which I'm not sure all of the ARM CI boxes have?
> Just guessing.
Its not only on arm, its also on i386[2]:
The following command failed with exit code 1
/usr/bin/iva --threads 1 --trimmomatic /usr/share/java/trimmomatic.jar --pcr_primers hiv_pcr_primers.fa -f reads_1.fq.gz -r reads_2.fq.gz iva.out
The output was:
The following command failed with exit code 134
bash run_kmc.sh
The output was:
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
run_kmc.sh: line 2: 5740 Aborted kmc -fa -m4 -k95 -sf1 -ci25 -cs1000000 -cx1000000 /tmp/tmp.m0F6lCZm21/test/iva.out/tmp.common_kmers.40prfn0y/reads.fa kmc_out $PWD > /dev/null
Running iva in test mode...
The logs for armhf[3] and ppc64el are showing the same error message
text as on arm64. So kmc seems to do a reliable job on amd64 only. No
idea how we can verify the "needs more RAM" idea or whether we should
simply restrict kmc to amd64. In any case it would be great if the code
would check for free memory first before running into a Segfault.
Kind regards
Andreas.
[1] https://ci.debian.net/data/autopkgtest/unstable/arm64/i/iva/8016157/log.gz
[2] https://ci.debian.net/data/autopkgtest/testing/i386/i/iva/8172852/log.gz
[3] https://ci.debian.net/data/autopkgtest/unstable/armhf/i/iva/7142297/log.gz
[4] https://ci.debian.net/data/autopkgtest/testing/ppc64el/i/iva/8176309/log.gz
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