On Mon, 16 Nov 2020 at 21:28, Andreas Tille <[email protected]> wrote:
> 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]:
>
JTFR, I tried running the tests on a arm64 porter box, and I get the
failure within a few seconds:
$ /bin/bash test-example
Running iva in test mode...
Copied input test files into here: /tmp/tmp.3MwLHzYtUY/test
Current working directory: /tmp/tmp.3MwLHzYtUY/test
Running iva on the test data with the command:
/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 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 139
bash run_kmc.sh
The output was:
run_kmc.sh: line 2: 10022 Segmentation fault kmc -fa -m4 -k95 -sf1
-ci25 -cs1000000 -cx1000000
/tmp/tmp.3MwLHzYtUY/test/iva.out/tmp.common_kmers.zu2h8c0q/reads.fa kmc_out
$PWD > /dev/null
On checking the ram consumption:
$ free -h
total used free shared buff/cache
available
Mem: 11Gi 622Mi 281Mi 60Mi 10Gi
10Gi
Swap: 15Gi 82Mi 15Gi
Looking at this, it does not _feel_ like a RAM issue - maybe it is
something else.
Nilesh
