On Mon, Nov 16, 2020 at 09:53:05PM +0530, Nilesh Patra wrote: > > > 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.
Thanks for checking. Once you have access to such a porter box, would you mind running it via strace or gdb to get some more information? Kind regards Andreas. -- http://fam-tille.de
