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Re: Help requested for htslib build failure on ppc64el

Hi Michael!

On 01/09/2019 06:08 PM, Michael Crusoe wrote:

https://buildd.debian.org/status/package.php?p=htslib&suite=experimental

http://metadata.ftp-master.debian.org/changelogs/main/h/htslib/htslib_1.9-9~floatingpoint0_changelog <http://metadata.ftp-master.debian.org/changelogs/main/h/htslib/htslib_1.9-9%7Efloatingpoint0_changelog>

Seems to work after all! Maybe a qemu bug?


Maybe, if host was amd64, etc... but hard to say with reproducing it and hunting.
I wonder if it's easy to trigger a build with -O3, just out of curiosity, to check it's gone.
btw, I didn't know you were using experimental instead of sid, but I suspected... :)

Thank you.

Best regards,
Gustavo


--
Michael R. Crusoe
Co-founder & Lead,
Common Workflow Language project
https://impactstory.org/u/0000-0002-2961-9670
mrc@commonwl.org <mailto:mrc@commonwl.org>

În mie., 9 ian. 2019, 19:38 Gustavo Romero <gromero@linux.vnet.ibm.com <mailto:gromero@linux.vnet.ibm.com> a scris:

    Ping.

    On 01/04/2019 08:01 PM, Gustavo Romero wrote:
     > Hi Michael,
     >
     > Thanks for the diff and the additional information on the failure.
     >
     > Since I could not reproduce the issue locally, would you mind to point a buildd machine (I tried the buildd logs for htslib without success) where it fails, please?
     >
     > Thank you.
     >
     > Regards,
     > Gustavo
     >
     > On 01/02/2019 02:41 PM, Michael Crusoe wrote:
     >>
     >>
     >> În mie., 2 ian. 2019 la 15:27, Gustavo Romero <gromero@linux.vnet.ibm.com <mailto:gromero@linux.vnet.ibm.com> <mailto:gromero@linux.vnet.ibm.com <mailto:gromero@linux.vnet.ibm.com>>> a scris:
     >>
     >>     Hello Michael,
     >>
     >>     On 12/31/2018 02:50 PM, Michael Crusoe wrote:
     >>      > În lun., 31 dec. 2018 la 06:42, Gustavo Romero <gromero@linux.vnet.ibm.com <mailto:gromero@linux.vnet.ibm.com> <mailto:gromero@linux.vnet.ibm.com <mailto:gromero@linux.vnet.ibm.com>> <mailto:gromero@linux.vnet.ibm.com <mailto:gromero@linux.vnet.ibm.com> <mailto:gromero@linux.vnet.ibm.com <mailto:gromero@linux.vnet.ibm.com>>>> a scris:
     >>      >     diff --git a/sam.c b/sam.c
     >>      >     index aa94776..23233a0 100644
     >>      >     --- a/sam.c
     >>      >     +++ b/sam.c
     >>      >     @@ -1408,7 +1408,7 @@ int sam_parse1(kstring_t *s, bam_hdr_t *h, bam1_t *b)
     >>      >                    else if (type == 'S') while (q + 1 < p) { u16_to_le(strtoul(q + 1, &q, 0), (uint8_t *) str.s + str.l); str.l += 2; _skip_to_comma(q, p); }
     >>      >                    else if (type == 'i') while (q + 1 < p) { i32_to_le(strtol(q + 1, &q, 0), (uint8_t *) str.s + str.l); str.l += 4; _skip_to_comma(q, p); }
     >>      >                    else if (type == 'I') while (q + 1 < p) { u32_to_le(strtoul(q + 1, &q, 0), (uint8_t *) str.s + str.l); str.l += 4; _skip_to_comma(q, p); }
     >>      >     -            else if (type == 'f') while (q + 1 < p) { float_to_le(strtod(q + 1, &q), (uint8_t *) str.s + str.l); str.l += 4; _skip_to_comma(q, p); }
     >>      >     +            else if (type == 'f') while (q + 1 < p) { float_to_le(strtof(q + 1, &q), (uint8_t *) str.s + str.l); str.l += 4; _skip_to_comma(q, p); }
     >>      >                    else _parse_err_param(1, "unrecognized type B:%c", type);
     >>      >
     >>      >        #undef _skip_to_comma
     >>      >
     >>      >
     >>      > Applying this patch and compiling under a qemu-based sid-ppc64el builder gets us to only a single test failure (yay!)
     >>      >
     >>      > ===
     >>      > test_vcf_various:
     >>      >          /build/htslib-1.9/htsfile -c /build/htslib-1.9/test/formatcols.vcf
     >>      >          The outputs differ:
     >>      >                  /build/htslib-1.9/test/formatcols.vcf
     >>      >                  /build/htslib-1.9/test/formatcols.vcf.new
     >>      > .. failed ...
     >>      > ===
     >>
     >>     Thanks for testing it!
     >>
     >>     hmm right... I'm not able to reproduce that failure on my setup.
     >>
     >>
     >> I've added the patch our git repo, so maybe try again by upcommenting it at https://salsa.debian.org/med-team/htslib/blob/master/debian/patches/series ;?
     >>
     >>
     >>     Could you share the differences when it fails? I think a 'diff -u formatcols.vcf formatcols.vcf.new' suffices.
     >>
     >> root@mrcdev:/build/htslib-1.9# diff -u /build/htslib-1.9/test/formatmissing-out.vcf /build/htslib-1.9/test/formatmissing-out.vcf.new
     >> --- /build/htslib-1.9/test/formatmissing-out.vcf        2018-07-18 08:33:10.000000000 +0000
     >> +++ /build/htslib-1.9/test/formatmissing-out.vcf.new    2019-01-02 16:14:27.000000000 +0000
     >> @@ -3,4 +3,4 @@
     >>   ##contig=<ID=1>
     >>   ##FORMAT=<ID=S,Number=1,Type=String,Description="Text">
     >>   #CHROM POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  S1      S2      S3
     >> -1      100     a       A       T       .       .       .       .       .       .       .
     >> +1      100     a       A       T       3.40282e+38     .       .       .       .       .       .
     >>
     >> root@mrcdev:/build/htslib-1.9# diff -u /build/htslib-1.9/test/formatcols.vcf /build/htslib-1.9/test/formatcols.vcf.new
     >> --- /build/htslib-1.9/test/formatcols.vcf       2018-07-18 08:33:10.000000000 +0000
     >> +++ /build/htslib-1.9/test/formatcols.vcf.new   2019-01-02 16:14:27.000000000 +0000
     >> @@ -3,4 +3,4 @@
     >>   ##contig=<ID=1>
     >>   ##FORMAT=<ID=S,Number=1,Type=String,Description="Text">
     >>   #CHROM POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  S1      S2      S3
     >> -1      100     a       A       T       .       .       .       S       a       bbbbbbb ccccccccc
     >> +1      100     a       A       T       3.40282e+38     .       .       S       a       bbbbbbb ccccccccc
     >>
     >>      > In the meantime, to unclog a chain of packages that have been held back from migrating to testing, I've uploaded a version of the package that uses -O0 for ppc64el only; which I agree is not ideal.
     >>      >
     >>      > If you think this is a qemu-only test failure then I can upload a build to experimental so that real hardware is used (I don't have porter box access)
     >>
     >>     I don't know... but all debugging / testing at my side is on a ppc64el VM (qemu/kvm-only so), so probably not a VM vs baremetal issue.
     >>
     >>     Did you check if the same error happens on x86_64 when that patch is applied? Or it's still ppc64el-specific?
     >>
     >>
     >> amd64 builds just fine with the patch
     >>
     >>     Cheers,
     >>     Gustavo
     >>      >
     >>      >     Cheers,
     >>      >     Gustavo
     >>      >
     >>      >      > Cheers,
     >>      >      >
     >>      >      > Steffen
     >>      >      >
     >>      >      > On 27.12.18 15:41, Michael Crusoe wrote:
     >>      >      >> https://buildd.debian.org/status/fetch.php?pkg=htslib&arch=ppc64el&ver=1.9-7&stamp=1545236716&raw=0
     >>      >      >>
     >>      >      >> Can I get some assistance here? Rebuilding using Qemu and the earlier source packages produces the same error, so maybe this is a regression in the compiler?
     >>      >      >>
     >>      >      >> --
     >>      >      >> Michael R. Crusoe
     >>      >      >> Co-founder & Lead, Common Workflow Language project <http://www.commonwl.org/>
     >>      >      >> Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania
     >>      >      >> https://orcid.org/0000-0002-2961-9670 <https://impactstory.org/u/0000-0002-2961-9670>
     >>      >      >> mrc@commonwl.org <mailto:mrc@commonwl.org> <mailto:mrc@commonwl.org <mailto:mrc@commonwl.org>> <mailto:mrc@commonwl.org <mailto:mrc@commonwl.org> <mailto:mrc@commonwl.org <mailto:mrc@commonwl.org>>> <mailto:mrc@commonwl.org <mailto:mrc@commonwl.org> <mailto:mrc@commonwl.org <mailto:mrc@commonwl.org>> <mailto:mrc@commonwl.org <mailto:mrc@commonwl.org> <mailto:mrc@commonwl.org <mailto:mrc@commonwl.org>>>>
     >>      >      >> +1 480 627 9108 / +370 653 11125
     >>      >      >
     >>      >
     >>      >
     >>      >
     >>      > --
     >>      > Michael R. Crusoe
     >>      > Co-founder & Lead, Common Workflow Language project <http://www.commonwl.org/>
     >>      > Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania
     >>      > https://orcid.org/0000-0002-2961-9670 <https://impactstory.org/u/0000-0002-2961-9670>
     >>      > mrc@commonwl.org <mailto:mrc@commonwl.org> <mailto:mrc@commonwl.org <mailto:mrc@commonwl.org>> <mailto:mrc@commonwl.org <mailto:mrc@commonwl.org> <mailto:mrc@commonwl.org <mailto:mrc@commonwl.org>>>
     >>      > +1 480 627 9108 / +370 653 11125
     >>
     >>
     >>
     >> --
     >> Michael R. Crusoe
     >> Co-founder & Lead, Common Workflow Language project <http://www.commonwl.org/>
     >> Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania
     >> https://orcid.org/0000-0002-2961-9670 <https://impactstory.org/u/0000-0002-2961-9670>
     >> mrc@commonwl.org <mailto:mrc@commonwl.org> <mailto:mrc@commonwl.org <mailto:mrc@commonwl.org>>
     >> +1 480 627 9108 / +370 653 11125
     >
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