[Debian-med-packaging] Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)

[Chris Chang]

Ok, I don't know why that particular line would fail, but I've added
another debug-print before it on GitHub.

On Fri, Feb 18, 2022 at 4:24 AM Andreas Tille <andreas at fam-tille.de> wrote:

> Hi Chris,
>
> Am Thu, Feb 17, 2022 at 07:13:49PM -0800 schrieb Chris Chang:
> > I was unable to replicate this issue on a Debian EC2 instance.  However,
> > there are very few things that happen between printing "End time:" and
> > program exit, so I have added a bunch of debug-prints (active when the
> > --debug flag is passed in) to the latest GitHub commit that should reveal
> > which of those few things is triggering the segfault; let me know if you
> > are able to run this build.
>
> I think the issue is a bit more complex.  Debian provides a wrapper
> which calls the best / most performant plink2.  The issue seems to
> occure for SFX=avx.  First I do:
>
>
>    /usr/lib/plink2/plink2-avx --debug --dummy 33 65537 0.1 dosage-freq=0.1
> --out tmp_data
>
> This works.  In the next step I fire up gdb then which results in
>
>
> (gdb) run
> Starting program: /usr/lib/plink2/plink2-avx --debug --pfile tmp_data
> --export vcf vcf-dosage=DS --out tmp_data2
> [Thread debugging using libthread_db enabled]
> Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
> [New Thread 0x7ffff4cc7640 (LWP 2931408)]
> [New Thread 0x7ffff44c6640 (LWP 2931409)]
> [New Thread 0x7fffebcc5640 (LWP 2931411)]
> PLINK v2.00a3 SSE4.2 (29 Jan 2022)
> www.cog-genomics.org/plink/2.0/
> (C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public
> License v3
> Logging to tmp_data2.log.
> Options in effect:
>   --debug
>   --export vcf vcf-dosage=DS
>   --out tmp_data2
>   --pfile tmp_data
>
> Start time: Fri Feb 18 11:58:49 2022
> 31998 MiB RAM detected; reserving 15999 MiB for main workspace.
> Using up to 4 compute threads.
> [New Thread 0x7ffff7fc5640 (LWP 2931412)]
>
> Thread 1 "plink2-avx" received signal SIGSEGV, Segmentation fault.
> plink2::LoadPsam (psamname=psamname at entry=0x7fffffffbe70 "tmp_data.psam",
> pheno_range_list_ptr=<optimized out>, fam_cols=..., pheno_ct_max=<optimized
> out>,
>     missing_pheno=<optimized out>, affection_01=0, max_thread_ct=4,
> piip=0x7fffffff8880, sample_include_ptr=0x7fffffff87a0,
> founder_info_ptr=0x7fffffff87b8, sex_nm_ptr=0x7fffffff87a8,
>     sex_male_ptr=0x7fffffff87b0, pheno_cols_ptr=0x7fffffff8780,
> pheno_names_ptr=0x7fffffff8790, raw_sample_ct_ptr=0x7fffffff8738,
> pheno_ct_ptr=0x7fffffff8730,
>     max_pheno_name_blen_ptr=0x7fffffff87c0) at ../plink2_psam.cc:611
> warning: Source file is more recent than executable.
> 611             pheno_cols[pheno_idx].nonmiss = nullptr;
>
>
> I also added some more debug lines in a patch[1].
>
> It seems that there is actually the weak part of the code since the
> output turns to
>
> ...
> Start time: Fri Feb 18 13:19:13 2022
> 31998 MiB RAM detected; reserving 15999 MiB for main workspace.
> Using up to 4 compute threads.
> [New Thread 0x7ffff7fc5640 (LWP 3957711)]
> --debug: setting pheno_cols[0].nonmiss. = nullptr
>
> Thread 1 "plink2-sse2" received signal SIGSEGV, Segmentation fault.
> 0x00005555556fb6ff in plink2::LoadPsam (psamname=psamname at entry=0x7fffffffbe70
> "tmp_data.psam", pheno_range_list_ptr=<optimized out>, fam_cols=...,
> pheno_ct_max=<optimized out>,
>     missing_pheno=<optimized out>, affection_01=0, max_thread_ct=4,
> piip=0x7fffffff8880, sample_include_ptr=0x7fffffff87a0,
> founder_info_ptr=0x7fffffff87b8, sex_nm_ptr=0x7fffffff87a8,
>     sex_male_ptr=0x7fffffff87b0, pheno_cols_ptr=0x7fffffff8780,
> pheno_names_ptr=0x7fffffff8790, raw_sample_ct_ptr=0x7fffffff8738,
> pheno_ct_ptr=0x7fffffff8730,
>     max_pheno_name_blen_ptr=0x7fffffff87c0) at ../plink2_psam.cc:614
> warning: Source file is more recent than executable.
> 614             pheno_cols[pheno_idx].nonmiss = nullptr;
>
>
> I hope this might help a bit to track down the issue
>
>     Andreas.
>
>
>
> [1]
> https://salsa.debian.org/med-team/plink2/-/blob/master/debian/patches/debug2.patch
>
> --
> http://fam-tille.de
>
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