[med-svn] [Git][med-team/plink2][master] Attempt to track down SIGSEGV

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / plink2


Commits:
f01ba65b by Andreas Tille at 2022-02-18T13:21:34+01:00
Attempt to track down SIGSEGV

- - - - -


2 changed files:

- + debian/patches/debug2.patch
- debian/patches/series


Changes:

=====================================
debian/patches/debug2.patch
=====================================
@@ -0,0 +1,47 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 18 Feb 2022 13:20:18 +0100
+Description: Attempt to track down SIGSEGV
+
+(gdb) run
+Starting program: /usr/lib/plink2/plink2-sse2 --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 3957708)]
+[New Thread 0x7ffff44c6640 (LWP 3957709)]
+[New Thread 0x7fffe3cc5640 (LWP 3957710)]
+PLINK v2.00a3 64-bit (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 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;
+
+
+--- a/plink2_psam.cc
++++ b/plink2_psam.cc
+@@ -608,6 +608,9 @@ PglErr LoadPsam(const char* psamname, co
+       }
+       for (uint32_t pheno_idx = 0; pheno_idx != pheno_ct; ++pheno_idx) {
+         // ensure cleanup works if initialization fails in the middle
++        if (g_debug_on) {
++          fprintf(stdout, "--debug: setting pheno_cols[%d].nonmiss. = nullptr\n", pheno_idx); fflush(stdout);
++        }
+         pheno_cols[pheno_idx].nonmiss = nullptr;
+       }
+       uint32_t cat_pheno_idx = 0;


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ Fix_Makefile.patch
 use_packaged_libdeflate.patch
 baseline
 debug.patch
+debug2.patch



View it on GitLab: https://salsa.debian.org/med-team/plink2/-/commit/f01ba65b332a116f195a4488ca320cf55b399ab7

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View it on GitLab: https://salsa.debian.org/med-team/plink2/-/commit/f01ba65b332a116f195a4488ca320cf55b399ab7
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