What compiler version are you using? This implies that the pgl_malloc inline function is not being compiled to the expected code; there is an existing non-inlined version that is used for very old gcc versions, but it looks like it may also be needed here.
On Fri, Feb 18, 2022 at 11:40 AM Andreas Tille <andr...@an3as.eu> wrote: > Hi again, > > I applied this patch and now I get: > > (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 4060797)] > [New Thread 0x7fffec4c6640 (LWP 4060798)] > [New Thread 0x7fffebcc5640 (LWP 4060799)] > 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 19:06:45 2022 > 31998 MiB RAM detected; reserving 15999 MiB for main workspace. > Using up to 4 compute threads. > [New Thread 0x7ffff7fc5640 (LWP 4060800)] > sizeof(PhenoCol): 40 pheno_cols: 0 > --debug: setting pheno_cols[0].nonmiss. = nullptr > > Thread 1 "plink2-sse2" received signal SIGSEGV, Segmentation fault. > 0x00005555556fb82e in plink2::LoadPsam (psamname=psamname@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=0x7fffffff8790, > founder_info_ptr=0x7fffffff87a8, sex_nm_ptr=0x7fffffff8798, > sex_male_ptr=0x7fffffff87a0, pheno_cols_ptr=0x7fffffff8770, > pheno_names_ptr=0x7fffffff8780, raw_sample_ct_ptr=0x7fffffff8728, > pheno_ct_ptr=0x7fffffff8720, > max_pheno_name_blen_ptr=0x7fffffff87b0) at ../plink2_psam.cc:615 > warning: Source file is more recent than executable. > 615 pheno_cols[pheno_idx].nonmiss = nullptr; > > Kind regards > > Andreas. > > Am Fri, Feb 18, 2022 at 08:45:12AM -0800 schrieb 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 <andr...@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@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@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 > > > > > -- > http://fam-tille.de >
