Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)
Just a heads-up, today's release contains a fix for an infinite-loop-instead-of-error bug in the previous release. On Sun, Feb 20, 2022 at 12:36 PM Andreas Tille wrote: > Cool! This finally works. Thanks a lot for your patience, Andreas. > > Am Sun, Feb 20, 2022 at 09:43:10AM -0800 schrieb Chris Chang: > > Hmm. Ordinarily, that download link would be fine. I had not updated it > > this time because the issue only affects gcc 11+, so it did not affect > any > > of the precompiled binaries and I wanted to keep the posted source > > identical to that used to compile those binaries. > > > > On the other hand, the only difference (in the non-gcc-11+ case) between > > the binaries and the updated source is the version date. I guess this is > > insignificant enough that a temporary discordance is less disruptive than > > making you change your packing process, so I've updated the website > source > > link to point to the newer code; let me know if you still run into any > > problems. > > > > On Sat, Feb 19, 2022 at 11:53 PM Andreas Tille wrote: > > > > > Hi Chris, > > > > > > Am Sat, Feb 19, 2022 at 11:37:34PM -0800 schrieb Chris Chang: > > > > To elaborate: when I look at > > > > https://salsa.debian.org/med-team/plink2/-/tree/master , I can see > that > > > > plink2.cc, include/plink2_base.h, and include/plink2_base.cc don't > have > > > the > > > > same contents as the v2.00a3-20220218 GitHub tag/release. So I don't > > > know > > > > where you grabbed the code from this time, but it does not appear to > be > > > > from GitHub. > > > > > > That's true since on Github the source code of plink1.9 and plink2 is > not > > > separated. Thus I download the tarball from > > > > > >https://www.cog-genomics.org/plink/2.0/ > > > > > > which points to > > > > > >https://www.cog-genomics.org/static/bin/plink2_src_220217.zip > > > > > > I confirm that the tag on Github says v2.00a3-20220218 which seems to > be > > > later than 220217. In principle I could point the packaging metadata > to > > > Github and exclude everything that I do not need for plink2 packaging > (so > > > remove 1.9 directory and code copies of libdeflate, simde and zstd in > 2.0) > > > > > > In case you consider this the safer way to download plink2 code I'll > do so. > > > > > > Kind regards and thanks a lot for comparing the code base > > > > > > Andreas. > > > > > > > On Sat, Feb 19, 2022 at 7:54 AM Chris Chang > > > wrote: > > > > > > > > > If you build off the current head, the version string should say > "18 > > > Feb > > > > > 2022", not "17 Feb 2022". > > > > > > > > > > On Sat, Feb 19, 2022 at 7:02 AM Andreas Tille > > > wrote: > > > > > > > > > >> Hi again, > > > > >> > > > > >> Am Sat, Feb 19, 2022 at 12:28:21AM -0800 schrieb Chris Chang: > > > > >> > Ok, new release/tag created. > > > > >> > > > > >> I've built the new version now. The bad news is that it keeps on > > > > >> SEGFAULTing for me: > > > > >> > > > > >> ... > > > > >> (gdb) run > > > > >> Starting program: /usr/lib/plink2/plink2-sse3 --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 0x74cc7640 (LWP 985019)] > > > > >> [New Thread 0x744c6640 (LWP 985020)] > > > > >> [New Thread 0x7fffebcc5640 (LWP 985021)] > > > > >> PLINK v2.00a3 64-bit (17 Feb 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: Sat Feb 19 1
Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)
Hmm. Ordinarily, that download link would be fine. I had not updated it this time because the issue only affects gcc 11+, so it did not affect any of the precompiled binaries and I wanted to keep the posted source identical to that used to compile those binaries. On the other hand, the only difference (in the non-gcc-11+ case) between the binaries and the updated source is the version date. I guess this is insignificant enough that a temporary discordance is less disruptive than making you change your packing process, so I've updated the website source link to point to the newer code; let me know if you still run into any problems. On Sat, Feb 19, 2022 at 11:53 PM Andreas Tille wrote: > Hi Chris, > > Am Sat, Feb 19, 2022 at 11:37:34PM -0800 schrieb Chris Chang: > > To elaborate: when I look at > > https://salsa.debian.org/med-team/plink2/-/tree/master , I can see that > > plink2.cc, include/plink2_base.h, and include/plink2_base.cc don't have > the > > same contents as the v2.00a3-20220218 GitHub tag/release. So I don't > know > > where you grabbed the code from this time, but it does not appear to be > > from GitHub. > > That's true since on Github the source code of plink1.9 and plink2 is not > separated. Thus I download the tarball from > >https://www.cog-genomics.org/plink/2.0/ > > which points to > >https://www.cog-genomics.org/static/bin/plink2_src_220217.zip > > I confirm that the tag on Github says v2.00a3-20220218 which seems to be > later than 220217. In principle I could point the packaging metadata to > Github and exclude everything that I do not need for plink2 packaging (so > remove 1.9 directory and code copies of libdeflate, simde and zstd in 2.0) > > In case you consider this the safer way to download plink2 code I'll do so. > > Kind regards and thanks a lot for comparing the code base > > Andreas. > > > On Sat, Feb 19, 2022 at 7:54 AM Chris Chang > wrote: > > > > > If you build off the current head, the version string should say "18 > Feb > > > 2022", not "17 Feb 2022". > > > > > > On Sat, Feb 19, 2022 at 7:02 AM Andreas Tille > wrote: > > > > > >> Hi again, > > >> > > >> Am Sat, Feb 19, 2022 at 12:28:21AM -0800 schrieb Chris Chang: > > >> > Ok, new release/tag created. > > >> > > >> I've built the new version now. The bad news is that it keeps on > > >> SEGFAULTing for me: > > >> > > >> ... > > >> (gdb) run > > >> Starting program: /usr/lib/plink2/plink2-sse3 --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 0x74cc7640 (LWP 985019)] > > >> [New Thread 0x744c6640 (LWP 985020)] > > >> [New Thread 0x7fffebcc5640 (LWP 985021)] > > >> PLINK v2.00a3 64-bit (17 Feb 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: Sat Feb 19 16:00:00 2022 > > >> 31998 MiB RAM detected; reserving 15999 MiB for main workspace. > > >> Using up to 4 compute threads. > > >> [New Thread 0x77fc5640 (LWP 985022)] > > >> > > >> Thread 1 "plink2-sse3" received signal SIGSEGV, Segmentation fault. > > >> plink2::LoadPsam (psamname=psamname@entry=0x7fffbe60 > > >> "tmp_data.psam", pheno_range_list_ptr=, fam_cols=..., > > >> pheno_ct_max=, > > >> missing_pheno=, affection_01=0, max_thread_ct=4, > > >> piip=0x7fff8870, sample_include_ptr=0x7fff8790, > > >> founder_info_ptr=0x7fff87a8, sex_nm_ptr=0x7fff8798, > > >> sex_male_ptr=0x7fff87a0, pheno_cols_ptr=0x7fff8770, > > >> pheno_names_ptr=0x7fff8780, raw_sample_ct_ptr=0x7fff8728, > > >> pheno_ct_ptr=0x7fff8720, > > >> max_pheno_name_blen_ptr=0x7fff87b0) at ../plink2_psam.cc:611 > > >> 611 pheno_cols[pheno_idx].nonmiss = nullptr; > > >> > > >> > > >> Please let me know if I can do further checks. > > >> > > >> Kind regards > > >> > > >> Andreas. > > >> > > >> -- > > >> http://fam-tille.de > > >> > > > > > -- > http://fam-tille.de >
Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)
To elaborate: when I look at https://salsa.debian.org/med-team/plink2/-/tree/master , I can see that plink2.cc, include/plink2_base.h, and include/plink2_base.cc don't have the same contents as the v2.00a3-20220218 GitHub tag/release. So I don't know where you grabbed the code from this time, but it does not appear to be from GitHub. On Sat, Feb 19, 2022 at 7:54 AM Chris Chang wrote: > If you build off the current head, the version string should say "18 Feb > 2022", not "17 Feb 2022". > > On Sat, Feb 19, 2022 at 7:02 AM Andreas Tille wrote: > >> Hi again, >> >> Am Sat, Feb 19, 2022 at 12:28:21AM -0800 schrieb Chris Chang: >> > Ok, new release/tag created. >> >> I've built the new version now. The bad news is that it keeps on >> SEGFAULTing for me: >> >> ... >> (gdb) run >> Starting program: /usr/lib/plink2/plink2-sse3 --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 0x74cc7640 (LWP 985019)] >> [New Thread 0x744c6640 (LWP 985020)] >> [New Thread 0x7fffebcc5640 (LWP 985021)] >> PLINK v2.00a3 64-bit (17 Feb 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: Sat Feb 19 16:00:00 2022 >> 31998 MiB RAM detected; reserving 15999 MiB for main workspace. >> Using up to 4 compute threads. >> [New Thread 0x77fc5640 (LWP 985022)] >> >> Thread 1 "plink2-sse3" received signal SIGSEGV, Segmentation fault. >> plink2::LoadPsam (psamname=psamname@entry=0x7fffbe60 >> "tmp_data.psam", pheno_range_list_ptr=, fam_cols=..., >> pheno_ct_max=, >> missing_pheno=, affection_01=0, max_thread_ct=4, >> piip=0x7fff8870, sample_include_ptr=0x7fff8790, >> founder_info_ptr=0x7fff87a8, sex_nm_ptr=0x7fff8798, >> sex_male_ptr=0x7fff87a0, pheno_cols_ptr=0x7fff8770, >> pheno_names_ptr=0x7fff8780, raw_sample_ct_ptr=0x7fff8728, >> pheno_ct_ptr=0x7fff8720, >> max_pheno_name_blen_ptr=0x7fff87b0) at ../plink2_psam.cc:611 >> 611 pheno_cols[pheno_idx].nonmiss = nullptr; >> >> >> Please let me know if I can do further checks. >> >> Kind regards >> >> Andreas. >> >> -- >> http://fam-tille.de >> >
Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)
If you build off the current head, the version string should say "18 Feb 2022", not "17 Feb 2022". On Sat, Feb 19, 2022 at 7:02 AM Andreas Tille wrote: > Hi again, > > Am Sat, Feb 19, 2022 at 12:28:21AM -0800 schrieb Chris Chang: > > Ok, new release/tag created. > > I've built the new version now. The bad news is that it keeps on > SEGFAULTing for me: > > ... > (gdb) run > Starting program: /usr/lib/plink2/plink2-sse3 --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 0x74cc7640 (LWP 985019)] > [New Thread 0x744c6640 (LWP 985020)] > [New Thread 0x7fffebcc5640 (LWP 985021)] > PLINK v2.00a3 64-bit (17 Feb 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: Sat Feb 19 16:00:00 2022 > 31998 MiB RAM detected; reserving 15999 MiB for main workspace. > Using up to 4 compute threads. > [New Thread 0x77fc5640 (LWP 985022)] > > Thread 1 "plink2-sse3" received signal SIGSEGV, Segmentation fault. > plink2::LoadPsam (psamname=psamname@entry=0x7fffbe60 "tmp_data.psam", > pheno_range_list_ptr=, fam_cols=..., pheno_ct_max= out>, > missing_pheno=, affection_01=0, max_thread_ct=4, > piip=0x7fff8870, sample_include_ptr=0x7fff8790, > founder_info_ptr=0x7fff87a8, sex_nm_ptr=0x7fff8798, > sex_male_ptr=0x7fff87a0, pheno_cols_ptr=0x7fff8770, > pheno_names_ptr=0x7fff8780, raw_sample_ct_ptr=0x7fff8728, > pheno_ct_ptr=0x7fff8720, > max_pheno_name_blen_ptr=0x7fff87b0) at ../plink2_psam.cc:611 > 611 pheno_cols[pheno_idx].nonmiss = nullptr; > > > Please let me know if I can do further checks. > > Kind regards > > Andreas. > > -- > http://fam-tille.de >
Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)
Ok, new release/tag created. On Fri, Feb 18, 2022 at 10:55 PM Andreas Tille wrote: > Hi Chris, > > Am Fri, Feb 18, 2022 at 07:27:20PM -0800 schrieb Chris Chang: > > I have confirmed that the original code segfaults when compiled with gcc > > 11.2 on my Debian instance, and that it runs to completion after the > latest > > patch. I have also confirmed that, after the latest patch, all other > tests > > pass. > > Very nice. It would be great if you could tag a new release which would > ease the maintenance. > > Thanks a lot for your great cooperation > > Andreas. > > -- > http://fam-tille.de >
Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)
I have confirmed that the original code segfaults when compiled with gcc 11.2 on my Debian instance, and that it runs to completion after the latest patch. I have also confirmed that, after the latest patch, all other tests pass. On Fri, Feb 18, 2022 at 1:27 PM Chris Chang wrote: > I am installing gcc-11 on my Debian instance now, and will be running more > extensive tests today searching for other things that may have stopped > working for the same reason. > > On Fri, Feb 18, 2022 at 1:22 PM Andreas Tille wrote: > >> I confirm its gcc-11. I'll check tomorrow. Thanks a lot for your quick >> and helpful responses, Andreas. >> >> Am Fri, Feb 18, 2022 at 12:53:58PM -0800 schrieb Chris Chang: >> > I have posted an update under the provisional assumption that it's gcc >> 11's >> > new ipa-modref pass that is causing this code to fail, since it does >> seem >> > to break some similar code. >> > >> > On Fri, Feb 18, 2022 at 11:49 AM Chris Chang >> wrote: >> > >> > > 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 >> 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 0x74cc7640 (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 0x77fc5640 (LWP 4060800)] >> > >> sizeof(PhenoCol): 40 pheno_cols: 0 >> > >> --debug: setting pheno_cols[0].nonmiss. = nullptr >> > >> >> > >> Thread 1 "plink2-sse2" received signal SIGSEGV, Segmentation fault. >> > >> 0x556fb82e in plink2::LoadPsam (psamname=psamname@entry >> =0x7fffbe70 >> > >> "tmp_data.psam", pheno_range_list_ptr=, fam_cols=..., >> > >> pheno_ct_max=, >> > >> missing_pheno=, affection_01=0, max_thread_ct=4, >> > >> piip=0x7fff8880, sample_include_ptr=0x7fff8790, >> > >> founder_info_ptr=0x7fff87a8, sex_nm_ptr=0x7fff8798, >> > >> sex_male_ptr=0x7fff87a0, pheno_cols_ptr=0x7fff8770, >> > >> pheno_names_ptr=0x7fff8780, raw_sample_ct_ptr=0x7fff8728, >> > >> pheno_ct_ptr=0x7fff8720, >> > >> max_pheno_name_blen_ptr=0x7fff87b0) 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
Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)
I am installing gcc-11 on my Debian instance now, and will be running more extensive tests today searching for other things that may have stopped working for the same reason. On Fri, Feb 18, 2022 at 1:22 PM Andreas Tille wrote: > I confirm its gcc-11. I'll check tomorrow. Thanks a lot for your quick > and helpful responses, Andreas. > > Am Fri, Feb 18, 2022 at 12:53:58PM -0800 schrieb Chris Chang: > > I have posted an update under the provisional assumption that it's gcc > 11's > > new ipa-modref pass that is causing this code to fail, since it does seem > > to break some similar code. > > > > On Fri, Feb 18, 2022 at 11:49 AM Chris Chang > wrote: > > > > > 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 > 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 0x74cc7640 (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 0x77fc5640 (LWP 4060800)] > > >> sizeof(PhenoCol): 40 pheno_cols: 0 > > >> --debug: setting pheno_cols[0].nonmiss. = nullptr > > >> > > >> Thread 1 "plink2-sse2" received signal SIGSEGV, Segmentation fault. > > >> 0x556fb82e in plink2::LoadPsam (psamname=psamname@entry > =0x7fffbe70 > > >> "tmp_data.psam", pheno_range_list_ptr=, fam_cols=..., > > >> pheno_ct_max=, > > >> missing_pheno=, affection_01=0, max_thread_ct=4, > > >> piip=0x7fff8880, sample_include_ptr=0x7fff8790, > > >> founder_info_ptr=0x7fff87a8, sex_nm_ptr=0x7fff8798, > > >> sex_male_ptr=0x7fff87a0, pheno_cols_ptr=0x7fff8770, > > >> pheno_names_ptr=0x7fff8780, raw_sample_ct_ptr=0x7fff8728, > > >> pheno_ct_ptr=0x7fff8720, > > >> max_pheno_name_blen_ptr=0x7fff87b0) 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 > > > >> 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 y
Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)
I have posted an update under the provisional assumption that it's gcc 11's new ipa-modref pass that is causing this code to fail, since it does seem to break some similar code. On Fri, Feb 18, 2022 at 11:49 AM Chris Chang wrote: > 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 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 0x74cc7640 (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 0x77fc5640 (LWP 4060800)] >> sizeof(PhenoCol): 40 pheno_cols: 0 >> --debug: setting pheno_cols[0].nonmiss. = nullptr >> >> Thread 1 "plink2-sse2" received signal SIGSEGV, Segmentation fault. >> 0x556fb82e in plink2::LoadPsam >> (psamname=psamname@entry=0x7fffbe70 >> "tmp_data.psam", pheno_range_list_ptr=, fam_cols=..., >> pheno_ct_max=, >> missing_pheno=, affection_01=0, max_thread_ct=4, >> piip=0x7fff8880, sample_include_ptr=0x7fff8790, >> founder_info_ptr=0x7fff87a8, sex_nm_ptr=0x7fff8798, >> sex_male_ptr=0x7fff87a0, pheno_cols_ptr=0x7fff8770, >> pheno_names_ptr=0x7fff8780, raw_sample_ct_ptr=0x7fff8728, >> pheno_ct_ptr=0x7fff8720, >> max_pheno_name_blen_ptr=0x7fff87b0) 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 >> 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 0x74cc7640 (LWP 2931408)] >> > > [New Thread 0x744c6640 (LWP 2931409)] >> > > [New Thread 0x7fffebcc5640 (LWP 2931411)] >> > > PLINK v2.00a3 SSE4.2 (29 Jan 2022) >> > > www.cog-genomics.org/plink/2.0/ >>
Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)
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 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 0x74cc7640 (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 0x77fc5640 (LWP 4060800)] > sizeof(PhenoCol): 40 pheno_cols: 0 > --debug: setting pheno_cols[0].nonmiss. = nullptr > > Thread 1 "plink2-sse2" received signal SIGSEGV, Segmentation fault. > 0x556fb82e in plink2::LoadPsam (psamname=psamname@entry=0x7fffbe70 > "tmp_data.psam", pheno_range_list_ptr=, fam_cols=..., > pheno_ct_max=, > missing_pheno=, affection_01=0, max_thread_ct=4, > piip=0x7fff8880, sample_include_ptr=0x7fff8790, > founder_info_ptr=0x7fff87a8, sex_nm_ptr=0x7fff8798, > sex_male_ptr=0x7fff87a0, pheno_cols_ptr=0x7fff8770, > pheno_names_ptr=0x7fff8780, raw_sample_ct_ptr=0x7fff8728, > pheno_ct_ptr=0x7fff8720, > max_pheno_name_blen_ptr=0x7fff87b0) 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 > 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 0x74cc7640 (LWP 2931408)] > > > [New Thread 0x744c6640 (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 0x77fc5640 (LWP 2931412)] > > > > > > Thread 1 "plink2-avx" received s
Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)
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 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 0x74cc7640 (LWP 2931408)] > [New Thread 0x744c6640 (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 0x77fc5640 (LWP 2931412)] > > Thread 1 "plink2-avx" received signal SIGSEGV, Segmentation fault. > plink2::LoadPsam (psamname=psamname@entry=0x7fffbe70 "tmp_data.psam", > pheno_range_list_ptr=, fam_cols=..., pheno_ct_max= out>, > missing_pheno=, affection_01=0, max_thread_ct=4, > piip=0x7fff8880, sample_include_ptr=0x7fff87a0, > founder_info_ptr=0x7fff87b8, sex_nm_ptr=0x7fff87a8, > sex_male_ptr=0x7fff87b0, pheno_cols_ptr=0x7fff8780, > pheno_names_ptr=0x7fff8790, raw_sample_ct_ptr=0x7fff8738, > pheno_ct_ptr=0x7fff8730, > max_pheno_name_blen_ptr=0x7fff87c0) 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 0x77fc5640 (LWP 3957711)] > --debug: setting pheno_cols[0].nonmiss. = nullptr > > Thread 1 "plink2-sse2" received signal SIGSEGV, Segmentation fault. > 0x556fb6ff in plink2::LoadPsam (psamname=psamname@entry=0x7fffbe70 > "tmp_data.psam", pheno_range_list_ptr=, fam_cols=..., > pheno_ct_max=, > missing_pheno=, affection_01=0, max_thread_ct=4, > piip=0x7fff8880, sample_include_ptr=0x7fff87a0, > founder_info_ptr=0x7fff87b8, sex_nm_ptr=0x7fff87a8, > sex_male_ptr=0x7fff87b0, pheno_cols_ptr=0x7fff8780, > pheno_names_ptr=0x7fff8790, raw_sample_ct_ptr=0x7fff8738, > pheno_ct_ptr=0x7fff8730, > max_pheno_name_blen_ptr=0x7fff87c0) 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 >
Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)
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. On Thu, Feb 17, 2022 at 11:47 AM Andreas Tille wrote: > Am Thu, Feb 17, 2022 at 11:39:30AM -0800 schrieb Chris Chang: > > Haven't yet replicated this on any of my usual non-Debian test machines, > > but I will spin up a Debian EC2 instance within the next two days and try > > to replicate the crash there. > > Thanks a lot, Andreas. > > -- > http://fam-tille.de >
Bug#1004037: Segmentation fault in plink2 (Was: src:plink2: fails to migrate to testing for too long: autopkgtest regression)
Haven't yet replicated this on any of my usual non-Debian test machines, but I will spin up a Debian EC2 instance within the next two days and try to replicate the crash there. On Wed, Feb 16, 2022 at 11:30 PM Andreas Tille wrote: > PS to last mail: Here > >https://salsa.debian.org/med-team/plink2/-/jobs/2479769 > > is a full test log in our Gitlab CI for the latest version which I just > injected into the packaging Git repository but did not upload yet. > > Kind regards > > Andreas. > > -- > http://fam-tille.de >
