bug#22125: bless: non-deterministic failure on x86_64

bug#22125: bless: non-deterministic failure on x86_64

[Mark H Weaver]

The following build of 'bless' on x86_64, the most recent at the time of
this writing, failed by timeout after 1 hour of silence:

  http://hydra.gnu.org/build/864760#tabs-buildsteps

Here's the tail of the failed build log:

--8<---------------cut here---------------start------------->8---
starting phase `build'
mpicxx -Wall -O3 -I ./boost/include -I ./google-sparsehash -I ./zlib/install/include -I ./klib -I ./kmc/kmc_api -fopenmp -std=c++11 -c  kmc/kmc_api/kmc_file.cpp -o kmc/kmc_api/kmc_file.o
mpicxx -Wall -O3 -I ./boost/include -I ./google-sparsehash -I ./zlib/install/include -I ./klib -I ./kmc/kmc_api -fopenmp -std=c++11 -c  kmc/kmc_api/kmer_api.cpp -o kmc/kmc_api/kmer_api.o
mpicxx -Wall -O3 -I ./boost/include -I ./google-sparsehash -I ./zlib/install/include -I ./klib -I ./kmc/kmc_api -fopenmp -std=c++11 -c  kmc/kmc_api/mmer.cpp -o kmc/kmc_api/mmer.o
mpicxx -Wall -O3 -I ./boost/include -I ./google-sparsehash -I ./zlib/install/include -I ./klib -I ./kmc/kmc_api -fopenmp -std=c++11 -c  murmurhash3/MurmurHash3.cpp -o murmurhash3/MurmurHash3.o
mpicxx -Wall -O3 -I ./boost/include -I ./google-sparsehash -I ./zlib/install/include -I ./klib -I ./kmc/kmc_api -fopenmp -std=c++11 -c  check_inputs.cpp -o check_inputs.o
mpicxx -Wall -O3 -I ./boost/include -I ./google-sparsehash -I ./zlib/install/include -I ./klib -I ./kmc/kmc_api -fopenmp -std=c++11 -c  correct_errors.cpp -o correct_errors.o
mpicxx -Wall -O3 -I ./boost/include -I ./google-sparsehash -I ./zlib/install/include -I ./klib -I ./kmc/kmc_api -fopenmp -std=c++11 -c  count_solid_kmers.cpp -o count_solid_kmers.o
mpicxx -Wall -O3 -I ./boost/include -I ./google-sparsehash -I ./zlib/install/include -I ./klib -I ./kmc/kmc_api -fopenmp -std=c++11 -c  main.cpp -o main.o
mpicxx -Wall -O3 -I ./boost/include -I ./google-sparsehash -I ./zlib/install/include -I ./klib -I ./kmc/kmc_api -fopenmp -std=c++11 -c  parse_args.cpp -o parse_args.o
mpicxx kmc/kmc_api/kmc_file.o kmc/kmc_api/kmer_api.o kmc/kmc_api/mmer.o murmurhash3/MurmurHash3.o check_inputs.o correct_errors.o count_solid_kmers.o main.o parse_args.o -o bless -lboost_filesystem -lboost_system -lboost_iostreams -lz -fopenmp -std=c++11
cd kmc; make CC=mpicxx
make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
make[1]: Entering directory '/tmp/nix-build-bless-1p02.drv-0/v1p02/kmc'
mpicxx -Wall -O3 -m64 -fopenmp -pthread -std=c++11 -c kmer_counter/kmer_counter.cpp -o kmer_counter/kmer_counter.o
building of `/gnu/store/iwp3cd4p94lvfgkhyvpyzrghfsrm8mvj-bless-1p02.drv' timed out after 3600 seconds of silence
@ build-failed /gnu/store/iwp3cd4p94lvfgkhyvpyzrghfsrm8mvj-bless-1p02.drv - timeout
guix build: error: build failed: build of `/gnu/store/iwp3cd4p94lvfgkhyvpyzrghfsrm8mvj-bless-1p02.drv' failed
--8<---------------cut here---------------end--------------->8---

      Mark

bug#22125: bless: non-deterministic failure on x86_64

[Ludovic Courtès]

Mark H Weaver <mhw@netris.org> skribis:

> mpicxx kmc/kmc_api/kmc_file.o kmc/kmc_api/kmer_api.o kmc/kmc_api/mmer.o murmurhash3/MurmurHash3.o check_inputs.o correct_errors.o count_solid_kmers.o main.o parse_args.o -o bless -lboost_filesystem -lboost_system -lboost_iostreams -lz -fopenmp -std=c++11
> cd kmc; make CC=mpicxx
> make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> make[1]: Entering directory '/tmp/nix-build-bless-1p02.drv-0/v1p02/kmc'
> mpicxx -Wall -O3 -m64 -fopenmp -pthread -std=c++11 -c kmer_counter/kmer_counter.cpp -o kmer_counter/kmer_counter.o
> building of `/gnu/store/iwp3cd4p94lvfgkhyvpyzrghfsrm8mvj-bless-1p02.drv' timed out after 3600 seconds of silence

Sounds like ‘make’ getting confused and waiting forever.
Possibly #:parallel-build? #f would help?

Ludo’.

bug#22125: bless: non deterministic failure

[Branson, Joshua A]

It looks like bless is building fine.  It had two recent failures (March 2017), but more recent correct builds.  

http://hydra.gnu.org/job/gnu/core-updates/bless-1p02.x86_64-linux

I also see other builds of bless working just fine here: 

http://hydra.gnu.org/job/gnu/master/bless-1p02.x86_64-linux

http://hydra.gnu.org/job/gnu/release-0.12.0/bless-1p02.x86_64-linux

Perhaps this is not a huge issue anymore?

Joshua

bug#22125: bless: non deterministic failure

[Leo Famulari]

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On Tue, Mar 28, 2017 at 05:42:36PM +0000, Branson, Joshua A wrote:
> It looks like bless is building fine.  It had two recent failures (March 2017), but more recent correct builds.  
> 
> http://hydra.gnu.org/job/gnu/core-updates/bless-1p02.x86_64-linux
> 
> I also see other builds of bless working just fine here: 
> 
> http://hydra.gnu.org/job/gnu/master/bless-1p02.x86_64-linux
> 
> http://hydra.gnu.org/job/gnu/release-0.12.0/bless-1p02.x86_64-linux
> 
> Perhaps this is not a huge issue anymore?

It may be an issue but not a huge issue. It would be good to know what's
going on, though.

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bug#22125: bless: non deterministic failure

[Andreas Enge]

Bless is still compiling well in 2018, closing this bug.

Andreas