Thread blocked indefinitely in an MVar (or STM) operation

[erikd]

General summary/comments (optional)

Steps to reproduce

git clone https://github.com/input-output-hk/cardano-ledger
cd cardano-ledger
stack build

Result in:

thread blocked indefinitely in an MVar operation
thread blocked indefinitely in an STM transaction

Restarting it will get a bit further before hitting the same issue again (and again (and again ...)).

Expected

There should not be any blocked threads.

Actual

$ stack build <args> --verbose
<output>

Stack version

$ stack --version
Version 2.1.1.1, Git revision 45c7a07ea3161f406eb371fbeaf9c553d0806aa1 (4 commits) x86_64

Method of installation

Build from the Hackage tarball and turned into a custom Debian package.

[ehildenb]

I think that haskell/haskell-ide-engine#1328 and I may also be experiencing this. For me, the issue only shows up on my Arch machine, when trying to build https://github.com/kframework/kore. This is on a fresh Arch lxc container which is brought up to date and then has these packages installed:

depends=('java-runtime' 'flex' 'gcc' 'gmp' 'mpfr' 'z3' 'clang' 'libyaml' 'jemalloc' 'opam' 'gawk' 'make' 'diffutils' 'patch' 'tar' 'grep' 'llvm' 'lld')
makedepends=('maven' 'jdk8-openjdk' 'cmake' 'boost' 'zlib' 'stack' 'pkg-config' 'bison' 'python' 'fakeroot')

I run:

$ git clone 'https://github.com/kframework/kore'
Cloning into 'kore'...
remote: Enumerating objects: 7, done.
remote: Counting objects: 100% (7/7), done.
remote: Compressing objects: 100% (7/7), done.
remote: Total 35899 (delta 0), reused 4 (delta 0), pack-reused 35892
Receiving objects: 100% (35899/35899), 35.97 MiB | 6.96 MiB/s, done.
Resolving deltas: 100% (21397/21397), done.

$ cd kore

$ stack build
Warning: /home/dev/kore/stack.yaml: Unrecognized fields in PLArchive:github: sha256, size
Preparing to install GHC (tinfo6) to an isolated location.
This will not interfere with any system-level installation.
Already downloaded.                       
Installing GHC ...                                                                  
thread blocked indefinitely in an STM transaction

Retrying doesn't seem to help.

[dbaynard]

Hi, thanks for reporting. Would you please paste the verbose output, @erikd (wrapped in <details> tags, please)?

Likewise, @ehildenb, please paste the verbose output, and I'll take a look.

[ehildenb]

From stack build --verbose:

Version 1.9.3.1, Git revision 43ff632b030f50898bff793c9e6c634637ba6001 (6217 commits) x86_64
Compiled with:
- Cabal-2.4.0.1
- Glob-0.10.0
- HUnit-1.6.0.0
- QuickCheck-2.13.1
- StateVar-1.1.1.1
- aeson-1.4.4.0
- aeson-compat-0.3.9
- annotated-wl-pprint-0.7.0
- ansi-terminal-0.9.1
- ansi-wl-pprint-0.6.9
- array-0.5.3.0
- asn1-encoding-0.9.5
- asn1-parse-0.9.4
- asn1-types-0.3.3
- async-2.2.2
- attoparsec-0.13.2.2
- attoparsec-iso8601-1.0.1.0
- auto-update-0.1.6
- base-4.12.0.0
- base-compat-0.10.5
- base-orphans-0.8.1
- base-prelude-1.3
- base16-bytestring-0.1.1.6
- base64-bytestring-1.0.0.2
- basement-0.0.11
- bifunctors-5.5.4
- binary-0.8.6.0
- bindings-uname-0.1
- bitarray-0.0.1.1
- blaze-builder-0.4.1.0
- blaze-html-0.9.1.1
- blaze-markup-0.8.2.2
- byteable-0.1.1
- bytestring-0.10.8.2
- call-stack-0.1.0
- case-insensitive-1.2.1.0
- cereal-0.5.8.1
- clock-0.8
- colour-2.3.5
- comonad-5.0.5
- conduit-1.3.1.1
- conduit-extra-1.3.2
- connection-0.3.0
- constraints-0.11
- containers-0.6.0.1
- contravariant-1.5.2
- cookie-0.4.4
- cryptohash-0.11.9
- cryptohash-sha256-0.11.101.0
- cryptonite-0.26
- cryptonite-conduit-0.2.2
- data-default-class-0.1.2.0
- deepseq-1.4.4.0
- digest-0.0.1.2
- directory-1.3.3.0
- distributive-0.6
- dlist-0.8.0.6
- easy-file-0.2.2
- echo-0.1.3
- ed25519-0.0.5.0
- either-5.0.1.1
- enclosed-exceptions-1.0.3
- exceptions-0.10.2
- extra-1.6.17
- fast-logger-2.4.16
- file-embed-0.0.11
- filelock-0.1.1.3
- filepath-1.4.2.1
- free-5.1.1
- fsnotify-0.3.0.1
- generic-deriving-1.12.4
- ghc-boot-th-8.6.5
- ghc-prim-0.5.3
- githash-0.1.3.1
- hackage-security-0.5.3.0
- hashable-1.2.7.0
- hinotify-0.4
- hourglass-0.2.12
- hpack-0.31.2
- hpc-0.6.0.3
- hspec-2.7.1
- hspec-core-2.7.1
- hspec-discover-2.7.1
- hspec-expectations-0.8.2
- hspec-smallcheck-0.5.2
- http-api-data-0.4.1
- http-client-0.6.4
- http-client-tls-0.3.5.3
- http-conduit-2.3.7.1
- http-types-0.12.3
- infer-license-0.2.0
- integer-gmp-1.0.2.0
- integer-logarithms-1.0.3
- libyaml-0.1.1.0
- lifted-async-0.10.0.4
- lifted-base-0.2.3.12
- logict-0.6.0.3
- megaparsec-7.0.5
- memory-0.14.18
- microlens-0.4.11.2
- microlens-th-0.4.3.2
- mime-types-0.1.0.9
- mintty-0.1.2
- monad-control-1.0.2.3
- monad-logger-0.3.30
- monad-loops-0.4.3
- mono-traversable-1.0.11.0
- mtl-2.2.2
- mustache-2.3.0
- neat-interpolation-0.3.2.4
- network-2.8.0.0
- network-uri-2.6.1.0
- old-locale-1.0.0.7
- old-time-1.1.0.3
- open-browser-0.2.1.0
- optparse-applicative-0.14.3.0
- optparse-simple-0.1.1.2
- parsec-3.1.13.0
- parser-combinators-1.0.3
- path-0.6.1
- path-io-1.4.2
- path-pieces-0.2.1
- pem-0.2.4
- persistent-2.9.2
- persistent-sqlite-2.9.3
- persistent-template-2.6.0
- pretty-1.1.3.6
- primitive-0.6.4.0
- process-1.6.5.0
- profunctors-5.4
- project-template-0.2.0.1
- quickcheck-io-0.2.0
- random-1.1
- regex-applicative-0.3.3
- regex-applicative-text-0.1.0.1
- resource-pool-0.2.3.2
- resourcet-1.2.2
- retry-0.8.0.1
- rio-0.1.10.0
- rts-1.0
- safe-0.3.17
- scientific-0.3.6.2
- semigroupoids-5.3.2
- setenv-0.1.1.3
- shelly-1.8.1
- silently-1.2.5
- smallcheck-1.1.5
- socks-0.6.0
- split-0.2.3.3
- splitmix-0.0.2
- stm-2.5.0.0
- stm-chans-3.0.0.4
- store-0.5.1.1
- store-core-0.4.4
- streaming-commons-0.2.1.1
- syb-0.7.1
- system-fileio-0.3.16.4
- system-filepath-0.4.14
- tagged-0.8.6
- tar-0.5.1.0
- template-haskell-2.14.0.0
- temporary-1.3
- text-1.2.3.1
- text-metrics-0.3.0
- tf-random-0.5
- th-abstraction-0.2.11.0
- th-expand-syns-0.4.4.0
- th-lift-0.7.11
- th-lift-instances-0.1.11
- th-orphans-0.13.7
- th-reify-many-0.1.9
- th-utilities-0.2.3.0
- time-1.8.0.2
- time-compat-1.9.2.2
- time-locale-compat-0.1.1.5
- tls-1.4.1
- transformers-0.5.6.2
- transformers-base-0.4.5.2
- transformers-compat-0.6.5
- typed-process-0.2.6.0
- unicode-transforms-0.3.6
- unix-2.7.2.2
- unix-compat-0.5.1
- unix-time-0.4.7
- unliftio-0.2.12
- unliftio-core-0.1.2.0
- unordered-containers-0.2.10.0
- uuid-types-1.0.3
- vector-0.12.0.3
- vector-algorithms-0.8.0.1
- void-0.7.3
- x509-1.7.5
- x509-store-1.6.7
- x509-system-1.6.6
- x509-validation-1.6.11
- yaml-0.11.1.0
- zip-archive-0.4.1
- zlib-0.6.2

Warning: this is an unsupported build that may use different versions of
dependencies and GHC than the officially released binaries, and therefore may
not behave identically.  If you encounter problems, please try the latest
official build by running 'stack upgrade --force-download'.

2019-07-16 00:45:54.024184: [debug] Checking for project config at: /home/dev/kore/stack.yaml
2019-07-16 00:45:54.024387: [debug] Loading project config file stack.yaml
2019-07-16 00:45:54.024849: [warn] Warning: /home/dev/kore/stack.yaml: Unrecognized fields in PLArchive:github: sha256, size
2019-07-16 00:45:54.025407: [debug] Decoding build plan from: /home/dev/.stack/build-plan/lts-13.22.yaml
2019-07-16 00:45:54.025441: [debug] Trying to decode /home/dev/.stack/build-plan-cache/lts-13.22.cache
2019-07-16 00:45:54.029963: [debug] Success decoding /home/dev/.stack/build-plan-cache/lts-13.22.cache
2019-07-16 00:45:54.030232: [debug] Run process: /sbin/ldconfig -p
2019-07-16 00:45:54.031426: [debug] Process finished in 1ms: /sbin/ldconfig -p
2019-07-16 00:45:54.032181: [debug] Did not find shared library libtinfo.so.5
2019-07-16 00:45:54.032229: [debug] Found shared library libtinfo.so.6 in /usr/lib
2019-07-16 00:45:54.032255: [debug] Found shared library libncursesw.so.6 in 'ldconfig -p' output
2019-07-16 00:45:54.032281: [debug] Found shared library libgmp.so.10 in 'ldconfig -p' output
2019-07-16 00:45:54.032321: [debug] Did not find shared library libgmp.so.3
2019-07-16 00:45:54.032341: [debug] Potential GHC builds: tinfo6, ncurses6
2019-07-16 00:45:54.032375: [debug] Found already installed GHC builds:
2019-07-16 00:45:54.264198: [debug] Trying to setup GHC build: tinfo6
2019-07-16 00:45:54.264335: [info] Preparing to install GHC (tinfo6) to an isolated location.
2019-07-16 00:45:54.264380: [info] This will not interfere with any system-level installation.
2019-07-16 00:45:54.265091: [info] Preparing to download ghc-tinfo6-8.6.5 ...
2019-07-16 00:45:54.265148: [debug] Downloading from https://github.com/commercialhaskell/ghc/releases/download/ghc-8.6.5-release/ghc-8.6.5-x86_64-fedora27-linux.tar.xz to /home/dev/.stack/programs/x86_64-linux/ghc
2019-07-16 00:45:54.265188: [debug] Will check against sha1 hash: 0b5b1b15dd36edf01eb29fadbb8566864f95838f
2019-07-16 00:45:54.265229: [debug] Will check against sha256 hash: cf78b53eaf336083e7a05f4a3000afbae4abe5bbc77ef80cc40e09d04ac5b4a1
2019-07-16 00:45:55.197113: [info] Already downloaded.
2019-07-16 00:45:55.227219: [debug] menv = fromList [("BROWSER","w3m"),("DBUS_SESSION_BUS_ADDRESS","unix:path=/run/user/1000/bus"),("DOTFILES","/home/dev/dotfiles"),("DOWNLOADS","/home/dev/dl"),("EDITOR","kak"),("E
2019-07-16 00:45:55.227647: [debug] ziptool: xz
2019-07-16 00:45:55.227673: [debug] make: make
2019-07-16 00:45:55.227691: [debug] tar: tar
2019-07-16 00:45:55.227711: [info] Unpacking GHC into /home/dev/.stack/programs/x86_64-linux/ghc-tinfo6-8.6.5.temp/ ...
2019-07-16 00:45:55.227730: [debug] Unpacking /home/dev/.stack/programs/x86_64-linux/ghc-tinfo6-8.6.5.tar.xz
2019-07-16 00:45:55.227863: [debug] Run process within /home/dev/.stack/programs/x86_64-linux/ghc-tinfo6-8.6.5.temp/: /usr/bin/tar Jxf /home/dev/.stack/programs/x86_64-linux/ghc-tinfo6-8.6.5.tar.xz
thread blocked indefinitely in an STM transaction

[ehildenb]

Hmmm, sudo stack upgrade (to version 2.1.3) and now I can run stack build. Makes it tough to make a PKGBUILD though with the default version of stack that Arch comes with.

[dbaynard]

I've flagged it on the aur — glad you've found a fix.

There have been some tar issues, recently (#4888) and I wonder whether this is related — I'll wait to see what @erikd reports.

[erikd]

I switched back to version 1.9.3 when I hit this issue and have not bothered to update since.

The version I had issue with (2.1.1.1) has been superseded and I will assume that this has been fixed. Closing this.