undefined reference to symbol 'pthread_setname_np@@GLIBC_2.12' while setting ghc for stack

[rajcspsg]

General summary/comments (optional)

Operating System - OpenSuse 42.3 Leap

Steps to reproduce

For example:

1. Install stack using curl -sSL https://get.haskellstack.org/ | sh as mentioned in https://docs.haskellstack.org/en/stable/README/.
2. update ~/.stack/global-project/stack.yaml file with key value resolver: ghc-8.2.1 .
3. run stack setup.
4. you will encounter some missing libraries. Install those libraries (For example glibc etc).
5. After installing any missing libraries run stack setup.
6. You will get error undefined reference to symbol 'pthread_setname_np@@GLIBC_2.12' /lib64/libpthread.so.0

Expected

stack setup should go through without any error.

Actual

Getting below error

stack setup
  The GHC located at /home/rajkumar/.stack/programs/x86_64-linux/ghc-8.2.1/bin/ghc failed to compile a sanity check. Please see:

  http://docs.haskellstack.org/en/stable/install_and_upgrade/

  for more information. Exception was:
  Running /home/rajkumar/.stack/programs/x86_64-linux/ghc-8.2.1/bin/ghc /tmp/stack-sanity-check3048/Main.hs -no-user-package-db in directory /tmp/stack-sanity-check3048/ exited with ExitFailure 1

  [1 of 1] Compiling Main             ( /tmp/stack-sanity-check3048/Main.hs, /tmp/stack-sanity-check3048/Main.o )
  Linking /tmp/stack-sanity-check3048/Main ...

 /usr/bin/ld.bfd: /home/rajkumar/.stack/programs/x86_64-linux/ghc-8.2.1/lib64/ghc-8.2.1/rts/libHSrts.a(OSThreads.o): undefined reference to symbol 'pthread_setname_np@@GLIBC_2.12'
 /lib64/libpthread.so.0: error adding symbols: DSO missing from command line
 collect2: error: ld returned 1 exit status
`gcc' failed in phase `Linker'. (Exit code: 1)

Stack version

stack --version
Version 1.5.1, Git revision 600c1f01435a10d127938709556c1682ecfd694e (4861 commits) x86_64 hpack-0.17.1

Method of installation

Install stack using curl -sSL https://get.haskellstack.org/ | sh as mentioned in https://docs.haskellstack.org/en/stable/README/.

I have asked question regarding this on stackoverflow. Here is the link.

Please let me know if you need more details.

[mgsloan]

Hmm, I wonder what is so different about that setup. Not sure if this will work, but it might be worth trying LDFLAGS="-pthread" stack setup or LDFLAGS="-lpthread".

[rajcspsg]

@mgsloan I tried both the options but still I am getting same error.

[rajcspsg]

@mgsloan . Looks like this issue is fixed. Now I'm able to stack set up in OpenSuse Tumbleweed 42.3. Stack version 1.6.1. I think this issue can be closed now.

[palday]

Still present in Stack 1.6.5 (installed using on curl -sSL https://get.haskellstack.org/ | sh) on Linux Mint 18.3 (based on Ubuntu 16.04 LTS).

[thalesrca]

I'm facing the same problem with version 1.6.1. I'm using solus

Stack version: Version 1.6.1, Git revision f25811329bbc40b0c21053a8160c56f923e1201b (5435 commits) x86_64 hpack-0.20.0

Error:

stack setup
Preparing to install GHC to an isolated location.
This will not interfere with any system-level installation.
Downloaded ghc-8.2.2.                                      
Installed GHC.                                                                   
The GHC located at /home/rodolfo/.stack/programs/x86_64-linux/ghc-8.2.2/bin/ghc failed to compile a sanity check. Please see:

    http://docs.haskellstack.org/en/stable/install_and_upgrade/

for more information. Exception was:
Running /home/rodolfo/.stack/programs/x86_64-linux/ghc-8.2.2/bin/ghc /tmp/stack-sanity-check24682/Main.hs -no-user-package-db in directory /tmp/stack-sanity-check24682/ exited with ExitFailure 1

[1 of 1] Compiling Main             ( /tmp/stack-sanity-check24682/Main.hs, /tmp/stack-sanity-check24682/Main.o )
Linking /tmp/stack-sanity-check24682/Main ...

/usr/bin/ld.bfd: /home/rodolfo/.stack/programs/x86_64-linux/ghc-8.2.2/lib/ghc-8.2.2/rts/libHSrts.a(OSThreads.o): undefined reference to symbol 'pthread_setname_np@@GLIBC_2.12'
/usr/lib64/libpthread.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
`gcc' failed in phase `Linker'. (Exit code: 1)

[InkBrownell]

I can also confirm this issue is still present in stack v1.6.5

$ stack --version
Version 1.6.5, Git revision 24ab0d6ff07f28276e082c3ce74dfdeb1a2ca9e9 (5514 commits) x86_64 hpack-0.20.0

$ LDFLAGS="-pthread" stack setup
The GHC located at /home/autopilot/.stack/programs/x86_64-linux/ghc-8.2.2/bin/ghc failed to compile a sanity check. Please see:

    http://docs.haskellstack.org/en/stable/install_and_upgrade/

for more information. Exception was:
Running /home/autopilot/.stack/programs/x86_64-linux/ghc-8.2.2/bin/ghc /tmp/stack-sanity-check16592/Main.hs -no-user-package-db in directory /tmp/stack-sanity-check16592/ exited with ExitFailure 1

[1 of 1] Compiling Main             ( /tmp/stack-sanity-check16592/Main.hs, /tmp/stack-sanity-check16592/Main.o )
Linking /tmp/stack-sanity-check16592/Main ...

/usr/bin/ld.bfd: /home/autopilot/.stack/programs/x86_64-linux/ghc-8.2.2/lib/ghc-8.2.2/rts/libHSrts.a(OSThreads.o): undefined reference to symbol 'pthread_setname_np@@GLIBC_2.12'
/usr/lib64/libpthread.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
`gcc' failed in phase `Linker'. (Exit code: 1)

$ LDFLAGS="-lpthread" stack setup
The GHC located at /home/autopilot/.stack/programs/x86_64-linux/ghc-8.2.2/bin/ghc failed to compile a sanity check. Please see:

    http://docs.haskellstack.org/en/stable/install_and_upgrade/

for more information. Exception was:
Running /home/autopilot/.stack/programs/x86_64-linux/ghc-8.2.2/bin/ghc /tmp/stack-sanity-check16635/Main.hs -no-user-package-db in directory /tmp/stack-sanity-check16635/ exited with ExitFailure 1

[1 of 1] Compiling Main             ( /tmp/stack-sanity-check16635/Main.hs, /tmp/stack-sanity-check16635/Main.o )
Linking /tmp/stack-sanity-check16635/Main ...

/usr/bin/ld.bfd: /home/autopilot/.stack/programs/x86_64-linux/ghc-8.2.2/lib/ghc-8.2.2/rts/libHSrts.a(OSThreads.o): undefined reference to symbol 'pthread_setname_np@@GLIBC_2.12'
/usr/lib64/libpthread.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
`gcc' failed in phase `Linker'. (Exit code: 1)

[InkBrownell]

Possible workaround: in your stack.yaml use the option resolver: ghc-8.4.1. This bug seems not to manifest with this version of GHC.

[luispedro]

UPDATE: The error below was due to $LD_LIBRARY_PATH being set and not including the system directories. Adding them to $LD_LIBRARY_PATH solved the issue.

I'm still seeing this on stack 1.7.1 even with resolver: nightly-2018-05-02 (which includes GHC 8.4.2).

In particular, I am seeing this when trying to build a Haskell package with stack in conda (which runs on a Centos 6 container).

The full error log is

Downloading nightly-2018-05-02 build plan ...
Downloaded nightly-2018-05-02 build plan.                                           
Preparing to install GHC (gmp4) to an isolated location.                            
This will not interfere with any system-level installation.                         
Preparing to download ghc-gmp4-8.4.2 ...                                            
ghc-gmp4-8.4.2: download has begun                                                  
[...]
ghc-gmp4-8.4.2:  132.33 MiB / 132.33 MiB (100.00%) downloaded...
Downloaded ghc-gmp4-8.4.2.                                                          
Unpacking GHC into /opt/conda/conda-bld/ngless_1525292274450/work/ngless-0.7.1/fake-    home/.stack/programs/x86_64-linux/ghc-gmp4-8.4.2.temp/ ...
Configuring GHC ...                       
Installing GHC ...                                                                  
Installed GHC.                                                                      
/opt/rh/devtoolset-2/root/usr/bin/ld.bfd: /opt/conda/conda-bld/ngless_1525292274450/work/ngless-0.7.1/fake-home/.stack/programs/x86_64-linux/ghc-gmp4-8.4.2/lib/ghc-8.4.2/rts/libHSrts.a(OSThreads.o): undefined reference to symbol 'pthread_setname_np@@GLIBC_2.12' 
/opt/rh/devtoolset-2/root/usr/bin/ld.bfd: note: 'pthread_setname_np@@GLIBC_2.12' is defined in DSO /lib64/libpthread.so.0 so try adding it to the linker command line/lib64/libpthread.so.0: could not read symbols: Invalid operation
collect2: error: ld returned 1 exit status                                          
`gcc' failed in phase `Linker'. (Exit code: 1)                                      
The GHC located at /opt/conda/conda-bld/ngless_1525292274450/work/ngless-0.7.1/fake-home/.stack/programs/x86_64-linux/ghc-gmp4-8.4.2/bin/ghc failed to compile a sanity check. Please see:                         

    http://docs.haskellstack.org/en/stable/install_and_upgrade/

for more information. Exception was:                                                
Received ExitFailure 1 when running                                                                                                                                      
Raw command: /opt/conda/conda-bld/ngless_1525292274450/work/ngless-0.7.1/fake-home/.stack/programs/x86_64-linux/ghc-gmp4-8.4.2/bin/ghc /tmp/stack-sanity-check2833/Main.hs -no-user-package-db                                                                                                                                                    
Run from: /tmp/stack-sanity-check2833/                                              
Standard output:                                                                                                                                                         

[1 of 1] Compiling Main             ( /tmp/stack-sanity-check2833/Main.hs, /tmp/stack-sanity-check2833/Main.o )                                                          
Linking /tmp/stack-sanity-check2833/Main ...

[davidsd]

I had a similar issue in building cpphs and happy using stack 2.1.1 with ghc-8.2.2. The precise error was

$ stack build
....
cpphs            > /opt/gnu/bin/ld.bfd: /home/dsd/.stack/programs/x86_64-linux/ghc-gmp4-8.2.2/lib/ghc-8.2.2/rts/libHSrts.a(OSThreads.o): undefined reference to symbol 'pthread_setname_np@@GLIBC_2.12'
cpphs            > /lib64/libpthread.so.0: error adding symbols: DSO missing from command line
cpphs            > collect2: error: ld returned 1 exit status
cpphs            > `gcc' failed in phase `Linker'. (Exit code: 1)
happy            > Linking .stack-work/dist/x86_64-linux-gmp4/Cabal-2.0.1.0/build/happy/happy ...
happy            > /opt/gnu/bin/ld.bfd: /home/dsd/.stack/programs/x86_64-linux/ghc-gmp4-8.2.2/lib/ghc-8.2.2/rts/libHSrts.a(OSThreads.o): undefined reference to symbol 'pthread_setname_np@@GLIBC_2.12'
happy            > /lib64/libpthread.so.0: error adding symbols: DSO missing from command line
happy            > collect2: error: ld returned 1 exit status
happy            > `gcc' failed in phase `Linker'. (Exit code: 1)

I resolved the error by editing the file ~/.stack/programs/x86_64-linux/ghc-gmp4-8.2.2/lib/ghc-8.2.2/settings and changing the following lines:

("C compiler flags", " -std=gnu99 -fno-stack-protector"),
=======>
("C compiler flags", " -std=gnu99 -fno-stack-protector -pthread"),

("C compiler link flags", " -fuse-ld=bfd"),
=======>
("C compiler link flags", " -fuse-ld=bfd -pthread"),

("ld flags", ""),
=======>
("ld flags", "-pthread"),

[dchenbecker]

Confirming that the workaround provided by @davidsd worked for me