permissions error

[folivetti]

permissions error

[folivetti]

could you patch the itea.py locally and change line 108 to

subprocess.call([f"stack run config {cfgname}"], shell=True, cwd=cwd)

and see if it works?
I have just patched this file, so if you redo the install script it should get the correct file. Let me know if it works.

I'm also trying to replicate a conda environment that works with stack without using sudo, but haven't got any luck so far.

[lacava]

I'm confused, did you want to add --allow-different-user to line 108 or do you want me to remove it?

I reran the install script and get

 bash itea_install.sh 
Cloning into 'ITEA'...
remote: Enumerating objects: 2192, done.
remote: Counting objects: 100% (2192/2192), done.
remote: Compressing objects: 100% (1296/1296), done.
remote: Total 2192 (delta 1011), reused 1886 (delta 726), pack-reused 0
Receiving objects: 100% (2192/2192), 25.76 MiB | 6.88 MiB/s, done.
Resolving deltas: 100% (1011/1011), done.
/home/bill/anaconda3/envs/srbench/bin/stack
Preparing to install GHC (tinfo6) to an isolated location.
This will not interfere with any system-level installation.
Downloaded ghc-tinfo6-8.10.4.                                      
configure: WARNING: Unknown vendor conda                                              
configure: WARNING: Unknown vendor conda
configure: WARNING: Unknown vendor conda
Installed GHC.     
WARNING: Ignoring MissingH's bounds on random (>=1.0.1.1 && <1.2); using random-1.2.0.
Reason: allow-newer enabled.
[1 of 2] Compiling Main             ( /home/bill/.stack/setup-exe-src/setup-mPHDZzAJ.hs, /home/bill/.stack/setup-exe-src/setup-mPHDZzAJ.o )
[2 of 2] Compiling StackSetupShim   ( /home/bill/.stack/setup-exe-src/setup-shim-mPHDZzAJ.hs, /home/bill/.stack/setup-exe-src/setup-shim-mPHDZzAJ.o )
Linking /home/bill/.stack/setup-exe-cache/x86_64-linux-tinfo6/tmp-Cabal-simple_mPHDZzAJ_3.2.1.0_ghc-8.10.4 ...
/home/bill/anaconda3/envs/srbench/bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lgmp
collect2: error: ld returned 1 exit status
`x86_64-conda-linux-gnu-cc' failed in phase `Linker'. (Exit code: 1)

--  While building simple Setup.hs (scroll up to its section to see the error) using:
      /home/bill/.stack/programs/x86_64-linux/ghc-tinfo6-8.10.4/bin/ghc-8.10.4 -rtsopts -threaded -clear-package-db -global-package-db -hide-all-packages -package base -main-is StackSetupShim.mainOverride -package Cabal-3.2.1.0 /home/bill/.stack/setup-exe-src/setup-mPHDZzAJ.hs /home/bill/.stack/setup-exe-src/setup-shim-mPHDZzAJ.hs -o /home/bill/.stack/setup-exe-cache/x86_64-linux-tinfo6/tmp-Cabal-simple_mPHDZzAJ_3.2.1.0_ghc-8.10.4
    Process exited with code: ExitFailure 1

[folivetti]

I'm confused, did you want to add --allow-different-user to line 108 or do you want me to remove it?

I meant to replace line 108 with the one I posted. But it doesn't matter, by rerunning the installation script this is solved.

Now the problem is that it cannot find gmp inside the conda environment.

I'm simulating this issue in a sandbox environment, but I couldn't find a solution that didn't involve the use of sudo to install the necessary libs. I'm still investigating alternatives, but one (ugly) possibility would be to provide a precompiled binary together with the libraries in the same directory.

[folivetti]

@lacava is it ok to provide a compiled executable file? In order to run in your environment, it would require to add the following in your environment.yml (I can make a pull request, if you like):

  - libblas=3.9.0=8_openblas
  - liblapack=3.9.0=8_openblas
  - gmp=6.2.1=h58526e2_0
  - gsl=2.6=he838d99_2
  - libffi=3.3=h58526e2_2

and in your install.sh script insert right after line 4:

export LD_LIBRARY_PATH=~/.conda/envs/srbench/lib:$LD_LIBRARY_PATH

I'm assuming srbench env will be under home directory.

If that's ok to you, I can compile the binary and change the python wrapper and installation scripts accondingly.

[lacava]

i'm fine with it! Just need something that A) works on github actions and B) will install in the HPC environment i'm running the experiments in.

[folivetti]

@lacava great! I just need to know if the HPC runs under the same OS as github actions (Ubuntu 20). The main thing is what is the GLIBC version I need to compile with (the output of ldd --version)

[lacava]

It's running CentOS, centos-release-7-9.2009.1.el7.centos.x86_64 . gcc version 10.2.0

[lacava]

ldd version 2.17

[folivetti]

done! I'm making a PR into srbench that should fix everything related to ITEA. If you find any problem, please reopen this issue.
Thanks for the input!

[lacava]

Great. One note:

I'm assuming srbench env will be under home directory.

You should be able to use the $CONDA_PREFIX environment variable to point to the environment location

[folivetti]

Yes, I'm using that now :-)
See the PR comments, I had to add a line in configure.sh so that I can actually use this variable. It passed on the CI of my fork.