Setup_lxplus.sh gives errors

Issues
1

Dear developers,

I just found an issue I did not have in the past. When I try to run source etc/scripts/setup_lxplus.sh on LXPLUS, I obtain the following error output. Do you recognize such an error from your experience?

Thanks,
Cheers,

Lorenzo de Cilladi

[ldecilla@lxplus773 tmp]$ cd /afs/cern.ch/work/l/ldecilla/private/
[ldecilla@lxplus773 private]$ git clone https://gitlab.cern.ch/allpix-squared/allpix-squared.git
Cloning into 'allpix-squared'...
remote: Enumerating objects: 202, done.
remote: Counting objects: 100% (202/202), done.
remote: Compressing objects: 100% (148/148), done.
remote: Total 38280 (delta 113), reused 101 (delta 54), pack-reused 38078
Ricezione degli oggetti: 100% (38280/38280), 11.82 MiB | 23.52 MiB/s, done.
Risoluzione dei delta: 100% (29928/29928), done.
[ldecilla@lxplus773 private]$ git pull
fatal: Not a git repository (or any parent up to mount point /afs)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
[ldecilla@lxplus773 private]$ cd allpix-squared/
[ldecilla@lxplus773 allpix-squared]$ mkdir build
[ldecilla@lxplus773 allpix-squared]$ source etc/scripts/setup_lxplus.sh 
Compiler type set to LLVM, version clang8.
Traceback (most recent call last):
  File "/cvmfs/sft.cern.ch/lcg/views/LCG_97/x86_64-centos7-gcc9-opt/lib/python2.7/site-packages/site.py", line 73, in <module>
    __boot()
  File "/cvmfs/sft.cern.ch/lcg/views/LCG_97/x86_64-centos7-gcc9-opt/lib/python2.7/site-packages/site.py", line 3, in __boot
import os
ImportError: No module named os
Traceback (most recent call last):
  File "/cvmfs/sft.cern.ch/lcg/views/LCG_97/x86_64-centos7-gcc9-opt/lib/python2.7/site-packages/site.py", line 73, in <module>
    __boot()
  File "/cvmfs/sft.cern.ch/lcg/views/LCG_97/x86_64-centos7-gcc9-opt/lib/python2.7/site-packages/site.py", line 3, in __boot
    import os
ImportError: No module named os
Traceback (most recent call last):
  File "/cvmfs/sft.cern.ch/lcg/views/LCG_97/x86_64-centos7-gcc9-opt/lib/python2.7/site-packages/site.py", line 73, in <module>
__boot()
  File "/cvmfs/sft.cern.ch/lcg/views/LCG_97/x86_64-centos7-gcc9-opt/lib/python2.7/site-packages/site.py", line 3, in __boot
    import os
ImportError: No module named os
dirname: operando mancante
Try 'dirname --help' for more information.
dirname: operando mancante
Try 'dirname --help' for more information.
Error in find.package("RInside") : there is no package called ‘RInside’
Calls: cat -> find.package
Esecuzione interrotta
Error in find.package("Rcpp") : there is no package called ‘Rcpp’
Calls: cat -> find.package
Esecuzione interrotta
Error in find.package("readr") : there is no package called ‘readr’
Calls: cat -> find.package
Esecuzione interrotta
dirname: operando mancante
Try 'dirname --help' for more information.

dirname: operando mancante
Try ‘dirname --help’ for more information.
[ldecilla@lxplus773 allpix-squared]$

2

Hi Lorenzo,

I am not 100% sure here, I didn’t work on lxplus much. It seems like this is using python2.7, which it shouldn’t. Are you by any chance sourcing anything (python version, other software setups) in the .bashrc or before doing this?

Cheers
Paul

3

Dear @pschutze,

thanks, this solved my issue. My .bashrc was including the following line, which was the origin of the error:

source /cvmfs/sft.cern.ch/lcg/views/LCG_97/x86_64-centos7-gcc9-opt/setup.sh

Thanks again,
Best,

Lorenzo