Re: [easybuild] no sqlite3 in python builds

[Ward Poelmans]

On Thu, Jan 22, 2015 at 9:57 PM, Heywood, Todd  wrote:
> I have built Python2 and Python3 using standard easyconfigs and the goolf
> toolchain. But they don¹t include the sqlite3 module:

Hi Todd,

We're aware of the issue [1]. If you want to fix it, it should be as
simple as adding sqlite as a dependencies in the easyconfig of python.

Ward

[1] https://github.com/hpcugent/easybuild-easyconfigs/issues/1304

[easybuild] no sqlite3 in python builds

[Heywood, Todd]

I have built Python2 and Python3 using standard easyconfigs and the goolf
toolchain. But they don¹t include the sqlite3 module:

heywood@bnbmgmt2:~$ which python
/sonas-hs/it/hpc/home/easybuild/install/software/MPI/GCC/4.8.2/OpenMPI/1.6.
5/Python/2.7.8/bin/python
heywood@bnbmgmt2:~$ python
Python 2.7.8 (default, Jan 22 2015, 11:28:14)
[GCC 4.8.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sqlite3
Traceback (most recent call last):
  File "", line 1, in 
  File 
"/sonas-hs/it/hpc/home/easybuild/install/software/MPI/GCC/4.8.2/OpenMPI/1.6
.5/Python/2.7.8/lib/python2.7/sqlite3/__init__.py", line 24, in 
from dbapi2 import *
  File 
"/sonas-hs/it/hpc/home/easybuild/install/software/MPI/GCC/4.8.2/OpenMPI/1.6
.5/Python/2.7.8/lib/python2.7/sqlite3/dbapi2.py", line 28, in 
from _sqlite3 import *
ImportError: No module named _sqlite3
>>> quit()



The system python has the module, and I find this:

heywood@bnbmgmt2:~$ find /usr/lib64 -name _sqlite3.so
find: `/usr/lib64/audit': Permission denied
/usr/lib64/python2.6/lib-dynload/_sqlite3.so
heywood@bnbmgmt2:~$



But that is not found under the easybuild build:

heywood@bnbmgmt2:~$ find
/sonas-hs/it/hpc/home/easybuild/install/software/MPI/GCC/4.8.2/OpenMPI/1.6.
5/Python/2.7.8 -name  _sqlite3.so
heywood@bnbmgmt2:~$



But some sqlite3 stuff was ³installed²:

heywood@bnbmgmt2:~$ ls -ltr
/sonas-hs/it/hpc/home/easybuild/install/software/MPI/GCC/4.8.2/OpenMPI/1.6.
5/Python/2.7.8/lib/python2.7/sqlite3/
total 88
-rw-r--r-- 1 heywood itstaffnew 2698 Jan 22 11:28 dbapi2.py
-rw-r--r-- 1 heywood itstaffnew 2804 Jan 22 11:28 dump.py
-rw-r--r-- 1 heywood itstaffnew 1037 Jan 22 11:28 __init__.py
-rw-r--r-- 1 heywood itstaffnew  247 Jan 22 11:29 __init__.pyc
-rw-r--r-- 1 heywood itstaffnew 3455 Jan 22 11:29 dbapi2.pyc
-rw-r--r-- 1 heywood itstaffnew 2320 Jan 22 11:29 dump.pyc
-rw-r--r-- 1 heywood itstaffnew  247 Jan 22 11:29 __init__.pyo
-rw-r--r-- 1 heywood itstaffnew 3455 Jan 22 11:29 dbapi2.pyo
-rw-r--r-- 1 heywood itstaffnew 2320 Jan 22 11:29 dump.pyo
drwxr-sr-x 2 heywood itstaffnew 8192 Jan 22 11:29 test
heywood@bnbmgmt2:~$



How can this be fixed?

Thanks,

Todd