Corrfunc: Cannot run tests on NERSC interactive node
General information
- Corrfunc version: 2.3.4
- platform:linux
- installation method (pip/source/other?): from source and then python -m pip install .
Issue description
a) I can run the tests on the login node of Cori and they finish successfully, however if I ask for an interactive node and I try to run the tests they fail (python tests.py). I tried to check at which point they fail and I found out that when it tries to read the catalogs I get the error below. What is even more confusing for me is that if I use the python console I can run this:
from Corrfunc.io import read_catalog x, y, z = read_catalog() print(x) line by line and it works.
b) This error occurs also in one of my codes (again, only on the interactive node) There, I generate at each step a new galaxy catalog and then I use Corrfunc to compute its 2PCF. What happens is that for the first galaxy catalog the Corrfunc provides me the 2PCF, but at the second step, it cannot even obtain the galaxy catalog because I get the error below.
I want to mention that I ask for a haswell interactive node.
Actual behavior
*** Error in `python’: break adjusted to free malloc space: 0x0000010000000000 *** Aborted
Thank you very much! Regards, Andrei
About this issue
- Original URL
- State: closed
- Created 3 years ago
- Comments: 22 (6 by maintainers)
Thanks, that’s good to know. Can you check if any Intel GSL is left in your environment:
printenv | grep gsl?If not, can you try to run the reproducer in #244? Basically, download the C code and the
setup.py, build the extension as per Manodeep’s comment, and try to import it from Python. This triggers the error for me with base NERSC Python and Intel GSL, but goes away with GNU GSL. And it contains no Corrfunc code, which is why I suspect it’s an environment issue!