Add runtime environment check for NERSC Cray hugepages

.github/workflows/ci.yml

@@ -10,38 +10,38 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-16.04", "ubuntu-18.04", "ubuntu-20.04", "macos-latest"]
-        compiler: [gcc-7, gcc-8, gcc-9, clang]
+        compiler: [gcc-7, gcc-9, gcc-10, clang]
         python-version: ["2.7", "3.5", "3.6", "3.7", "3.8"]
         numpy-version: ["1.14", "1.16", "1.18"]
         exclude:
 
           # Only run with 'clang' on OSX
           - os: "macos-latest"
             compiler: gcc-7
-          - os: "macos-latest"
-            compiler: gcc-8
           - os: "macos-latest"
             compiler: gcc-9
+          - os: "macos-latest"
+            compiler: gcc-10
 
           # Don't use 'clang' on linux
+          - os: "ubuntu-16.04"
+            compiler: clang
           - os: "ubuntu-18.04"
             compiler: clang
           - os: "ubuntu-20.04"
             compiler: clang
-          - os: "ubuntu-16.04"
-            compiler: clang
 
-          # only gcc-9 on 20.04
+          # only gcc-10 on 20.04
           - os: "ubuntu-20.04"
-            compiler: gcc-7
+            compiler: gcc-9
           - os: "ubuntu-20.04"
-            compiler: gcc-8
+            compiler: gcc-7
 
-          # only gcc-7 on 16.04
+          # only gcc-9 on 16.04
           - os: "ubuntu-16.04"
-            compiler: gcc-8
+            compiler: gcc-7
           - os: "ubuntu-16.04"
-            compiler: gcc-9
+            compiler: gcc-10
 
           # python3.8 only on 20.04
           - os: "ubuntu-16.04"

CHANGES.rst

@@ -17,6 +17,7 @@ Enhancements
 ------------
 - In the theoretical VPF calculation (``theory.vpf``), the total volume of the random spheres can now exceed the volume of the sample  [#238]
 - Gridlink (the binning of particles into cells) now uses a parallel algorithm for the theory module [#239]
+- Add detection of known-bad Cray hugepages library at NERSC [#246]
 
 Bug fixes
 ---------

Corrfunc/__init__.py

@@ -25,6 +25,8 @@
     from . import theory
     from . import mocks
 
+    utils.check_runtime_env()
+
 
 def read_text_file(filename, encoding="utf-8"):
     """

Corrfunc/utils.py

@@ -6,7 +6,10 @@
 from __future__ import (absolute_import, division, print_function,
                         unicode_literals)
 import sys
+import os
+import warnings
 from os.path import exists as file_exists
+
 import wurlitzer
 from contextlib import contextmanager
 
@@ -1054,6 +1057,22 @@ def sys_pipes():
     except:
         yield
 
+
+def check_runtime_env():
+    '''
+    Detect any computing environment conditions that may cause Corrfunc
+    to fail, and inform the user if there is any action they can take.
+    '''
+
+    # Check if Cray hugepages is enabled at NERSC, which will crash
+    # C Python extensions due to a hugepages bug
+    if 'NERSC_HOST' in os.environ and os.getenv('HUGETLB_DEFAULT_PAGE_SIZE'):
+        warnings.warn('Warning: Cray hugepages has a bug that may crash '
+                      'Corrfunc. You might be able to fix such a crash with '
+                      '`module unload craype-hugepages2M` (see '
+                      'https://github.com/manodeep/Corrfunc/issues/245 '
+                      'for details)')
+
 if __name__ == '__main__':
     import doctest
     doctest.testmod()