Parallel-NetCDF · wkliao · Aug 5, 2024 · Aug 5, 2024
diff --git a/Makefile b/Makefile
@@ -1,3 +1,8 @@
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 check:
 	cd test && make check
 	cd examples && make check
@@ -10,8 +15,8 @@ clean:
 	cd test && make clean
 	cd examples && make clean
 
-build-clean:
-	rm -rf 	build/
+build-clean: clean
+	rm -rf build
 	rm -rf src/pnetcdf.egg-info/
 	rm -rf src/pnetcdf/_Dimension.c
 	rm -rf src/pnetcdf/_Dimension.*.so
@@ -24,3 +29,6 @@ build-clean:
 	rm -rf src/pnetcdf/__pycache__/
 	rm -rf test/__pycache__/
 
+install-clean: build-clean
+	rm -rf dist
+
diff --git a/examples/Makefile b/examples/Makefile
@@ -1,3 +1,7 @@
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
 
 check_PROGRAMS = collective_write.py \
                  create_open.py \

diff --git a/examples/Pytorch_DDP/README.md b/examples/Pytorch_DDP/README.md
@@ -5,9 +5,8 @@ Distributed Data Parallel (DDP) module and MPI to run on multiple MPI processes
 in parallel. Detailed information describing the example programs is provided
 at the beginning of each file.
 
-## torch_ddp_skeleton_py
-[torch_ddp_skeleton.py](./torch_ddp_skeleton.py) shows how to set up the MPI and DDP
-environment to run a program in parallel.
+## [torch_ddp_skeleton.py](./torch_ddp_skeleton.py) shows how to set up the MPI
+and DDP environment to run a program in parallel.
 
 Command usage:
 ```sh

diff --git a/examples/Pytorch_DDP/torch_ddp_skeleton.py b/examples/Pytorch_DDP/torch_ddp_skeleton.py
@@ -1,3 +1,7 @@
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+
 # This is a skeleton program to show how to run Pytorch distributed environment
 # with MPI
 

diff --git a/examples/collective_write.py b/examples/collective_write.py
@@ -1,9 +1,8 @@
-####################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-####################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 """
  This example mimics the coll_perf.c from ROMIO. It creates a netcdf file and 
  writes a number of 3D integer non-record variables. The measured write bandwidth

diff --git a/examples/create_open.py b/examples/create_open.py
@@ -1,9 +1,8 @@
-####################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-####################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 """
  This example shows how to use `File` class constructor to create a netCDF file and to 
  open the file for read only.

diff --git a/examples/fill_mode.py b/examples/fill_mode.py
@@ -1,9 +1,8 @@
-####################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-####################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 """
  This example shows how to use `Variable` class methods and `File` class methods 
  to set the fill mode of variables and fill values.

diff --git a/examples/flexible_api.py b/examples/flexible_api.py
@@ -1,9 +1,8 @@
-####################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-####################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 """
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
   This example shows how to use `Variable` method put_var() and iput_var() to write a 2D 4-byte

diff --git a/examples/get_info.py b/examples/get_info.py
@@ -1,9 +1,8 @@
-####################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-####################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 """
 
  Example commands for MPI run and outputs from running ncmpidump on the

diff --git a/examples/get_vara.py b/examples/get_vara.py
@@ -1,9 +1,8 @@
-####################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-####################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 """
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
   This example is the read counterpart of example put_vara.py. It shows how to

diff --git a/examples/ghost_cell.py b/examples/ghost_cell.py
@@ -1,9 +1,8 @@
-####################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-####################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 """
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 This example shows how to use `Variable` method to write a 2D array buffer with 

diff --git a/examples/global_attribute.py b/examples/global_attribute.py
@@ -1,9 +1,8 @@
-####################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-####################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 """
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
   This example shows how to use `File` API to write a 2D 4-byte

diff --git a/examples/hints.py b/examples/hints.py
@@ -1,9 +1,8 @@
-####################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-####################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 """
  * This example sets two PnetCDF hints: nc_header_align_size and nc_var_align_size 
  and prints the hint values as well as the header size, header extent, and two variables' 

diff --git a/examples/nonblocking_write.py b/examples/nonblocking_write.py
@@ -1,9 +1,8 @@
-####################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-####################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 """
     This example is similar to collective_write.py but using nonblocking APIs.
      It creates a netcdf file in CDF-5 format and writes a number of

diff --git a/examples/nonblocking_write_def.py b/examples/nonblocking_write_def.py
@@ -1,9 +1,8 @@
-####################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-####################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 """
     This example is the same as nonblocking_write.py expect all nonblocking
     write requests (calls to iput and bput) are posted in define mode.

diff --git a/examples/put_vara.py b/examples/put_vara.py
@@ -1,9 +1,8 @@
-####################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-####################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 """
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
   This example shows how to use `Variable` method put_var() to write a 2D 4-byte

diff --git a/examples/put_varn_int.py b/examples/put_varn_int.py
@@ -1,9 +1,8 @@
-####################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-####################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 """
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
   This example shows how to use a single call of `Variable` method put_var() to 

diff --git a/examples/transpose.py b/examples/transpose.py
@@ -1,9 +1,8 @@
-####################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-####################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 """
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
   This example shows how to use `Variable` method put_var() to write six 3D integer array

diff --git a/examples/transpose2D.py b/examples/transpose2D.py
@@ -1,9 +1,8 @@
-####################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-####################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 """
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
   This example shows how to use `Variable` method put_var() write a 2D integer array

diff --git a/include/PnetCDF.pxi b/include/PnetCDF.pxi
@@ -1,3 +1,8 @@
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 # # size_t, ptrdiff_t are defined in stdlib.h
 # cdef extern from "stdlib.h":
 #    ctypedef long size_t
@@ -313,4 +318,4 @@ cdef extern from "numpy/arrayobject.h":
     void* PyArray_DATA(ndarray) nogil
     char* PyArray_BYTES(ndarray) nogil
     npy_intp* PyArray_STRIDES(ndarray) nogil
-    void import_array()
+    void import_array()
diff --git a/include/mpi-compat.h b/include/mpi-compat.h
@@ -1,5 +1,7 @@
-/* Author:  Lisandro Dalcin   */
-/* Contact: [email protected] */
+/*
+ * Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+ * See COPYRIGHT notice in top-level directory.
+*/
 
 #ifndef MPI_COMPAT_H
 #define MPI_COMPAT_H
@@ -16,4 +18,4 @@ typedef void *PyMPI_MPI_Session;
 #define MPI_Session PyMPI_MPI_Session
 #endif
 
-#endif/*MPI_COMPAT_H*/
+#endif /*MPI_COMPAT_H*/
diff --git a/setup.cfg b/setup.cfg
@@ -1,9 +1,7 @@
-###############################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-###############################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
 
 # Follow instructions below for editing.
 [options]

diff --git a/setup.py b/setup.py
@@ -1,9 +1,7 @@
-###############################################################################
-# 
-#  Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-#  See COPYRIGHT notice in top-level directory.
-# 
-###############################################################################
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
 
 import os
 import sys

diff --git a/test/Makefile b/test/Makefile
@@ -1,3 +1,7 @@
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
 
 check_PROGRAMS = tst_atts.py \
                  tst_default_format.py \

diff --git a/test/tst_atts.py b/test/tst_atts.py
@@ -1,3 +1,8 @@
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 import math
 import subprocess
 import sys

diff --git a/test/tst_default_format.py b/test/tst_default_format.py
@@ -1,9 +1,7 @@
-# This file is part of pnetcdf, a Python interface to the PnetCDF library.
-#
 #
 # Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-# See COPYRIGHT notice in top-level directory
-# License:  
+# See COPYRIGHT notice in top-level directory.
+#
 
 """
    This test program is intended to illustrate the use of the pnetCDF python API.

diff --git a/test/tst_dims.py b/test/tst_dims.py
@@ -1,3 +1,8 @@
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
 import sys
 import unittest
 import os

diff --git a/test/tst_file_fill.py b/test/tst_file_fill.py
@@ -1,9 +1,7 @@
-# This file is part of pnetcdf, a Python interface to the PnetCDF library.
-#
 #
 # Copyright (C) 2024, Northwestern University and Argonne National Laboratory
-# See COPYRIGHT notice in top-level directory
-# License:  
+# See COPYRIGHT notice in top-level directory.
+#
 
 """
    This example program is intended to illustrate the use of the pnetCDF python API. The