Merge pull request #45 from wkliao/copy_attr

add test program to test attribute copy

Author: wkliao

test/Makefile

@@ -4,6 +4,7 @@
 #
 
 check_PROGRAMS = tst_atts.py \
+                 tst_copy_attr.py \
                  tst_default_format.py \
                  tst_dims.py \
                  tst_file_fill.py \

test/README.md

@@ -98,5 +98,12 @@ installation information.
   + Test non-blocking APIs and then use `wait/wait_all` method of `File` class
     to flush out the pending I/O requests.
 
-
+* **tst_copy_attr.py**
+  + Copying an attribute from one file to another in python can be done without
+    `ncmpi_copy_att()`. For exampl, this can be done in two lines of python
+    codes below:
+    ```
+    att = source_file.get_att("history")
+    destition_file.put_att('history', att)
+    ```
 

test/tst_copy_attr.py

@@ -0,0 +1,148 @@
+#
+# Copyright (C) 2024, Northwestern University and Argonne National Laboratory
+# See COPYRIGHT notice in top-level directory.
+#
+
+"""
+This program tests how to copy an attribute from a file to another. Note that
+there is no ncmpi_copy_att() function in PnetCDF-Python. This is because
+copying a python object is much simpler than in C. In C, without
+ncmpi_copy_att(), one have to do the followings.
+1. find the size and type of the attribute from the source file
+2. malloc space, read from the source file
+3. write to the destination file
+4. free the buffer
+
+In python, this can be done in two lines of codes:
+   att = source_file.get_att("history")
+   destition_file.put_att('history', att)
+
+To run:
+  % mpiexec -n num_process python3 tst_copy_attr.py [test_file_name]
+
+  Example commands for MPI run and outputs from running ncmpidump on the
+  output netCDF file produced by this example program:
+
+  % mpiexec -n num_process python3 tst_copy_attr.py testfile.nc
+
+  % ncmpidump testfile.nc
+    netcdf testfile {
+    // file format: CDF-1
+    variables:
+        int var0 ;
+                var0:history = "today" ;
+
+    // global attributes:
+                :history = "today" ;
+    data:
+
+     var0 = 0 ;
+    }
+"""
+
+import sys, os, argparse
+import numpy as np
+from mpi4py import MPI
+import pnetcdf
+
+
+def parse_help():
+    help_flag = "-h" in sys.argv or "--help" in sys.argv
+    if help_flag and rank == 0:
+        help_text = (
+            "Usage: {} [-h] | [-v] [file_name]\n"
+            "       [-h] Print help\n"
+            "       [-v] Verbose mode\n"
+            "       [-k format] file format: 1 for CDF-1, 2 for CDF-2, 5 for CDF-5\n"
+            "       [filename] (Optional) output netCDF file name\n"
+        ).format(sys.argv[0])
+        print(help_text)
+    return help_flag
+
+
+# Create two files and copy attributes from one file to another
+def pnetcdf_io(filename, file_format):
+
+    # Create the file
+    f0 = pnetcdf.File(filename = filename, mode = 'w', format = file_format,
+                      comm = comm, info = None)
+
+    filename_dup = filename + "_dup.nc"
+    f1 = pnetcdf.File(filename = filename_dup, mode = 'w', format = file_format,
+                      comm = comm, info = None)
+
+    # define a variable in each file
+    v0 = f0.def_var('var0', 'i4', ())
+    v1 = f1.def_var('var1', 'i4', ())
+
+    # put a new global attribute in f0
+    f0.put_att('history','today')
+
+    # put a new attribute to variable v0 in f0
+    v0.put_att('history','today')
+
+    # retrieve the global attribute from f0
+    att = f0.get_att("history")
+
+    # copy it to f1
+    f1.put_att('history', att)
+
+    # retrieve v0's attribute from f0
+    v_att = v0.get_att("history")
+
+    # copy it to variable v1 in f1
+    v1.put_att('history', v_att)
+
+    # close files
+    f0.close()
+    f1.close()
+
+    # Open file f1 and check the attribute contents
+    f1 = pnetcdf.File(filename_dup, 'r', comm = comm)
+    assert("today" == f1.get_att("history"))
+
+    v1=f1.variables['var1']
+    assert("today" == v1.get_att("history"))
+
+    # close files
+    f1.close()
+
+
+if __name__ == "__main__":
+    comm = MPI.COMM_WORLD
+    rank = comm.Get_rank()
+    nprocs = comm.Get_size()
+
+    if parse_help():
+        MPI.Finalize()
+        sys.exit(1)
+
+    # get command-line arguments
+    args = None
+    parser = argparse.ArgumentParser()
+    parser.add_argument("dir", nargs="?", type=str, help="(Optional) output directory name",\
+                         default = ".")
+    parser.add_argument("-v", help="Verbose mod ", action="store_true")
+    parser.add_argument("-k", help="File format: 1 for CDF-1, 2 for CDF-2, 5 for CDF-5")
+    args = parser.parse_args()
+
+    verbose = True if args.v else False
+
+    file_format = None
+    if args.k:
+        kind_dict = {'1':None, '2':"NC_64BIT_OFFSET", '5':"NC_64BIT_DATA"}
+        file_format = kind_dict[args.k]
+
+    filename = os.path.join(args.dir, "tst_copy_attr.nc")
+
+    if verbose and rank == 0:
+        print("{}: test copying attributes ".format(os.path.basename(__file__)))
+
+    try:
+        pnetcdf_io(filename, file_format)
+    except BaseException as err:
+        print("Error: type:", type(err), str(err))
+        raise
+
+    MPI.Finalize()
+