Merge pull request #373 from NOAA-GFDL/372.split-vars

Restore split_ncvars.pl splitting behavior post NCO 5.1.9

Author: ceblanton

.gitignore

@@ -3,7 +3,7 @@
 *.tar
 *.gz
 build.fre-nctools*
-build
+build*
 _build
 *.exe
 *.1

site-configs/gfdl-ws/env.sh

@@ -32,18 +32,17 @@
 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
 # Variables to control versions used
-env_version=2024.02
-gcc_version=13.2.0
+env_version=2025.01
+gcc_version=13.3.0
 ncc_version=4.9.2
 ncf_version=4.6.1
-mpi_version=4.2.1
+mpi_version=4.2.3
 
 # Ensure the base spack modules are first in MODULEPATH
 module remove-path MODULEPATH /app/spack/${env_version}/modulefiles/linux-rhel8-x86_64
 module prepend-path MODULEPATH /app/spack/${env_version}/modulefiles/linux-rhel8-x86_64
 
-# bats, and python are needed for tests
-module load bats
+# python is needed for tests
 module load python
 module load nco
 

site-configs/gfdl/env.sh

@@ -32,18 +32,17 @@
 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
 # Variables to control versions used
-env_version=2024.02
-gcc_version=13.2.0
+env_version=2025.01
+gcc_version=13.3.0
 ncc_version=4.9.2
 ncf_version=4.6.1
-mpi_version=4.2.1
+mpi_version=4.2.3
 
 # Ensure the base spack modules are first in MODULEPATH
 module remove-path MODULEPATH /app/spack/${env_version}/modulefiles/linux-rhel8-x86_64
 module prepend-path MODULEPATH /app/spack/${env_version}/modulefiles/linux-rhel8-x86_64
 
-# bats, and python are needed for tests
-module load bats
+# python is needed for tests
 module load python
 module load nco
 

src/split_ncvars/split_ncvars.pl.in

@@ -363,9 +363,9 @@ foreach my $file (@ifiles) {
         print "   var=$var; timename=$timename; vlist=$vlist\n" if $Opt{VERBOSE} > 2;
         my $appendopt = "";
         $appendopt = "-A" if ( -f "$cwd/$tmp_var_filename" );
-        print "$ncks -h $appendopt -v $vlist $file $tmp_var_filename\n" if $Opt{VERBOSE};
+        print "$ncks -C -h $appendopt -v $vlist $file $tmp_var_filename\n" if $Opt{VERBOSE};
         next                                                            if $TEST;
-        system("$ncks -h $appendopt -v $vlist $file $tmp_var_filename");
+        system("$ncks -C -h $appendopt -v $vlist $file $tmp_var_filename");
         $ncstatus += $?;
 
         # remove dimensions called "scalar_axis" (i.e., length = 1)
@@ -502,8 +502,8 @@ foreach my $file (@ifiles) {
     # for an existing variable in a netCDF4 file. The netCDF4 format (unlike netCDF3) does not permit this.
     if ( $Opt{onefile} ) {
         my $vlist = join ",", @vlist;
-        print "$ncks -6 -h -A -v $vlist $file $Opt{onefile}\n" if $Opt{VERBOSE} > 0;
-        system("$ncks -6 -h -A -v $vlist $file $Opt{onefile}");
+        print "$ncks -C -6 -h -A -v $vlist $file $Opt{onefile}\n" if $Opt{VERBOSE} > 0;
+        system("$ncks -C -6 -h -A -v $vlist $file $Opt{onefile}");
         $ncstatus += $?;
 
         my @ncatted_opts = set_ncatted_opts( $Opt{onefile}, tailname( $Opt{onefile} ) );

tests/Makefile.am

@@ -143,6 +143,7 @@ TESTS = \
     plevel/plevel-nctypes \
     plevel/plevel-t \
     split_ncvars/split_ncvars \
+    split_ncvars/split_ncvars-f \
     split_ncvars/split_ncvars-i \
     split_ncvars/split_ncvars-l \
     split_ncvars/split_ncvars-o \

tests/create_plevel_test_ncfile.c

@@ -108,6 +108,7 @@ int main(int argc, char **argv) {
     check_err(nc_put_att_text(ncid, pfull_id, "long_name", 23, "ref full pressure level"), __LINE__);
     check_err(nc_put_att_text(ncid, pfull_id, "cartesian_axis", 1, "Z"), __LINE__);
     check_err(nc_put_att_text(ncid, pfull_id, "positive", 4, "down"), __LINE__);
+    check_err(nc_put_att_text(ncid, pfull_id, "formula_terms", 6, "ps: ps"), __LINE__);
 
     check_err(nc_def_var(ncid, "pk", NC_FLOAT, 1, &phalf_dim, &pk_id), __LINE__);
     check_err(nc_put_att_text(ncid, pk_id, "units", 6, "pascal"), __LINE__);

tests/split_ncvars/split_ncvars-f

@@ -0,0 +1,54 @@
+#!/bin/sh
+
+# Copyright (C) 2024 Geophysical Fluid Dynamics Laboratory
+
+# This file is part of the GFDL FRE NetCDF tools package (FRE-NCTools).
+
+# FRE-NCtools is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or (at
+# your option) any later version.
+
+# FRE-NCtools is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+# for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with FRE-NCTools.  If not, see
+# <http://www.gnu.org/licenses/>.
+
+if test "$VERBOSE" = yes
+then
+    set -x
+    command -v split_ncvars.pl --version
+fi
+
+. ${srcdir=.}/init.sh; path_prepend_ ../../src
+
+# Need to use the included list_ncvars.sh script.  Otherwise,
+# split_ncvars will look for list_ncvars.sh in the installed bin
+# directory.
+export LIST_NCVARS=$(readlink -f ../../src/list_ncvars.sh)
+
+# list_ncvars.sh needs to know where to find the built list_ncvars
+# executable.
+export PKGLIBEXECDIR=$(readlink -f ../../src)
+
+# Use the test netCDF files from plevel
+${builddir=..}/create_plevel_test_ncfile || framework_failure_ "failed to create plevel test files"
+mkdir idir || framework_failure_ "failed to create idir"
+mv test_input.nc idir || framework_failure_ "failed to move test_input.nc to idir"
+
+# Extract a static variable whose formula_terms contains a variable that contains time.
+# The output file should NOT contain time.
+split_ncvars.pl -v pfull -i idir test_input.nc -f output.nc || fail_ split_ncvars.pl test_input.nc failed
+
+# Check that the output.nc file was created, that it has pfull in it, and does not have time in it
+test -f output.nc || fail_ output.nc not created
+if ncdump -v time output.nc
+then
+    # Expected failure
+    fail_ "output.nc incorrectly contains time"
+fi
+ncdump -v pfull output.nc || fail_ "output.nc does not contain output variable pfull"