CMakeLists.txt

@@ -151,6 +151,12 @@ endif()
 
 set(CMAKE_REQUIRED_LIBRARIES ${NETCDF_LIBRARY})
 
+check_library_exists(${NETCDF_LIBRARY} nc_rename_grp "" has_nc_rename_grp)
+if (has_nc_rename_grp)
+  message("-- Found nc_rename_grp in: " ${NETCDF_LIBRARY})
+  add_definitions(-DHAVE_NC_RENAME_GRP)
+endif()
+
 check_library_exists(${NETCDF_LIBRARY} nc_inq_path "" has_nc_inq_path)
 if (has_nc_inq_path)
   message("-- Found nc_inq_path in: " ${NETCDF_LIBRARY})
@@ -536,7 +542,7 @@ target_link_libraries (ncwa ${nco_LIB} ${LIB_DEP})
 
 
 #//////////////////////////
-#ANLR
+#ANTLR
 #cmake can detect relative paths, e.g, antlr/AST.hpp
 #detect a user defined system environment variable ANTLR_ROOT
 #this sets the include path to ANTLR_INCLUDE directly

bld/Makefile

@@ -14,15 +14,15 @@
 
 # Machine build parameters
 #                         Source     Method   Packages Compiler
-# aerosol.ess.uci.edu: NCO          Configure All else clang
+# aerosol.ess.uci.edu: NCO          Configure All else GCC
 # AppVeyor CI        : NCO          CMake     All else MSVC
 # cheyenne.ucar.edu  : NCO          Makefile  All else Intel
 # cooley.alcf.anl.g  : NCO          Configure All else GCC
 # edison.nersc.gov   : NCO          Configure All else Intel
-# firn.ess.uci.edu   : NCO          Configure All else clang
+# firn.ess.uci.edu   : NCO          Configure All else GCC
 # frazil.ess.uci.edu : NCO          Configure All else clang
 # glace.ess.uci.edu  : NCO          CMake     All else GCC
-# grele.ess.uci.edu  : NCO          Makefile  All else GCC
+# grele.ess.uci.edu  : NCO + netCDF Makefile  All else GCC
 # katabatic.ess.uci.e: NCO          CMake     All else clang
 # rhea.ccs.ornl.gov  : NCO          Makefile  All else GCC
 # skyglow.ess.uci.edu: NCO + netCDF Configure All else GCC
@@ -42,7 +42,7 @@
 # Usage (Compilation):
 # cd ~/nco/qt;qmake;make;cd -        # Qt
 # cd ~/nco/bld;make;cd -             # Default build
-# cd ~/nco/bld;make USR_TKN='-DNC_HAVE_RENAME_GRP';cd - # New API
+# cd ~/nco/bld;make USR_TKN='-DHAVE_NC_RENAME_GRP';cd - # New API
 # cd ~/nco/bld;make UDUNITS_INC='/usr/include/udunits2';cd - # Fedora build
 # cd ~/nco/bld;make cln bin_cln;cd - # Clean all dependencies for fresh build
 # cd ~/nco/bld;make dir all; cd -    # Create target directories then build

bld/nco.spec

@@ -2,17 +2,17 @@
 # http://cvs.fedoraproject.org/viewvc/devel/nco/nco.spec?view=co
 
 Name:           nco
-Version:        4.7.5
+Version:        4.7.6
 Release:        1%{?dist}
 Summary:        Programs that manipulate netCDF files
 Group:          Applications/Engineering
 License:        GPL3
 URL:            http://nco.sf.net/
 
-# Obtain NCO version 4.7.5-1 tar.gz from Sourceforge using CVS:
+# Obtain NCO version 4.7.6-1 tar.gz from Sourceforge using CVS:
 # cvs -d:pserver:anonymous@nco.cvs.sf.net:/cvsroot/nco login
-# cvs -z3 -d:pserver:anonymous@nco.cvs.sf.net:/cvsroot/nco co -r nco-4.7.5-1 -d nco-%{version} nco
-# tar czf nco-%{version}.tar.gz --exclude='nco-4.7.5/debian*' --exclude='.cvsignore' --exclude=ncap_lex.c --exclude='ncap_yacc.[ch]' ./nco-%{version}
+# cvs -z3 -d:pserver:anonymous@nco.cvs.sf.net:/cvsroot/nco co -r nco-4.7.6-1 -d nco-%{version} nco
+# tar czf nco-%{version}.tar.gz --exclude='nco-4.7.6/debian*' --exclude='.cvsignore' --exclude=ncap_lex.c --exclude='ncap_yacc.[ch]' ./nco-%{version}
 Source0:        nco-%{version}.tar.gz
 #Patch0:		nco_install_C_headers.patch
 #Patch1:         nco_find_udunits-dat.patch
@@ -108,6 +108,9 @@ fi
 # %{_libdir}/libnco++.so
 
 %changelog
+* Sat Aug 11 2018 Charlie Zender <zender@uci.edu> - 4.7.6-1
+- new upstream 4.7.6
+
 * Sun Jun 10 2018 Charlie Zender <zender@uci.edu> - 4.7.5-1
 - new upstream 4.7.5
 

bld/nco_dst.pl

@@ -5,20 +5,20 @@
 
 # Usage:
 # Export tagged, public versions
-# /usr/bin/scp ${DATA}/nco-4.7.5.tar.gz zender,nco@web.sf.net:/home/project-web/nco/htdocs/src
-
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln nco-4.7.5 # Build, do not release on SF
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln --sf nco-4.7.5 # Build, release on SF
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --nst_all nco-4.7.5 # Install, do not build
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln --nst_all nco-4.7.5 # Build and install
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --acd_cnt nco-4.7.5
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --acd_prs nco-4.7.5
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --cgd_cnt nco-4.7.5
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --cray_prs nco-4.7.5
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --bbl_cnt nco-4.7.5
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --blk_cnt nco-4.7.5
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --dat_cnt nco-4.7.5
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --ute_prs nco-4.7.5
+# /usr/bin/scp ${DATA}/nco-4.7.6.tar.gz zender,nco@web.sf.net:/home/project-web/nco/htdocs/src
+
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln nco-4.7.6 # Build, do not release on SF
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln --sf nco-4.7.6 # Build, release on SF
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --nst_all nco-4.7.6 # Install, do not build
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln --nst_all nco-4.7.6 # Build and install
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --acd_cnt nco-4.7.6
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --acd_prs nco-4.7.6
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --cgd_cnt nco-4.7.6
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --cray_prs nco-4.7.6
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --bbl_cnt nco-4.7.6
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --blk_cnt nco-4.7.6
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --dat_cnt nco-4.7.6
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --ute_prs nco-4.7.6
 
 # Export daily snapshot
 # ${HOME}/nco/bld/nco_dst.pl --dbg=2 
@@ -256,7 +256,7 @@ if($bld){
 # Set up FTP server
     chdir $dst_pth_pfx or die "$prg_nm: ERROR unable to chdir to $dst_pth_pfx: $!\n"; # $! is system error string
     cmd_prc("$cp_cmd $doc_fl ./$dst_vrs/doc"); # Copy derived documentation to source directory
-    cmd_prc("$tar_cmd cvzf $dst_fl --exclude='nco-4.7.5/debian*' --exclude='.cvsignore' --exclude=ncap_lex.c --exclude=ncap_yacc.[ch] ./$dst_vrs"); # Create gzipped tarfile
+    cmd_prc("$tar_cmd cvzf $dst_fl --exclude='nco-4.7.6/debian*' --exclude='.cvsignore' --exclude=ncap_lex.c --exclude=ncap_yacc.[ch] ./$dst_vrs"); # Create gzipped tarfile
     cmd_prc("$rsh_cmd $www_mch $rm_cmd $www_drc/src/$dst_fl"); # Remove any distribution with same name
     if($dly_snp){cmd_prc("$rsh_cmd $www_mch $rm_cmd -r $www_drc/src/nco-????????.tar.gz");} # Remove previous daily snapshots from WWW server
     cmd_prc("$rcp_cmd $dst_fl $www_mch:$www_drc/src"); # Copy local tarfile to WWW server

bm/NCO_rgr.pm

@@ -501,6 +501,20 @@ if($USER eq 'zender'){
     NCO_bm::tst_run(\@tst_cmd);
     $#tst_cmd=0; # Reset array
 
+# ncap2 #18
+   $dsc_sng="Run script to test pack() function";
+    $tst_cmd[0]="ncap2 -h -O $fl_fmt $nco_D_flg -v -S '../data/pack.nco' $in_pth_arg in.nc %tmp_fl_00%";
+    $tst_cmd[1]="ncpdq -O -U %tmp_fl_00% %tmp_fl_01%";
+    $tst_cmd[2]="ncap2 -O -h -C $fl_fmt $nco_D_flg -v -s 'n2=p_three_dmn_var_dbl.total();' %tmp_fl_01% %tmp_fl_02%";
+    $tst_cmd[3]="ncks -C -H --trd -v n2 -s '%.2f' %tmp_fl_02%";
+    $tst_cmd[4]="2802.00";
+    $tst_cmd[5]="SS_OK";
+    NCO_bm::tst_run(\@tst_cmd);
+    $#tst_cmd=0; # Reset array
+    
+
+
+    
     if($dodap eq "FALSE"){
 ####################
 #### ncatted tests #
@@ -1652,6 +1666,7 @@ if($USER eq 'zender'){
     $opr_nm='ncks';
 ####################
 
+    
 #ncks #01   
     $dsc_sng="Create T42 variable named one, uniformly 1.0 over globe in %tmp_fl_03%. (FAILURE with netCDF4 ncrename nco821)";
     $tst_cmd[0]="ncks -h -O $fl_fmt $nco_D_flg -v lat_T42,lon_T42,gw_T42 $in_pth_arg in.nc %tmp_fl_03%";
@@ -3041,6 +3056,52 @@ if($RUN_NETCDF4_TESTS_VERSION_GE_431){
     NCO_bm::tst_run(\@tst_cmd);
     $#tst_cmd=0; # Reset array
 
+# ncks #124    
+    $dsc_sng="netCDF4 test --cal switch" ;
+    $tst_cmd[0]="ncks -H -C -O $fl_fmt $nco_D_flg --cal -d time,0 -v time $in_pth_arg in.nc|grep '\"1964-03-13 21:09:00\"'";
+    $tst_cmd[1]="    time = \"1964-03-13 21:09:00\" ;";
+    $tst_cmd[2]="SS_OK";
+    NCO_bm::tst_run(\@tst_cmd);
+    $#tst_cmd=0; # Reset array
+    
+    # Check that xmllint exists  
+    my $xmllint_code=system("xmllint --version 1>: 2>&1");
+
+    if($xmllint_code == 0){
+	# 20180701: csz xmllint produces more false negatives than Emacs XML-validator, only catches egregious mistakes
+	# ncks #125
+	$dsc_sng="ncks test --xml switch with groups" ;
+	$tst_cmd[0]="ncks --xml $fl_fmt $nco_D_flg $in_pth_arg in_grp.nc > %tmp_fl_00%";
+	$tst_cmd[1]="xmllint --schema '../data/ncml-2.2.xsd' %tmp_fl_00% > /dev/null 2>&1 && echo xml_ok";
+	$tst_cmd[2]="xml_ok";   
+	$tst_cmd[3]="SS_OK";   
+	NCO_bm::tst_run(\@tst_cmd);
+	$#tst_cmd=0; # Reset array
+
+	# ncks #126    
+	$dsc_sng="ncks test --xml switch with regular in.nc" ;
+	$tst_cmd[0]="ncks --xml $fl_fmt $nco_D_flg $in_pth_arg in.nc > %tmp_fl_00%";
+	$tst_cmd[1]="xmllint --schema '../data/ncml-2.2.xsd' %tmp_fl_00% > /dev/null 2>&1 && echo xml_ok";
+	$tst_cmd[2]="xml_ok";   
+	$tst_cmd[3]="SS_OK";   
+	NCO_bm::tst_run(\@tst_cmd);
+	$#tst_cmd=0; # Reset array
+    } # !XML
+
+# ncks #127    
+# ncatted -O -a standard_name,,d,, ~/nco/data/in.nc ~/foo.nc
+# ncks -O -X 150.,210.,-15.,45. -v gds_var,gds_3dvar ~/foo.nc ~/foo1.nc
+# ncap2 -v -O -S '../data/chk-aux-subset.nco' ~/foo1.nc ~/foo2.nc
+# ncks -O -C -H --trd -v nbr_err -s '%d' ~/foo2.nc;
+    $dsc_sng="ncks test auxiliary coords WITHOUT standard_name";
+    $tst_cmd[0]="ncatted -O $fl_fmt $nco_D_flg -a standard_name,,d,, $in_pth_arg in.nc %tmp_fl_00%";
+    $tst_cmd[1]="ncks -O $fl_fmt $nco_D_flg -X 150.,210.,-15.,45. -v gds_var,gds_3dvar %tmp_fl_00% %tmp_fl_01%";
+    $tst_cmd[2]="ncap2 -v -O $fl_fmt $nco_D_flg -S '../data/chk-aux-subset.nco' %tmp_fl_01% %tmp_fl_02%";
+    $tst_cmd[3]="ncks -O -C -H --trd -v nbr_err -s '%d' %tmp_fl_02%";
+    $tst_cmd[4]="0";
+    $tst_cmd[5]="SS_OK";
+    NCO_bm::tst_run(\@tst_cmd);
+    $#tst_cmd=0; # Reset array
 
 #####################
 #### ncpdq tests #### -OK !
@@ -5015,7 +5076,7 @@ if(0){
     $dsc_sng="test wrapped ttl with dbl_prc patch (harmless failure expected/OK on all chips since wrap behavior is not IEEE-specified)";
     $tst_cmd[0]="ncwa $omp_flg -h -O $fl_fmt $nco_D_flg -y ttl -v val_max_max_sht $in_pth_arg in.nc %tmp_fl_00% 2> %tmp_fl_02%";
     $tst_cmd[1]="ncks -C -H --trd -s '%d' -v val_max_max_sht %tmp_fl_00%";
-#    $nsr_xpc= -31536 ; # Expected on Pentium IV GCC Debian 3.4.3-13, PowerPC xlc
+#    $nsr_xpc= -31536 ; # Expected on Pentium IV GCC Debian 3.4.3-13, PowerPC xlmlc
 #    $nsr_xpc= -32768 ; # Expected on Xeon GCC Fedora 3.4.2-6.fc3
 #    $nsr_xpc= -32768 ; # Expected on Opteron
 #    $nsr_xpc= -32768 ; # Expected on PentiumIII (Coppermine) gcc 3.4 MEPIS

cmake/bld.bat

-:: cmake build all NCO dependencies obtained with 'git clone'
+:: bld.bat
+:: Windows script to build NCO on the command line, using Visual Studio 
+:: 1) clones all NCO dependecies 
+:: 2) cmake builds all NCO dependencies obtained with 'git clone'
+:: 3) cmake builds NCO
+:: 4) tests the netcdf build by reading a remote file with the built ncdump
+:: 5) tests the NCO build by using the built ncks to read 2 files (in.nc, in_grp.nc)
+:: and dumping content to a text file; this text file is compared using the FC tool with pre-existing output (generated in Linux)
+:: Notes:
+:: 1) must be run from ~/nco/cmake
+:: 2) requires manual editing of the 'hdf5' and 'netcdf' generated Visual Studio projects,
+:: so that dependencies ZLIB and SZIP are detected. This is explained in ~/nco/cmake/README.md
+:: 3) the existence of a NCO build is tested with the existence of a built ncks with
+:: if exist %build%\Debug\ncks.exe
+:: to force another cmake build, '%build%\Debug\ncks.exe' can be deleted and retyping
+:: $bld.bat
 :: Pedro Vicente
 
 @echo off
@@ -409,6 +424,9 @@ set data=%root_win%\..\data
 %build%\netcdf-c\build\ncgen\ncgen.exe -k netCDF-4 -b -o %data%\in.nc %data%\in.cdl
 %build%\Debug\ncks.exe --jsn_fmt 2 -C -g g10 -v two_dmn_rec_var %data%\in_grp.nc
 
+:: generation of comparison files in UNIX done with
+:: pvicente@glace:~/nco/data$ ../cmake/ncks in_grp.nc > in_grp.nc.txt
+:: pvicente@glace:~/nco/data$ ../cmake/ncks in.nc > in.nc.txt
 :: generate text files in_grp.nc.gen.txt from in_grp.nc and in.nc and use tool FC to compare contents 
 :: with pre-existing in_grp.nc.txt, in.nc.txt, generated in Linux
 :: generation of in_grp.nc.gen.txt must be done in 'data' folder so that paths match

cmake/in.nc.txt

@@ -1675,7 +1675,7 @@ netcdf in {
 
     RDM = 1, 9, 36, 84, 126, 126, 84, 36, 9, 1 ;
 
-    SALT = -9.96921e+33, 0.032, 0.033, 0.034, 0.035, 0.036, 0.037, 0.038, -9.96921e+33, -9.96921e+33 ;
+    SALT = _, 0.032, 0.033, 0.034, 0.035, 0.036, 0.037, 0.038, _, _ ;
 
     albers_conical_equal_area = "" ;
 
@@ -1841,9 +1841,9 @@ netcdf in {
     "/data/zender/dstccm04/dstccm04_8589_09.nc", 
     "/data/zender/dstccm04/dstccm04_8589_10.nc" ;
 
-    fll_val = 73, -999, 73, -999 ;
+    fll_val = 73, _, 73, _ ;
 
-    fll_val_mss_val = 73, -999, 73, -999 ;
+    fll_val_mss_val = 73, _, 73, _ ;
 
     float_var = 10 ;
 
@@ -2044,21 +2044,21 @@ netcdf in {
 
     mmr_CO2 = 0.000611 ;
 
-    msk_prt_mss_prt = 0.5, 1e+36, 1.5, 1e+36 ;
+    msk_prt_mss_prt = 0.5, _, 1.5, _ ;
 
-    mss_val = 73, 1e+36, 73, 1e+36 ;
+    mss_val = 73, _, 73, _ ;
 
-    mss_val_all = 1e+36, 1e+36, 1e+36, 1e+36 ;
+    mss_val_all = _, _, _, _ ;
 
-    mss_val_fst = -999, 73, -999, 73 ;
+    mss_val_fst = _, 73, _, 73 ;
 
-    mss_val_scl = 1e+36 ;
+    mss_val_scl = _ ;
 
-    mss_val_scl_sml = 10000 ;
+    mss_val_scl_sml = _ ;
 
     nan_arr = 0, 73 ;
 
-    nan_scl = 1 ;
+    nan_scl = _ ;
 
     nbdate = 640224 ;
 
@@ -2089,33 +2089,33 @@ netcdf in {
 
     one_dmn_rec_var = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 ;
 
-    one_dmn_rec_var__FillValue = 1, 2, 3, 4, 5, 6, 7, 8, 9, 1e+36 ;
+    one_dmn_rec_var__FillValue = 1, 2, 3, 4, 5, 6, 7, 8, 9, _ ;
 
     one_dmn_rec_var_dbl = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 ;
 
     one_dmn_rec_var_flt = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 ;
 
-    one_dmn_rec_var_flt_mss = 1e+36, 2, 3, 4, 5, 6, 7, 8, 9, 1e+36 ;
+    one_dmn_rec_var_flt_mss = _, 2, 3, 4, 5, 6, 7, 8, 9, _ ;
 
-    one_dmn_rec_var_flt_mss_scl = 1e+36, 2, 3, 4, 5, 6, 7, 8, 9, 1e+36 ;
+    one_dmn_rec_var_flt_mss_scl = _, 2, 3, 4, 5, 6, 7, 8, 9, _ ;
 
     one_dmn_rec_var_flt_scl = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 ;
 
     one_dmn_rec_var_mdn = 1, 1, 2, 2, 2, 2, 10, 10, 10, 10 ;
 
-    one_dmn_rec_var_mdn__FillValue = 1, -999, 2, 2, -999, -999, 10, 10, 10, -999 ;
+    one_dmn_rec_var_mdn__FillValue = 1, _, 2, 2, _, _, 10, 10, 10, _ ;
 
     one_dmn_rec_var_missing_value = 1, 2, 3, 4, 5, 6, 7, 8, 9, 1e+36 ;
 
-    one_dmn_rec_var_mss_val = 1e+36, 1e+36, 1e+36, 1e+36, 1e+36, 1e+36, 1e+36, 1e+36, 1e+36, 1e+36 ;
+    one_dmn_rec_var_mss_val = _, _, _, _, _, _, _, _, _, _ ;
 
-    one_dmn_rec_var_mss_val_arr = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 ;
+    one_dmn_rec_var_mss_val_arr = _, 2, 3, 4, 5, 6, 7, 8, 9, 10 ;
 
     one_dmn_rec_var_sng = "Hello Worl" ;
 
     one_dmn_rec_var_unsorted = 10, 4, 6, 2, 8, 1, 9, 7, 3, 5 ;
 
-    one_dmn_rec_var_unsorted__FillValue = 1e+36, 4, 6, 2, 8, 1, 9, 7, 3, 5 ;
+    one_dmn_rec_var_unsorted__FillValue = _, 4, 6, 2, 8, 1, 9, 7, 3, 5 ;
 
     one_dmn_rec_wgt = 2, 1, 0, 0, 0, 0, 0, 0, 0, 0 ;
 
@@ -2197,43 +2197,43 @@ netcdf in {
 
     rec_var_dbl = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 ;
 
-    rec_var_dbl_mss_val_dbl_pck = -999, 32767, 21845, 10922, 0, -10922, -21845, -32767, -999, -999 ;
+    rec_var_dbl_mss_val_dbl_pck = _, 32767, 21845, 10922, 0, -10922, -21845, -32767, _, _ ;
 
-    rec_var_dbl_mss_val_dbl_pck_lng = -999, 32767, 21845, 10922, 0, -10922, -21845, -32767, -999, -999 ;
+    rec_var_dbl_mss_val_dbl_pck_lng = _, 32767, 21845, 10922, 0, -10922, -21845, -32767, _, _ ;
 
-    rec_var_dbl_mss_val_dbl_upk = -999, 2, 3, 4, 5, 6, 7, 8, -999, -999 ;
+    rec_var_dbl_mss_val_dbl_upk = _, 2, 3, 4, 5, 6, 7, 8, _, _ ;
 
-    rec_var_dbl_mss_val_sht_pck = -999, 32767, 21845, 10922, 0, -10922, -21845, -32767, -999, -999 ;
+    rec_var_dbl_mss_val_sht_pck = _, 32767, 21845, 10922, 0, -10922, -21845, -32767, _, _ ;
 
-    rec_var_dbl_mss_val_sht_pck_sht = -999, 32767, 21845, 10922, 0, -10922, -21845, -32767, -999, -999 ;
+    rec_var_dbl_mss_val_sht_pck_sht = _, 32767, 21845, 10922, 0, -10922, -21845, -32767, _, _ ;
 
-    rec_var_dbl_mss_val_sht_upk = -999, 2, 3, 4, 5, 6, 7, 8, -999, -999 ;
+    rec_var_dbl_mss_val_sht_upk = _, 2, 3, 4, 5, 6, 7, 8, _, _ ;
 
     rec_var_dbl_pck = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 ;
 
     rec_var_flt = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 ;
 
-    rec_var_flt_mss_val_dbl = 1e+36, 2, 3, 4, 5, 6, 7, 8, 1e+36, 1e+36 ;
+    rec_var_flt_mss_val_dbl = _, 2, 3, 4, 5, 6, 7, 8, _, _ ;
 
-    rec_var_flt_mss_val_flt = 1e+36, 2, 3, 4, 5, 6, 7, 8, 1e+36, 1e+36 ;
+    rec_var_flt_mss_val_flt = _, 2, 3, 4, 5, 6, 7, 8, _, _ ;
 
-    rec_var_flt_mss_val_flt_all = 1e+36, 1e+36, 1e+36, 1e+36, 1e+36, 1e+36, 1e+36, 1e+36, 1e+36, 1e+36 ;
+    rec_var_flt_mss_val_flt_all = _, _, _, _, _, _, _, _, _, _ ;
 
-    rec_var_flt_mss_val_flt_all_but_one = 1e+36, 1e+36, 1e+36, 1e+36, 5, 1e+36, 1e+36, 1e+36, 1e+36, 1e+36 ;
+    rec_var_flt_mss_val_flt_all_but_one = _, _, _, _, 5, _, _, _, _, _ ;
 
-    rec_var_flt_mss_val_flt_all_but_two = 1e+36, 1e+36, 1e+36, 1e+36, 5, 1e+36, 1e+36, 1e+36, 1e+36, 10 ;
+    rec_var_flt_mss_val_flt_all_but_two = _, _, _, _, 5, _, _, _, _, 10 ;
 
-    rec_var_flt_mss_val_flt_pck_flt = -9.96921e+33, 0.032, 0.033, 0.034, 0.035, 0.036, 0.037, 0.038, -9.96921e+33, -9.96921e+33 ;
+    rec_var_flt_mss_val_flt_pck_flt = _, 0.032, 0.033, 0.034, 0.035, 0.036, 0.037, 0.038, _, _ ;
 
-    rec_var_flt_mss_val_int = -999, 2, 3, 4, 5, 6, 7, 8, -999, -999 ;
+    rec_var_flt_mss_val_int = _, 2, 3, 4, 5, 6, 7, 8, _, _ ;
 
     rec_var_flt_pck = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 ;
 
-    rec_var_int_mss_val_dbl = -999, 2, 3, 4, 5, 6, 7, 8, -999, -999 ;
+    rec_var_int_mss_val_dbl = _, 2, 3, 4, 5, 6, 7, 8, _, _ ;
 
-    rec_var_int_mss_val_flt = -999, 2, 3, 4, 5, 6, 7, 8, -999, -999 ;
+    rec_var_int_mss_val_flt = _, 2, 3, 4, 5, 6, 7, 8, _, _ ;
 
-    rec_var_int_mss_val_int = -999, 2, 3, 4, 5, 6, 7, 8, -999, -999 ;
+    rec_var_int_mss_val_int = _, 2, 3, 4, 5, 6, 7, 8, _, _ ;
 
     rec_var_pck_scale_factor_only = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 ;
 
@@ -2266,20 +2266,20 @@ netcdf in {
     13, 14, 15, 16, 
     17, 18, 19, 20, 
     21, 22, 23, 24, 
-    -99, -99, -99, -99, 
-    -99, -99, -99, -99, 
+    _, _, _, _, 
+    _, _, _, _, 
     33, 34, 35, 36, 
     37, 38, 39, 40, 
     41, 42, 43, 44, 
     45, 46, 47, 48, 
     49, 50, 51, 52, 
     53, 54, 55, 56, 
-    -99, 58, 59, 60, 
+    _, 58, 59, 60, 
     61, 62, 63, 64, 
     65, 66, 67, 68, 
     69, 70, 71, 72, 
-    -99, 74, 75, 76, 
-    77, 78, 79, -99 ;
+    _, 74, 75, 76, 
+    77, 78, 79, _ ;
 
     three = 3 ;
 
@@ -2350,64 +2350,64 @@ netcdf in {
     13, 14, 15, 16, 
     17, 18, 19, 20, 
     21, 22, 23, 24, 
-    -99, -99, -99, -99, 
-    -99, -99, -99, -99, 
+    _, _, _, _, 
+    _, _, _, _, 
     33, 34, 35, 36, 
     37, 38, 39, 40, 
     41, 42, 43, 44, 
     45, 46, 47, 48, 
     49, 50, 51, 52, 
     53, 54, 55, 56, 
-    -99, 58, 59, 60, 
+    _, 58, 59, 60, 
     61, 62, 63, 64, 
     65, 66, 67, 68, 
     69, 70, 71, 72, 
-    -99, 74, 75, 76, 
-    77, 78, 79, -99 ;
+    _, 74, 75, 76, 
+    77, 78, 79, _ ;
 
     three_dmn_var_int = 
     1, 2, 3, 4, 
     5, 6, 7, 8, 
     9, 10, 11, 12, 
     13, 14, 15, 16, 
-    -99, -99, -99, -99, 
-    -99, -99, -99, -99, 
+    _, _, _, _, 
+    _, _, _, _, 
     25, 26, 27, 28, 
     29, 30, 31, 32, 
     33, 34, 35, 36, 
     37, 38, 39, 40, 
-    41, -99, 43, 44, 
+    41, _, 43, 44, 
     45, 46, 47, 48, 
     49, 50, 51, 52, 
     53, 54, 55, 56, 
-    -99, 58, 59, 60, 
-    -99, 62, 63, 64, 
-    65, -99, 67, 68, 
+    _, 58, 59, 60, 
+    _, 62, 63, 64, 
+    65, _, 67, 68, 
     69, 70, 71, 72, 
-    -99, 74, 75, -99, 
+    _, 74, 75, _, 
     77, 78, 79, 80 ;
 
     three_dmn_var_sht = 
     1, 2, 3, 4, 
     5, 6, 7, 8, 
-    -99, 10, 11, 12, 
+    _, 10, 11, 12, 
     13, 14, 15, 16, 
     17, 18, 19, 20, 
     21, 22, 23, 24, 
     25, 26, 27, 28, 
     29, 30, 31, 32, 
-    -99, 34, 35, -99, 
+    _, 34, 35, _, 
     37, 38, 39, 40, 
     41, 42, 43, 44, 
-    -99, 46, 47, 48, 
+    _, 46, 47, 48, 
     49, 50, 51, 52, 
     53, 54, 55, 56, 
-    57, 58, 59, -99, 
+    57, 58, 59, _, 
     61, 62, 63, 64, 
     65, 66, 67, 68, 
     69, 70, 71, 72, 
-    -99, -99, -99, -99, 
-    -99, -99, -99, -99 ;
+    _, _, _, _, 
+    _, _, _, _ ;
 
     time = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 ;
 
@@ -2645,9 +2645,9 @@ netcdf in {
 
     val_one_int = 1 ;
 
-    val_one_mss = 1, 1e+36 ;
+    val_one_mss = 1, _ ;
 
-    val_one_mss_int = 1, -99 ;
+    val_one_mss_int = 1, _ ;
 
     val_one_one_int = 1, 1 ;
 
@@ -2667,19 +2667,19 @@ netcdf in {
     0, 1, 0, 0, 
     1, 1, 0, 2 ;
 
-    var_mss_0 = 1e+36, 1, 2, 3 ;
+    var_mss_0 = _, 1, 2, 3 ;
 
-    var_mss_1 = 0, 1e+36, 2, 3 ;
+    var_mss_1 = 0, _, 2, 3 ;
 
-    var_mss_2 = 0, 1, 1e+36, 3 ;
+    var_mss_2 = 0, 1, _, 3 ;
 
-    var_mss_3 = 0, 1, 2, 1e+36 ;
+    var_mss_3 = 0, 1, 2, _ ;
 
     var_mss_nil = 0, 1, 2, 3 ;
 
     var_nm-dash = 1 ;
 
-    vld_rng = 273, -999, 180, 179, 273, 360, 361, 1e+36, -1e+36, 273 ;
+    vld_rng = 273, _, 180, 179, 273, 360, 361, 1e+36, -1e+36, 273 ;
 
     vmr_CO2 = 0.0004 ;
 
@@ -2688,22 +2688,22 @@ netcdf in {
     wgt_one = 1, 1 ;
 
     wnd_spd = 
-    -999, 0.5, 1.5, 0.5, 
+    _, 0.5, 1.5, 0.5, 
     1.5, 0.5, 1.5, 0.5, 
-    0.5, -999, 0.5, 0.5, 
+    0.5, _, 0.5, 0.5, 
     0.5, 0.5, 0.5, 0.5, 
-    0.5, 1.5, -999, 1.5, 
+    0.5, 1.5, _, 1.5, 
     0.5, 1.5, 0.5, 1.5, 
-    0.5, 0.5, 0.5, -999, 
+    0.5, 0.5, 0.5, _, 
     0.5, 0.5, 0.5, 0.5, 
     1.5, 1.5, 1.5, 1.5, 
-    -999, 1.5, 1.5, 1.5, 
+    _, 1.5, 1.5, 1.5, 
     0.5, 0.5, 0.5, 0.5, 
-    0.5, -999, 0.5, 0.5, 
+    0.5, _, 0.5, 0.5, 
     2.5, 2.5, 2.5, 2.5, 
-    2.5, 2.5, -999, 2.5, 
+    2.5, 2.5, _, 2.5, 
     0.5, 0.5, 0.5, 0.5, 
-    0.5, 0.5, 0.5, -999, 
+    0.5, 0.5, 0.5, _, 
     0.5, 0.5, 0.5, 0.5, 
     0.5, 0.5, 0.5, 0.5, 
     0.5, 0.5, 2.5, 0.5, 

cmake/in_grp.nc.txt

@@ -70,6 +70,7 @@ netcdf in_grp {
       non_coord:purpose = "Test whether netCDF4 supports renaming non-coordinates to coordinates" ;
 
     float one ;
+      one:long_name = "one" ;
 
     double ppc_big(time) ;
 
@@ -141,10 +142,9 @@ netcdf in_grp {
 
     unique = 73 ;
 
-    val_one_mss = 1, 1e+36 ;
+    val_one_mss = 1, _ ;
 
   group: g1 {
-
     variables:
       int g1v1 ;
 
@@ -190,7 +190,6 @@ netcdf in_grp {
       v1 = 1 ;
 
     group: g1g1 {
-
       variables:
         double ppc_big(time) ;
 
@@ -231,7 +230,6 @@ netcdf in_grp {
     } // group /g1/g1\:g2
   } // group /g1
   group: g2 {
-
     variables:
       float lon(lon) ;
 
@@ -248,7 +246,6 @@ netcdf in_grp {
 
   } // group /g2
   group: g4 {
-
     variables:
       int one_dmn_rec_var(time) ;
         one_dmn_rec_var:long_name = "one dimensional record variable" ;
@@ -299,7 +296,6 @@ netcdf in_grp {
 
   } // group /g5
   group: g6 {
-
     variables:
       float area(lat) ;
 
@@ -311,7 +307,6 @@ netcdf in_grp {
       area1 = 21, 31 ;
 
     group: g6g1 {
-
       variables:
         float area(lat) ;
 
@@ -321,7 +316,6 @@ netcdf in_grp {
     } // group /g6/g6g1
   } // group /g6
   group: g7 {
-
     variables:
       float gds_crd(gds_crd) ;
         gds_crd:long_name = "Geodesic coordinate" ;
@@ -367,7 +361,6 @@ netcdf in_grp {
       ppc_flt = 0, 0.1, 0.12, 0.123, 0.1234, 0.12345, 0.123456, 0.1234567, 0.1234568, 0.1234568 ;
 
     group: g7g1 {
-
       variables:
         float gds_var(gds_crd) ;
           gds_var:units = "meter" ;
@@ -392,7 +385,6 @@ netcdf in_grp {
   } // group /g8
   group: g9 {
     group: g9g1 {
-
       variables:
         int v6 ;
 
@@ -407,7 +399,6 @@ netcdf in_grp {
           group: g9g1g1g1g1 {
             group: g9g1g1g1g1g1 {
               group: g9g1g1g1g1g1g1 {
-
                 variables:
                   double ppc_big(time) ;
 
@@ -440,7 +431,6 @@ netcdf in_grp {
     } // group /g9/g9g1
   } // group /g9
   group: g10 {
-
     variables:
       float three_dmn_rec_var(time,lat,lon) ;
         three_dmn_rec_var:units = "watt meter-2" ;
@@ -484,7 +474,6 @@ netcdf in_grp {
 
   } // group /g10
   group: g11 {
-
     variables:
       byte byte_var ;
         byte_var:long_name = "byte-type variable" ;

config.h.in

@@ -241,6 +241,9 @@
 /* Define to 1 if compiler finds external `nc_inq_path' function */
 #undef HAVE_NC_INQ_PATH
 
+/* Define to 1 if compiler finds external `nc_rename_grp' function */
+#undef HAVE_NC_RENAME_GRP
+
 /* Define to 1 if compiler finds external `nc_set_log_level' function */
 #undef HAVE_NC_SET_LOG_LEVEL
 
@@ -520,6 +523,9 @@
 /* Define to 1 if compiler needs external `nc_inq_path' function */
 #undef NEED_NC_INQ_PATH
 
+/* Define to 1 if compiler needs external `nc_rename_grp' function */
+#undef NEED_NC_RENAME_GRP
+
 /* Define to 1 if compiler needs external `nc_set_log_level' function */
 #undef NEED_NC_SET_LOG_LEVEL
 

configure

 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for NCO netCDF Operators 4.7.5.
+# Generated by GNU Autoconf 2.69 for NCO netCDF Operators 4.7.6.
 #
 # Report bugs to <nco-bugs@lists.sourceforge.net>.
 #
@@ -592,8 +592,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='NCO netCDF Operators'
 PACKAGE_TARNAME='nco'
-PACKAGE_VERSION='4.7.5'
-PACKAGE_STRING='NCO netCDF Operators 4.7.5'
+PACKAGE_VERSION='4.7.6'
+PACKAGE_STRING='NCO netCDF Operators 4.7.6'
 PACKAGE_BUGREPORT='nco-bugs@lists.sourceforge.net'
 PACKAGE_URL=''
@@ -1388,7 +1388,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures NCO netCDF Operators 4.7.5 to adapt to many kinds of systems.
+\`configure' configures NCO netCDF Operators 4.7.6 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1459,7 +1459,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of NCO netCDF Operators 4.7.5:";;
+     short | recursive ) echo "Configuration of NCO netCDF Operators 4.7.6:";;
    esac
   cat <<\_ACEOF
@@ -1621,7 +1621,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-NCO netCDF Operators configure 4.7.5
+NCO netCDF Operators configure 4.7.6
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2487,7 +2487,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
-It was created by NCO netCDF Operators $as_me 4.7.5, which was
+It was created by NCO netCDF Operators $as_me 4.7.6, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -3742,7 +3742,7 @@ fi
 # Define the identity of the package.
  PACKAGE='nco'
- VERSION='4.7.5'
+ VERSION='4.7.6'
 cat >>confdefs.h <<_ACEOF
@@ -18405,6 +18405,20 @@ cat >>confdefs.h <<_ACEOF
 #define NEED_NC_SET_LOG_LEVEL 1
 _ACEOF
+fi
+ac_fn_c_check_func "$LINENO" "nc_rename_grp" "ac_cv_func_nc_rename_grp"
+if test "x$ac_cv_func_nc_rename_grp" = xyes; then :
+
+cat >>confdefs.h <<_ACEOF
+#define HAVE_NC_RENAME_GRP 1
+_ACEOF
+
+else
+
+cat >>confdefs.h <<_ACEOF
+#define NEED_NC_RENAME_GRP 1
+_ACEOF
+
 fi
 ac_fn_c_check_func "$LINENO" "getopt" "ac_cv_func_getopt"
@@ -21496,7 +21510,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by NCO netCDF Operators $as_me 4.7.5, which was
+This file was extended by NCO netCDF Operators $as_me 4.7.6, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -21562,7 +21576,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-NCO netCDF Operators config.status 4.7.5
+NCO netCDF Operators config.status 4.7.6
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"

configure.ac

@@ -54,7 +54,7 @@
 # 20170808: Choose between traditional version and Git-based version
 # If Git, consider that Linux dynamic libraries will have full messy name, MacOSX will not
 # https://stackoverflow.com/questions/43526939/how-to-insert-git-based-version-in-autoconf-managed-project
-AC_INIT([NCO netCDF Operators],[4.7.5],[nco-bugs@lists.sourceforge.net],[nco])
+AC_INIT([NCO netCDF Operators],[4.7.6],[nco-bugs@lists.sourceforge.net],[nco])
 
 # Print GNU copyright in configure script
 AC_COPYRIGHT
@@ -388,7 +388,7 @@ esac
 # "#define HAVE_XXX 1" and "#undef NEED_XXX" when function xxx() is found and
 # "#undef HAVE_XXX" and "#define NEED_XXX 1" when function xxx() is not found
 # Purpose: CPP macros like "if(NEED_XXX)" are simpler to read than "if(!HAVE_xxx)"
-NCO_CHECK_FUNCS([nc_inq_format nc_inq_path nc_set_log_level])
+NCO_CHECK_FUNCS([nc_inq_format nc_inq_path nc_set_log_level nc_rename_grp])
 NCO_CHECK_FUNCS([getopt getopt_long])
 NCO_CHECK_FUNCS([atan2])
 NCO_CHECK_FUNCS([acosf asinf atanf atan2f cosf expf fabsf fmodf log10f logf powf sinf sqrtf tanf])

configure.eg

@@ -311,6 +311,7 @@ make install
 # Latest sysadmin-compiled module usage: 
 # Personal recipe last modified: 20180405
 # Personal recipe last used successfully: 20180406
+# NB: aims4 and acme1 only accept connections from whitelisted domains (e.g., uci.edu)
 export GNU_TRP=`~/nco/autobld/config.guess`
 cd ~/nco;/bin/rm -f *.${GNU_TRP}.foo;make distclean
 export PATH=/usr/local/uvcdat/2016-01-21/Externals/bin:${PATH}
@@ -328,6 +329,7 @@ scp nco.configure.${GNU_TRP}.foo nco.config.log.${GNU_TRP}.foo nco.libtool.${GNU
 # Latest sysadmin-compiled module usage: 
 # Personal recipe last modified: 2016??
 # Personal recipe last used successfully: 20180406
+# NB: aims4 and acme1 only accept connections from whitelisted domains (e.g., uci.edu)
 export GNU_TRP=`~/nco/autobld/config.guess`
 cd ~/nco;/bin/rm -f *.${GNU_TRP}.foo;make distclean
 ANTLR_ROOT=${HOME} CC='gcc' CXX='g++' NETCDF_ROOT='/usr/local/uvcdat/2016-01-21/Externals' UDUNITS2_PATH='/usr/local/uvcdat/2016-01-21/Externals' ./configure --prefix=${HOME} --bindir=${MY_BIN_DIR} --datadir=${HOME}/nco/data --libdir=${MY_LIB_DIR} --mandir=${HOME}/nco/man > nco.configure.${GNU_TRP}.foo 2>&1
@@ -344,18 +346,19 @@ scp nco.configure.${GNU_TRP}.foo nco.config.log.${GNU_TRP}.foo nco.libtool.${GNU
 # Sysadmin upgrade request: support@lcrc.anl.gov
 # Latest ticket: AREQ0215917 on 20180413
 # Latest sysadmin-compiled module usage: soft add +netcdf-4.6.1 soft add +nco-4.7.4 # 20180417
-# Personal recipe last modified: 20161223
-# Personal recipe last used successfully: 20180406
-# fails to link to udunits...why?
+# Personal recipe last modified: 20180729
+# Personal recipe last used successfully: 20180729 (up to ncap2 linking with antlr)
+# Fails to link to system-installed udunits...why?
 # nm -a /soft/udunits/2.1.21/lib/libudunits2.a | grep ut_read_xml
-# First use: 20161223 Latest use: 20161223
 # soft add +antlr-2.7.7 # 20161223 this ANTLR appears to be stock and not NCO-compatible
 # soft add +udunits-2.1.21 # 20161223 this UDUnits was compiled without -fPIC so fails with NCO
-soft add +netcdf-4.3.3.1-gnu5.2-serial
+soft add +gcc-5.3
+soft add +netcdf-c-4.4.1.1-f77-4.4.4-gcc-5.3.0-serial
 soft add +gsl-2.3
 export GNU_TRP=`~/nco/autobld/config.guess`
 cd ~/nco;/bin/rm -f *.${GNU_TRP}.foo;make distclean
-ANTLR_ROOT=${HOME} CC='gcc' CXX='g++' NETCDF_ROOT='/soft/netcdf_serial/4.3.3.1/gnu-5.2' UDUNITS2_PATH=${HOME} ./configure --prefix=${HOME} --bindir=${MY_BIN_DIR} --datadir=${HOME}/nco/data --libdir=${MY_LIB_DIR} --mandir=${HOME}/nco/man > nco.configure.${GNU_TRP}.foo 2>&1
+ANTLR_ROOT=${HOME} CC='gcc' CXX='g++' NETCDF_ROOT='/soft/spack-0.10.0/opt/spack/linux-centos6-x86_64/gcc-5.3.0/netcdf-4.4.1.1-2dtwbu4ojkwj5tqd4uqvomnu6ecmh6tx' UDUNITS2_PATH=${HOME} ./configure --prefix=${HOME} --bindir=${MY_BIN_DIR} --datadir=${HOME}/nco/data --libdir=${MY_LIB_DIR} --mandir=${HOME}/nco/man > nco.configure.${GNU_TRP}.foo 2>&1
+ANTLR_ROOT='/soft/antlr/2.7.7' CC='gcc' CXX='g++' NETCDF_ROOT='/soft/spack-0.10.0/opt/spack/linux-centos6-x86_64/gcc-5.3.0/netcdf-4.4.1.1-2dtwbu4ojkwj5tqd4uqvomnu6ecmh6tx' UDUNITS2_PATH=${HOME} ./configure --prefix=${HOME} --bindir=${MY_BIN_DIR} --datadir=${HOME}/nco/data --libdir=${MY_LIB_DIR} --mandir=${HOME}/nco/man > nco.configure.${GNU_TRP}.foo 2>&1
 /bin/cp -f config.log nco.config.log.${GNU_TRP}.foo
 /bin/cp -f libtool nco.libtool.${GNU_TRP}.foo
 make clean;make > nco.make.${GNU_TRP}.foo 2>&1
@@ -368,7 +371,7 @@ scp nco.configure.${GNU_TRP}.foo nco.config.log.${GNU_TRP}.foo nco.libtool.${GNU
 # Latest ticket: 216373 on 20180413
 # Latest sysadmin-compiled module usage: module load netcdf/4.6.1 module load nco/4.7.4 # 20180417
 # Personal recipe last modified: 20180427
-# Personal recipe last used successfully: 20180427 (getopt errors were eliminated by removing ~/include/getopt*.h)
+# Personal recipe last used successfully: 20180711 (getopt errors were eliminated by removing ~/include/getopt*.h)
 module purge
 module load ncarenv intel ncarcompilers mpt netcdf
 module add intel
@@ -424,7 +427,7 @@ scp nco.configure.${GNU_TRP}.foo nco.config.log.${GNU_TRP}.foo nco.libtool.${GNU
 # Latest ticket: INC0118469 on 20180413
 # Latest sysadmin-compiled module usage: module load nco/4.7.4 # 20180430 (without ncap2)
 # Personal recipe last modified: 20170807
-# Personal recipe last used successfully: 20180302 (20180406 but can't find antlr)
+# Personal recipe last used successfully: 20180808 (but must manually link to -L${HOME}/lib_edison to find antlr)
 module load szip
 module load gsl
 module load udunits2
@@ -723,7 +726,15 @@ To build NCO with netCDF4, we require changes from the default process:
 ************************************************************************
 End NETCDF4
 ************************************************************************
-
+cd
+/bin/rm -r -f nco
+git clone git@github.com:nco/nco.git
+cd nco
+<configure>
+make install
+cd ~/nco/data
+make
+cd ~/nco
 ************************************************************************
 Start LINUXAMD64
 Status: Appears to work. Make sure to compile netCDF and DAP with CFLAGS+='-fPIC'
@@ -737,7 +748,12 @@ x86_64-unknown-linux-gnu
 # Zender uses this on MACOSX aerosol/firn as well
 export GNU_TRP=`~/nco/autobld/config.guess`
 cd ~/nco;/bin/rm -f *.${GNU_TRP}.foo;make distclean
+# Pre-20180729 (antlr from macports seemed to have stopped linking, so build it from scratch)
 CC='gcc' CFLAGS='' CXX='g++' CXXFLAGS='' ./configure --prefix=${HOME} --bindir=${MY_BIN_DIR} --datadir=${HOME}/nco/data --libdir=${MY_LIB_DIR} --mandir=${HOME}/nco/man > nco.configure.${GNU_TRP}.foo 2>&1
+# Firn 20180729
+ANTLR_ROOT=${HOME} CC='gcc' CFLAGS='' CXX='g++' CXXFLAGS='' ./configure --prefix=${HOME} --bindir=${MY_BIN_DIR} --datadir=${HOME}/nco/data --libdir=${MY_LIB_DIR} --mandir=${HOME}/nco/man > nco.configure.${GNU_TRP}.foo 2>&1
+# Aerosol 20180729
+ANTLR_ROOT=${HOME} CC=${LINUX_CC} CFLAGS='' CXX=${LINUX_CXX} CXXFLAGS='' ./configure --prefix=${HOME} --bindir=${MY_BIN_DIR} --datadir=${HOME}/nco/data --libdir=${MY_LIB_DIR} --mandir=${HOME}/nco/man > nco.configure.${GNU_TRP}.foo 2>&1
 /bin/cp -f config.log nco.config.log.${GNU_TRP}.foo
 /bin/cp -f libtool nco.libtool.${GNU_TRP}.foo
 make clean;make > nco.make.${GNU_TRP}.foo 2>&1
@@ -778,7 +794,7 @@ make check >> nco.make.${GNU_TRP}.foo 2>&1
 make install >> nco.make.${GNU_TRP}.foo 2>&1
 scp nco.configure.${GNU_TRP}.foo nco.config.log.${GNU_TRP}.foo nco.libtool.${GNU_TRP}.foo nco.make.${GNU_TRP}.foo dust.ess.uci.edu:Sites/nco/rgr
 
-# gcc/g++ Zender uses this to debug NCO with pre-built netCDF binaries in /usr (frazil, skyglow)
+# gcc/g++ Zender uses this to debug NCO with pre-built netCDF binaries in /usr (skyglow)
 export GNU_TRP=`~/nco/autobld/config.guess`
 cd ~/nco;/bin/rm -f *.${GNU_TRP}.foo;make distclean
 # Pre-20170810 GCC7 dies on nco_yyget_leng() prototype with --enable-debug-custom option

data/chk-aux-subset.nco

+
+// Purpose: Script to test subsetting with auxiliary coordinates 
+//  print("Test script for subsetting of auxiliary coordinates\n");
+
+// Count number of errors
+nbr_err=0;
+
+if( $gds_crd.size != 2 )
+{
+
+  print("ERROR: gds_crd dim wrong size\n");
+  nbr_err++;
+
+ }
+
+
+if( lat_gds.type() != NC_DOUBLE || lat_gds.min() != 0.0d   || lat_gds.max() != 30.0d)
+{
+
+  print("ERROR: lat_gds coord wrong\n");
+  nbr_err++;
+
+ }
+
+if( lon_gds.type() != NC_DOUBLE || lon_gds.min() !=180.0d || lon_gds.max() != 180.0d )
+{
+
+  print("ERROR: lon_gds coord wrong\n");
+  nbr_err++;
+
+}
+
+
+if( gds_var.type() != NC_FLOAT || gds_var.ndims() != 1 )
+{
+
+  print("ERROR: gds_var shape wrong\n");
+  nbr_err++;
+
+}
+
+
+if( fabs(gds_var.min() -  273.5d)>1e-1d || fabs(gds_var.total() -  547.2d)>1e-1d )
+{
+
+  print("ERROR: gds_var values wrong\n");
+  nbr_err++;
+
+}
+
+if( gds_3dvar.type() != NC_FLOAT || gds_3dvar.ndims() != 2 )
+{
+
+  print("ERROR: gds_3dvar shape wrong\n");
+  nbr_err++;
+
+}
+
+
+if( fabs(gds_3dvar.min() -  273.5d)>1e-1d || fabs(gds_3dvar.total() - 5562.0d)>1e-1d )
+{
+
+  print("ERROR: gds_3dvar values wrong\n");
+  nbr_err++;
+
+}
+
+
+
+
+
+// Results summany
+print("RESULTS SUMMARY: total errors=");print(nbr_err,"%d");

data/enum.cdl

@@ -35,9 +35,12 @@ netcdf enum {
 				       name2\ \,\ with_comma=2,
    				       lost_value=128};
 
+   int64 enum Months {Jan=1, Feb=2, Mar=3, Apr=4, May=5, June=6, July=7, Aug=8, Sept=9, Oct=10, Nov=11, Dec=12, MISSING=9223372036854775807} ;
+ 
  dimensions:
    lat=2;
    lon=4;
+   sss=3;
    rec=8;
 
  variables:
@@ -58,6 +61,8 @@ netcdf enum {
    special_characters_type character_test(lon);
    special_characters_type character_test:_FillValue=lost_value;
 
+   Months Summer(sss);
+
     data:
    cld_flg=Stratus,_,Cumulonimbus,Clear;
    size=_,Small,Medium,Large;
@@ -77,4 +82,5 @@ netcdf enum {
 
  character_test=name\ with\ spaces,name1_\,_with_comma,name2\ \,\ with_comma,_;
 
+ Summer = June, July, Aug;
 } //end root group

data/in_grp.cdl

@@ -85,6 +85,7 @@ netcdf in_grp {
  non_coord:purpose = "Test whether netCDF4 supports renaming non-coordinates to coordinates";
   
   float one;
+ one:long_name = "one";
   
   float val_one_mss(lat);
   val_one_mss:long_name = "one regular value, one missing value";

data/mlt_rcd.cdl

+// -*-C++-*-
+// Purpose: CDL file to test multiple record dimensions
+
+// Usage:
+// ncgen -k netCDF-4 -b -o ~/nco/data/mlt_rcd.nc ~/nco/data/mlt_rcd.cdl
+// ncrcat -O -p ~/nco/data mlt_rcd.nc mlt_rcd.nc ~/foo.nc
+
+netcdf mlt_rcd {
+
+ dimensions:
+  time1=unlimited; 
+  time2=unlimited; 
+  time3=unlimited; 
+
+ variables:
+  int var1(time1);
+  int var2(time2);
+  int var3(time3);
+
+ data:
+  var1=1;
+  var2=2,2;
+  var3=3,3,3;
+
+} // end root group
+

data/ncclimo

@@ -872,7 +872,7 @@ if [ "${mdl_typ}" = 'mpas' ]; then
 fi # !mdl_typ
 # http://stackoverflow.com/questions/965053/extract-filename-and-extension-in-bash
 # http://stackoverflow.com/questions/17420994/bash-regex-match-string
-# NB: Order and 'elif' ensures name matches only fullest rx
+# NB: Order and 'elif' ensure name matches only fullest rx
 if [[ "${caseid}" =~ ^(.*)([0-9][0-9][0-9][0-9][01][0-9].nc.?)$ ]]; then
     nm_typ='yyyymm'
 elif [[ "${caseid}" =~ ^(.*)([0-9][0-9][0-9][0-9]-[01][0-9]-01.nc.?)$ ]]; then
@@ -978,13 +978,17 @@ fi # !no_stg_grd
 if [ "${par_typ}" = 'bck' ]; then 
     par_opt=' &'
     par_opt_cf=''
+    par_sng='Background'
 elif [ "${par_typ}" = 'mpi' ]; then 
     mpi_flg='Yes'
     par_opt=' &'
     par_opt_cf=''
+    par_sng='MPI'
     if [ -n "${UVCDAT_SETUP_PATH}" ]; then
 	printf "${spt_nm}: UVCDAT has been initialized in the shell running this job, and MPI-mode parallelization of ${spt_nm} is requested. Unfortunately UVCDAT's environment and the MPI-mode of ${spt_nm} do not play well together. The Workflow group is working toward a solution. The current workarounds are 1) do not use MPI-mode when UVCDAT is loaded or 2) do not initialize UVCDAT when invoking MPI-mode.\n"
     fi # !UVCDAT_SETUP_PATH
+elif [ "${par_typ}" = 'nil' ] || [ -z "${par_typ}" ]; then 
+    par_sng='Serial'
 fi # !par_typ
 if [ -n "${rgr_map}" ]; then 
     if [ ! -f "${rgr_map}" ]; then
@@ -1488,6 +1492,7 @@ else
 fi # !caseid
 printf "Running climatology script ${spt_nm} from directory ${drc_spt}\n"
 printf "NCO binaries version ${nco_vrs} from directory ${drc_nco}\n"
+printf "Parallelism mode = ${par_sng}\n"
 if [ "${sbs_flg}" = 'Yes' ]; then
     if [ ${inp_std} = 'No' ]; then 
 	if [ "${drc_in_usr_flg}" = 'Yes' ]; then

data/ncml-2.2.xsd

+<?xml version="1.0" encoding="UTF-8"?>
+<xsd:schema targetNamespace="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2"
+            xmlns:xsd="http://www.w3.org/2001/XMLSchema"
+            xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2"
+            elementFormDefault="qualified">
+  
+  <!-- XML encoding of Netcdf container object -->
+  <xsd:element name="netcdf">
+    <xsd:complexType>
+      <xsd:sequence>
+        <xsd:choice minOccurs="0">
+          <xsd:element name="readMetadata"/>
+          <xsd:element name="explicit"/>
+        </xsd:choice>
+
+        <xsd:element name="iospParam" minOccurs="0" />
+
+        <xsd:choice minOccurs="0" maxOccurs="unbounded">
+          <xsd:element ref="enumTypedef"/>
+          <xsd:element ref="group"/>
+          <xsd:element ref="dimension"/>
+          <xsd:element ref="variable"/>
+          <xsd:element ref="attribute"/>
+          <xsd:element ref="remove"/>
+        </xsd:choice>
+
+        <xsd:element ref="aggregation" minOccurs="0"/>
+      </xsd:sequence>
+
+      <xsd:attribute name="location" type="xsd:anyURI"/>
+      <xsd:attribute name="id" type="xsd:string"/>
+      <xsd:attribute name="title" type="xsd:string"/>
+      <xsd:attribute name="enhance" type="xsd:string"/>
+      <xsd:attribute name="addRecords" type="xsd:boolean"/>
+
+      <!-- iosp class name -->
+      <xsd:attribute name="iosp" type="xsd:string"/>
+      <!-- iosp parameter -->
+      <xsd:attribute name="iospParam" type="xsd:string"/>
+      <!-- raf buffer size -->
+      <xsd:attribute name="bufferSize" type="xsd:int"/>
+
+      <!-- for aggregations -->
+      <xsd:attribute name="ncoords" type="xsd:string"/>
+      <xsd:attribute name="coordValue" type="xsd:string"/>
+      <xsd:attribute name="section" type="xsd:string"/>
+    </xsd:complexType>
+  </xsd:element>
+
+  <!-- XML encoding of group object -->
+  <xsd:element name="group">
+    <xsd:complexType>
+      <xsd:choice minOccurs="0" maxOccurs="unbounded">
+        <xsd:element ref="enumTypedef"/>
+        <xsd:element ref="dimension"/>
+        <xsd:element ref="variable"/>
+        <xsd:element ref="attribute"/>
+        <xsd:element ref="group"/>
+        <xsd:element ref="remove"/>
+      </xsd:choice>
+      <xsd:attribute name="name" type="xsd:string" use="required"/>
+      <xsd:attribute name="orgName" type="xsd:string"/>
+    </xsd:complexType>
+  </xsd:element>
+
+  <!-- XML encoding of dimension object -->
+  <xsd:element name="dimension">
+    <xsd:complexType>
+      <xsd:attribute name="name" type="xsd:token" use="required"/>
+      <xsd:attribute name="length" type="xsd:string"/>
+      <xsd:attribute name="isUnlimited" type="xsd:boolean" default="false"/>
+      <xsd:attribute name="isVariableLength" type="xsd:boolean" default="false"/>
+      <xsd:attribute name="isShared" type="xsd:boolean" default="true"/>
+      <xsd:attribute name="orgName" type="xsd:string"/>
+    </xsd:complexType>
+  </xsd:element>
+
+  <!-- XML encoding of Variable object -->
+  <xsd:element name="variable">
+    <xsd:complexType>
+      <xsd:sequence>
+        <xsd:element ref="attribute" minOccurs="0" maxOccurs="unbounded"/>
+        <xsd:element ref="values" minOccurs="0"/>
+        <xsd:element ref="variable" minOccurs="0" maxOccurs="unbounded"/>
+        <xsd:element ref="logicalSection" minOccurs="0"/>
+        <xsd:element ref="logicalSlice" minOccurs="0"/>
+        <xsd:element ref="logicalReduce" minOccurs="0"/>
+        <xsd:element ref="remove" minOccurs="0" maxOccurs="unbounded"/>
+      </xsd:sequence>
+      <xsd:attribute name="name" type="xsd:token" use="required"/>
+      <xsd:attribute name="type" type="DataType"/>
+      <xsd:attribute name="typedef" type="xsd:string"/>
+      <xsd:attribute name="shape" type="xsd:token"/>
+      <xsd:attribute name="orgName" type="xsd:string"/>
+    </xsd:complexType>
+  </xsd:element>
+
+  <!-- XML encoding of values -->
+  <xsd:element name="values">
+    <xsd:complexType mixed="true">
+      <xsd:attribute name="start" type="xsd:float"/>
+      <xsd:attribute name="increment" type="xsd:float"/>
+      <xsd:attribute name="npts" type="xsd:int"/>
+      <xsd:attribute name="separator" type="xsd:string"/>
+      <xsd:attribute name="fromAttribute" type="xsd:string"/>
+    </xsd:complexType>
+  </xsd:element>
+
+  <!-- XML encoding of Attribute object -->
+  <xsd:element name="attribute">
+    <xsd:complexType mixed="true">
+      <xsd:attribute name="name" type="xsd:token" use="required"/>
+      <xsd:attribute name="type" type="DataType" default="String"/>
+      <xsd:attribute name="value" type="xsd:string"/>
+      <xsd:attribute name="separator" type="xsd:string"/>
+      <xsd:attribute name="orgName" type="xsd:string"/>
+      <xsd:attribute name="isUnsigned" type="xsd:boolean"/>
+    </xsd:complexType>
+  </xsd:element>
+
+  <!-- possible data types for Variable, Attribute objects -->
+  <xsd:simpleType name="DataType">
+    <xsd:restriction base="xsd:token">
+      <xsd:enumeration value="byte"/>
+      <xsd:enumeration value="char"/>
+      <xsd:enumeration value="short"/>
+      <xsd:enumeration value="int"/>
+      <xsd:enumeration value="long"/>
+      <xsd:enumeration value="float"/>
+      <xsd:enumeration value="double"/>
+      <xsd:enumeration value="String"/>
+      <xsd:enumeration value="string"/>
+      <xsd:enumeration value="Structure"/>
+      <xsd:enumeration value="Sequence"/>
+      <xsd:enumeration value="opaque"/>
+      <xsd:enumeration value="enum1"/>
+      <xsd:enumeration value="enum2"/>
+      <xsd:enumeration value="enum4"/>
+    </xsd:restriction>
+  </xsd:simpleType>
+
+  <!-- XML encoding of enum typedef object -->
+ <xsd:element name="enumTypedef">
+    <xsd:complexType>
+      <xsd:sequence>
+        <xsd:element name="enum" minOccurs="1" maxOccurs="unbounded">
+          <xsd:complexType mixed="true">
+            <xsd:attribute name="key" type="xsd:int" use="required"/>
+          </xsd:complexType>
+        </xsd:element>
+      </xsd:sequence>
+      <xsd:attribute name="name" type="xsd:token" use="required"/>
+      <xsd:attribute name="type" type="DataType" default="enum1"/>
+    </xsd:complexType>
+  </xsd:element>
+
+
+  <!-- Dataset **********************************************************************-->
+
+  <xsd:element name="remove">
+    <xsd:complexType>
+      <xsd:attribute name="type" type="ObjectType" use="required"/>
+      <xsd:attribute name="name" type="xsd:string" use="required"/>
+    </xsd:complexType>
+  </xsd:element>
+
+  <xsd:simpleType name="ObjectType">
+    <xsd:restriction base="xsd:string">
+      <xsd:enumeration value="attribute"/>
+      <xsd:enumeration value="dimension"/>
+      <xsd:enumeration value="variable"/>
+      <xsd:enumeration value="group"/>
+    </xsd:restriction>
+  </xsd:simpleType>
+
+  <!-- logical view: use only a section of original  -->
+  <xsd:element name="logicalSection">
+    <xsd:complexType>
+      <xsd:attribute name="section" type="xsd:token" use="required"/>  <!-- creates anonymous dimension -->
+    </xsd:complexType>
+  </xsd:element>
+
+  <xsd:element name="logicalSlice">
+    <xsd:complexType>
+      <xsd:attribute name="dimName" type="xsd:token" use="required"/>
+      <xsd:attribute name="index" type="xsd:int" use="required"/>
+    </xsd:complexType>
+  </xsd:element>
+
+  <xsd:element name="logicalReduce">
+     <xsd:complexType>
+       <xsd:attribute name="dimNames" type="xsd:string" use="required"/>
+     </xsd:complexType>
+   </xsd:element>
+
+   <!-- aggregation  -->
+  <xsd:element name="aggregation">
+    <xsd:complexType>
+      <xsd:sequence>
+
+        <!-- experimental - modify each dataset in aggregation  -->
+        <xsd:choice minOccurs="0" maxOccurs="unbounded">
+          <xsd:element ref="group"/>
+          <xsd:element ref="dimension"/>
+          <xsd:element ref="variable"/>
+          <xsd:element ref="attribute"/>
+          <xsd:element ref="remove"/>
+        </xsd:choice>
+
+        <xsd:element name="variableAgg" minOccurs="0" maxOccurs="unbounded">
+          <xsd:complexType>
+            <xsd:attribute name="name" type="xsd:string" use="required"/>
+          </xsd:complexType>
+        </xsd:element>
+
+        <xsd:element ref="promoteGlobalAttribute" minOccurs="0" maxOccurs="unbounded"/>
+        <xsd:element ref="cacheVariable" minOccurs="0" maxOccurs="unbounded"/>
+        <xsd:element ref="netcdf" minOccurs="0" maxOccurs="unbounded"/>
+
+        <xsd:element name="scan" minOccurs="0" maxOccurs="unbounded">
+          <xsd:complexType>
+            <xsd:attribute name="location" type="xsd:string" use="required"/>
+            <xsd:attribute name="regExp" type="xsd:string"/>
+            <xsd:attribute name="suffix" type="xsd:string"/>
+            <xsd:attribute name="subdirs" type="xsd:boolean" default="true"/>
+            <xsd:attribute name="olderThan" type="xsd:string"/>
+
+            <xsd:attribute name="dateFormatMark" type="xsd:string"/>
+            <xsd:attribute name="enhance" type="xsd:boolean"/>
+          </xsd:complexType>
+        </xsd:element>
+
+        <!-- fmrcSingle only  -->
+        <xsd:element name="scanFmrc" minOccurs="0" maxOccurs="unbounded">
+          <xsd:complexType>
+            <xsd:attribute name="location" type="xsd:string" use="required"/>
+            <xsd:attribute name="regExp" type="xsd:string"/>
+            <xsd:attribute name="suffix" type="xsd:string"/>
+            <xsd:attribute name="subdirs" type="xsd:boolean" default="true"/>
+            <xsd:attribute name="olderThan" type="xsd:string"/>
+
+            <xsd:attribute name="runDateMatcher" type="xsd:string"/>
+            <xsd:attribute name="forecastDateMatcher" type="xsd:string"/>
+            <xsd:attribute name="forecastOffsetMatcher" type="xsd:string"/>
+          </xsd:complexType>
+        </xsd:element>
+
+      </xsd:sequence>
+
+      <xsd:attribute name="type" type="AggregationType" use="required"/>
+      <xsd:attribute name="dimName" type="xsd:token"/>
+      <xsd:attribute name="recheckEvery" type="xsd:string"/>
+      <xsd:attribute name="timeUnitsChange" type="xsd:boolean"/>
+
+      <!-- fmrc, fmrcSingle only  -->
+      <xsd:attribute name="fmrcDefinition" type="xsd:string"/>
+
+    </xsd:complexType>
+  </xsd:element>
+
+  <!-- type of aggregation -->
+  <xsd:simpleType name="AggregationType">
+    <xsd:restriction base="xsd:string">
+      <xsd:enumeration value="forecastModelRunCollection"/>
+      <xsd:enumeration value="forecastModelRunSingleCollection"/>
+      <xsd:enumeration value="joinExisting"/>
+      <xsd:enumeration value="joinNew"/>
+      <xsd:enumeration value="tiled"/>
+      <xsd:enumeration value="union"/>
+    </xsd:restriction>
+  </xsd:simpleType>
+
+ <!-- promote global attribute to variable -->
+ <xsd:element name="promoteGlobalAttribute">
+   <xsd:complexType>
+     <xsd:attribute name="name" type="xsd:token" use="required"/>
+     <xsd:attribute name="orgName" type="xsd:string"/>
+   </xsd:complexType>
+ </xsd:element>
+
+  <!-- cache a Variable for efficiency -->
+ <xsd:element name="cacheVariable">
+   <xsd:complexType>
+     <xsd:attribute name="name" type="xsd:token" use="required"/>
+   </xsd:complexType>
+ </xsd:element>
+
+ </xsd:schema>

data/pack.nco

+p_three_dmn_var_dbl=pack(three_dmn_var_dbl);
+p_time=pack(time,0,1.0);
+p_three_dmn_var_dbl1=pack(three_dmn_var_dbl,0.0,1.0);
+p_time_udunits=pack(time_udunits,0.0,1.0);
+p_three_dmn_var_dbl2=pack(three_dmn_var_dbl,0.0,1.0);
+