Squashed 'src/externals/pio2/' changes from e41e6a6..1ff0f44

1ff0f44 Merge pull request #1653 from jedwards4b/short_type_in_fortran
b089073 Merge branch 'master' into short_type_in_fortran
30a1b79 Merge pull request #1650 from NCAR/ejh_fix_warnings_2
1c448af fix mem error
038b3a7 Correct -D_PNETCDF flag
14140f8 revert travis
b78ee97 bionic didnt work try Xenial
750209f try updating travis build
f44b71e update genf90 external
01452c3 add short data type to fortran interface and tests
b049420 add a short datatype to the fortran interface
ceff4ea fixed warnings in tests
a4fb42f Merge pull request #1644 from NCAR/ejh_netcdf_4_7_4_more
82e781c changed test to always use deflate of 1
20c529c Merge pull request #1643 from NCAR/ejh_netcdf_4_7_4
e722b81 turned off logging in test
ed7c53a restored test
8365a2c no longer try to set deflate on scalar vars
f8a3275 adjusted dispatch table for netcdf-c-4.7.4

git-subtree-dir: src/externals/pio2
git-subtree-split: 1ff0f44

scripts/genf90.pl

@@ -9,8 +9,8 @@
 # to generate F90 code for all of the desired specific types.
 #
 # Keywords are delimited by curly brackets: {}
-# 
-# {TYPE} and {DIMS} are used to generate the specific subroutine names from the 
+#
+# {TYPE} and {DIMS} are used to generate the specific subroutine names from the
 #            generic template
 # {TYPE} : Variable type name; implemented types are character, 4 or 8 byte real,
 #          and 4 or 8 byte integer.
@@ -20,7 +20,7 @@
 #                if {TYPE}=double then {VTYPE} is "real(r8)"
 # {ITYPE}, {ITYPENAME} : Used to generate CPP statements for the specific type.
 # {MPITYPE} : Used to generate MPI types corresponding to the specific type.
-# 
+#
 # {DIMS} : Rank of arrays, "0" for scalar.
 #                allowed values: 0-7
 #                default values : 0-5
@@ -33,40 +33,46 @@
 #                expands to this:
 #                foo(1, bar), foo(2, bar), foo(3, bar), ...
 
-# defaults 
-my @types = qw(text real double int);
-my $vtype = {'text' => 'character(len=*)', 
-	     'real' => 'real(r4)', 
+# defaults
+my @types = qw(text real double int short);
+my $vtype = {'text' => 'character(len=*)',
+	     'real' => 'real(r4)',
 	     'double' => 'real(r8)',
 	     'int'    => 'integer(i4)',
+	     'short'  => 'integer(i2)',
 	     'long'   => 'integer(i8)',
              'logical' => 'logical' };
-my $itype = {'text' => 100, 
-	     'real' => 101, 
+my $itype = {'text' => 100,
+	     'real' => 101,
 	     'double' => 102,
 	     'int'    => 103,
 	     'long'   => 104,
-             'logical' => 105};
-my $itypename = {'text' => 'TYPETEXT', 
-	     'real' =>  'TYPEREAL', 
+             'logical' => 105,
+             'short'  => 106};
+my $itypename = {'text' => 'TYPETEXT',
+	     'real' =>  'TYPEREAL',
 	     'double' => 'TYPEDOUBLE',
 	     'int'    => 'TYPEINT',
+	     'short'  => 'TYPESHORT',
 	     'long'   =>  'TYPELONG',
              'logical' => 'TYPELOGICAL'};
 my $mpitype = {'text' => 'MPI_CHARACTER',
 	       'real' => 'MPI_REAL4',
+	       'short' => 'MPI_SHORT',
 	       'double' => 'MPI_REAL8',
 	       'int' => 'MPI_INTEGER'};
 # Netcdf C datatypes
 my $nctype = {'text' => 'text',
 	      'real' => 'float',
+	      'short' => 'short',
 	      'double' => 'double',
 	      'int' => 'int'};
 # C interoperability types
 my $ctype = {'text' => 'character(C_CHAR)',
 	     'real' => 'real(C_FLOAT)',
 	     'double' => 'real(C_DOUBLE)',
-	     'int' => 'integer(C_INT)'};
+	     'int' => 'integer(C_INT)',
+             'short' => 'integer(C_SHORT)'};
 
 
 
@@ -108,9 +114,9 @@
     my @unit;
     my $unitcnt=0;
     my $date = localtime();
-    my $preamble = 
+    my $preamble =
 "!===================================================
-! DO NOT EDIT THIS FILE, it was generated using $0 
+! DO NOT EDIT THIS FILE, it was generated using $0
 ! Any changes you make to this file may be lost
 !===================================================\n";
     my @output ;
@@ -134,7 +140,7 @@
 	$itypeflag=1 if($line =~ /TYPEINT/);
 	$itypeflag=1 if($line =~ /TYPELONG/);
 
-	
+
         if($contains==0){
 	    if($line=~/\s*!\s*DIMS\s+[\d,]+!*/){
 		$dimmodifier=$line;
@@ -186,12 +192,12 @@
 	    if(defined $dimmodifier){
 		$line = $dimmodifier.$line;
 		undef $dimmodifier;
-	    } 
+	    }
 	    if(defined $typemodifier){
 		$line = $typemodifier.$line;
 		undef $typemodifier;
-	    } 
-	    
+	    }
+
 	    push(@output, buildout($line));
             if(($line =~ /^\s*contains\s*!*/i && ! $in_type_block) or
                ($line =~ /^\s*!\s*Not a module/i)){
@@ -218,7 +224,7 @@
                 }
 	    }
 
-	       
+
 	    push(@{$unit[$unitcnt]},$line);
 	    if ($line=~/^\s*interface/i) {
 		$block_type="interface";
@@ -242,10 +248,10 @@
 	if(defined($unit[$i])){
 		my $func = join('',@{$unit[$i]});
 		push(@output, buildout($func));
-	}	
+	}
     }
     push(@output,@{$unit[$#unit]}) if($unitcnt==$#unit);
-    push(@output, $end);	
+    push(@output, $end);
     if($itypeflag==1){
 	my $str;
 	$str.="#include \"dtypes.h\"\n";
@@ -283,9 +289,9 @@ sub build_repeatstr{
 
 sub writedtypes{
     open(F,">dtypes.h");
-    print F 
+    print F
 "#define TYPETEXT 100
-#define TYPEREAL 101	
+#define TYPEREAL 101
 #define TYPEDOUBLE 102
 #define TYPEINT 103
 #define TYPELONG 104
@@ -296,7 +302,7 @@ sub writedtypes{
 
 sub buildout{
     my ($func) = @_;
-    
+
     my $outstr;
     my(@ldims, @ltypes);
 
@@ -306,12 +312,12 @@ sub buildout{
 	@ldims = @dims;
     }
     if($func=~/\s*!\s*TYPE\s+([^!\s]+)\s*/){
-	@ltypes = split(/,/,$1);	
+	@ltypes = split(/,/,$1);
 #	print ">$func<>@ltypes<\n";
     }else{
 	@ltypes = @types;
     }
-    
+
 
     if(($func =~ /{TYPE}/ && $func =~ /{DIMS}/) ){
 	my ($type, $dims);
@@ -330,7 +336,7 @@ sub buildout{
 		}
 
 		my $repeatstr = build_repeatstr($dims);
-		
+
 		my $str = $func;
 		$str =~ s/{TYPE}/$type/g;
 		$str =~ s/{VTYPE}/$vtype->{$type}/g;
@@ -358,9 +364,9 @@ sub buildout{
 	    }else{
 		$dimstr='';
 	    }
-		
+
 	    my $repeatstr = build_repeatstr($dims);
-		
+
 	    my $str = $func;
 	    $str =~ s/{DIMS}/$dims/g;
 	    $str =~ s/{DIMSTR}/$dimstr/g;

set_flags.am

@@ -9,7 +9,7 @@ AM_CPPFLAGS = -I$(top_srcdir)/src/flib -D_NETCDF
 
 # Is the user building with pnetcdf?
 if BUILD_PNETCDF
-AM_CPPFLAGS += -D_PETCDF
+AM_CPPFLAGS += -D_PNETCDF
 endif
 
 # Is the user building with netCDF-4 parallel I/O?

src/clib/pio_darray.c

@@ -988,8 +988,19 @@ PIOc_read_darray(int ncid, int varid, int ioid, PIO_Offset arraylen,
     {
         if (!(tmparray = malloc(iodesc->piotype_size * iodesc->maplen)))
             return pio_err(ios, NULL, PIO_ENOMEM, __FILE__, __LINE__);
-        for (int m = 0; m < iodesc->maplen; m++)
+	if(iodesc->piotype_size == 1){
+	  for (int m = 0; m < iodesc->maplen; m++)
+            ((signed char *)array)[m] = -1;
+	}else if(iodesc->piotype_size == 2){
+	  for (int m = 0; m < iodesc->maplen; m++)
+            ((short *)array)[m] = -1;
+	}else if(iodesc->piotype_size == 4){
+	  for (int m = 0; m < iodesc->maplen; m++)
             ((int *)array)[m] = -1;
+	}else if(iodesc->piotype_size == 8){
+	  for (int m = 0; m < iodesc->maplen; m++)
+            ((double *)array)[m] = -1;
+	}
     }
     else
         tmparray = array;

src/clib/pio_nc.c

@@ -2280,8 +2280,8 @@ PIOc_def_var(int ncid, const char *name, nc_type xtype, int ndims,
 #ifdef _NETCDF4
         /* For netCDF-4 serial files, turn on compression for this
          * variable, unless this file was opened through the netCDF
-         * integration feature. */
-        if (!ierr && file->iotype == PIO_IOTYPE_NETCDF4C && !file->ncint_file)
+         * integration feature (or is a scalar). */
+        if (!ierr && file->iotype == PIO_IOTYPE_NETCDF4C && !file->ncint_file && ndims)
             ierr = nc_def_var_deflate(file->fh, varid, 0, 1, 1);
 
         /* For netCDF-4 parallel files, set parallel access to collective. */

src/clib/pio_nc4.c

@@ -49,6 +49,9 @@ PIOc_def_var_deflate(int ncid, int varid, int shuffle, int deflate,
     if (file->iotype != PIO_IOTYPE_NETCDF4P && file->iotype != PIO_IOTYPE_NETCDF4C)
         return pio_err(ios, file, PIO_ENOTNC4, __FILE__, __LINE__);
 
+    PLOG((1, "PIOc_def_var_deflate ncid = %d varid = %d shuffle = %d deflate = %d deflate_level = %d",
+	  ncid, varid, shuffle, deflate, deflate_level));
+
     /* If async is in use, and this is not an IO task, bcast the parameters. */
     if (ios->async)
     {
@@ -116,7 +119,7 @@ PIOc_def_var_deflate(int ncid, int varid, int shuffle, int deflate,
  * @param deflatep pointer to an int that will be set to non-zero if
  * deflation is in use for this variable. Ignored if NULL.
  * @param deflate_levelp pointer to an int that will get the deflation
- * level (from 1-9) if deflation is in use for this variable.  Ignored
+ * level (from 1-9) if deflation is in use for this variable. Ignored
  * if NULL.
  * @return PIO_NOERR for success, otherwise an error code.
  * @ingroup PIO_inq_var_c
@@ -140,6 +143,8 @@ PIOc_inq_var_deflate(int ncid, int varid, int *shufflep, int *deflatep,
     if (file->iotype != PIO_IOTYPE_NETCDF4P && file->iotype != PIO_IOTYPE_NETCDF4C)
         return pio_err(ios, file, PIO_ENOTNC4, __FILE__, __LINE__);
 
+    PLOG((1, "PIOc_inq_var_deflate ncid = %d varid = %d", ncid, varid));
+
     /* If async is in use, and this is not an IO task, bcast the parameters. */
     if (ios->async)
     {

src/flib/CMakeLists.txt

@@ -116,7 +116,7 @@ else ()
   ExternalProject_Add (genf90
     PREFIX ${CMAKE_CURRENT_BINARY_DIR}/genf90
     GIT_REPOSITORY https://github.com/PARALLELIO/genf90
-    GIT_TAG genf90_140121
+    GIT_TAG genf90_200608
     UPDATE_COMMAND ""
     CONFIGURE_COMMAND ""
     BUILD_COMMAND ""

src/flib/Makefile.am

@@ -7,7 +7,7 @@
 # The library we are building.
 lib_LTLIBRARIES = libpiof.la
 
-AM_CPPFLAGS = -D_NETCDF -D_NETCDF4 -D_PETCDF
+AM_CPPFLAGS = -D_NETCDF -D_NETCDF4 -D_PNETCDF
 
 # These linker flags specify libtool version info.
 # See http://www.gnu.org/software/libtool/manual/libtool.html#Libtool-versioning

src/flib/pio.F90

@@ -1,5 +1,5 @@
 !>
-!! @file 
+!! @file
 !! User interface Module for PIO, this is the only file a user program should 'use'.
 !! @author Jim Edwards
 !<
@@ -33,7 +33,7 @@ module pio
        pio_rearr_opt_t, pio_rearr_comm_fc_opt_t, pio_rearr_comm_fc_2d_enable,&
        pio_rearr_comm_fc_1d_comp2io, pio_rearr_comm_fc_1d_io2comp,&
        pio_rearr_comm_fc_2d_disable, pio_rearr_comm_unlimited_pend_req,&
-       pio_rearr_comm_p2p, pio_rearr_comm_coll,&
+       pio_rearr_comm_p2p, pio_rearr_comm_coll, pio_short, &
        pio_int, pio_real, pio_double, pio_noerr, iotype_netcdf, &
        iotype_pnetcdf,  pio_iotype_netcdf4p, pio_iotype_netcdf4c, &
        pio_iotype_pnetcdf,pio_iotype_netcdf, &
@@ -45,7 +45,7 @@ module pio
        pio_64bit_offset, pio_64bit_data, &
        pio_internal_error, pio_bcast_error, pio_return_error, pio_default
 
-  use piodarray, only : pio_read_darray, pio_write_darray, pio_set_buffer_size_limit  
+  use piodarray, only : pio_read_darray, pio_write_darray, pio_set_buffer_size_limit
 
   use pio_nf, only:        &
        PIO_enddef,            &
@@ -124,11 +124,11 @@ integer(C_INT) function PIOc_iam_iotask(iosysid, iotask) &
          logical(C_BOOL), intent(out) :: iotask
        end function PIOc_iam_iotask
     end interface
-    
+
     ierr = PIOc_iam_iotask(iosystem%iosysid, ctask)
     task = ctask
   end function pio_iam_iotask
-  
+
   !>
   !! Integer function returns rank of IO task.
   !! @author Jim Edwards
@@ -144,7 +144,7 @@ integer(C_INT) function PIOc_iotask_rank(iosysid, rank) &
          integer(C_INT), intent(out) :: rank
        end function PIOc_iotask_rank
     end interface
-    
+
     ierr = PIOc_iotask_rank(iosystem%iosysid, rank)
   end function pio_iotask_rank
 
@@ -172,4 +172,3 @@ end function PIOc_iosystem_is_active
   end subroutine pio_iosystem_is_active
 
 end module pio
-

src/flib/pio_kinds.F90

@@ -22,12 +22,13 @@ module pio_kinds
       char_len  = 360                    ,& !< char len
       log_kind  = kind(.true.)           ,& !< logical kind
       int_kind  = kind(1)                ,& !< int kind
+      i2        = selected_int_kind(4)   ,& !< i2 (short) kind
       i4        = selected_int_kind(6)   ,& !< i4 kind
       i8        = selected_int_kind(13)  ,& !< i8 kind
       r4        = selected_real_kind(6)  ,& !< r4 kind
       r8        = selected_real_kind(13)    !< r8 kind
 !
-!  MPI defines MPI_OFFSET_KIND as the byte size of the 
+!  MPI defines MPI_OFFSET_KIND as the byte size of the
 !  type, which is not nessasarily the type kind
 !
 !> Byte size of the MPI_OFFSET type.

src/flib/pio_types.F90

@@ -35,9 +35,10 @@
 !!
 !! @defgroup PIO_kinds PIO Fortran Type Kinds
 !! PIO supports different kinds of Fortran types.
-!!  - PIO_double : 8-byte reals or double precision
+!!  - PIO_doauble : 8-byte reals or double precision
 !!  - PIO_real : 4-byte reals
 !!  - PIO_int :  4-byte integers
+!!  - PIO_short : 2-byte integers
 !!  - PIO_char : character
 
 module pio_types
@@ -136,6 +137,7 @@ module pio_types
   integer, public, parameter :: PIO_double = nf_double       !< double type
   integer, public, parameter :: PIO_real   = nf_real         !< real type
   integer, public, parameter :: PIO_int    = nf_int          !< int type
+  integer, public, parameter :: PIO_short  = nf_short        !< short int type
   integer, public, parameter :: PIO_char   = nf_char         !< char type
   integer, public, parameter :: PIO_noerr  = nf_noerr        !< no error
   integer, public, parameter :: PIO_WRITE  = nf_write        !< read-write