re: github issues

#1168 #1163 #1162 This PR partially fixes memory leaks in the netcdf-c library, in the ncdump utility, and in some test cases. The netcdf-c library now runs memory clean with the assumption that the --disable-utilities option is used. The primary remaining problem is ncgen. Once that is fixed, I believe the netcdf-c library will run memory clean with no limitations. Notes ----------- 1. Memory checking was performed using gcc -fsanitize=address. Valgrind-based testing has yet to be performed. 2. The pnetcdf, hdf4, and examples code has not been tested. Misc. Non-leak changes 1. Make tst_diskless2 only run when netcdf4 is enabled (issue 1162) 2. Fix CmakeLists.txt to turn off logging if ENABLE_NETCDF_4 is OFF 3. Isolated all my debug scripts into a single top-level directory called debug 4. Fix some USE_NETCDF4 dependencies in nc_test and nc_test4 Makefile.am
Unidata · Oct 30, 2018 · 23f9ef8 · 23f9ef8
1 parent 8d5e66e
commit 23f9ef8
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -523,6 +523,9 @@ ENDIF()
 
 # Option Logging, only valid for netcdf4.
 OPTION(ENABLE_LOGGING "Enable Logging." OFF)
+IF(NOT ENABLE_NETCDF_4)
+SET(ENABLE_LOGGING OFF)
+ENDIF()
 IF(ENABLE_LOGGING)
   ADD_DEFINITIONS(-DLOGGING)
   ADD_DEFINITIONS(-DENABLE_SET_LOG_LEVEL)

diff --git a/configure.ac b/configure.ac
@@ -91,6 +91,7 @@ AC_DEFINE_UNQUOTED([NCIO_MINBLOCKSIZE], [$NCIO_MINBLOCKSIZE], [min blocksize for
 # Find valgrind, if available, and add targets for it.
 AX_VALGRIND_DFLT([sgcheck], [off])
 AX_VALGRIND_CHECK
+AM_CONDITIONAL(ENABLE_VALGRIND, [test "x$VALGRIND_ENABLED" = xyes])
 
 ###
 # Doxygen and doxygen-related options.

diff --git a/dap4_test/baseline/test_atomic_array.5.nc.d4d b/dap4_test/baseline/test_atomic_array.5.nc.d4d
@@ -1,14 +1,14 @@
 netcdf test_atomic_array.5.nc {
 types:
-  ubyte(*) _bytestring ;
+  opaque(16) opaque16_t ;
 dimensions:
 	_Anonymous1 = 1 ;
 	_Anonymous2 = 2 ;
 variables:
 	ubyte vu8(_Anonymous1, _Anonymous2) ;
 	double vd(_Anonymous1) ;
 	string vs(_Anonymous1, _Anonymous1) ;
-	_bytestring vo(_Anonymous1, _Anonymous1) ;
+	opaque16_t vo(_Anonymous1, _Anonymous1) ;
 
 // global attributes:
 		string :_dap4.ce = "/vu8[1][0:2:2];/vd[1];/vs[1][0];/vo[0][1]" ;
@@ -24,5 +24,6 @@ data:
   "Καλημέα" ;
 
  vo =
-  {171, 205, 239, 0, 0, 0, 0, 0} ;
+  0XABCDEF00000000000000000000000000 ;
+
 }
diff --git a/dap4_test/baseline/test_atomic_array.nc.d4d b/dap4_test/baseline/test_atomic_array.nc.d4d
@@ -4,7 +4,7 @@ types:
       Stratocumulus = 3, Cumulus = 4, Altostratus = 5, Nimbostratus = 6, 
       Altocumulus = 7, Cirrostratus = 8, Cirrocumulus = 9, Cirrus = 10, 
       Missing = 127} ;
-  ubyte(*) _bytestring ;
+  opaque(16) opaque16_t ;
 dimensions:
 	d1 = 1 ;
 	d2 = 2 ;
@@ -18,7 +18,7 @@ variables:
 	double vd(d2) ;
 	char vc(d2) ;
 	string vs(d2, d2) ;
-	_bytestring vo(d1, d2) ;
+	opaque16_t vo(d1, d2) ;
 	cloud_class_t primary_cloud(d5) ;
 		cloud_class_t primary_cloud:_FillValue = Missing ;
 
@@ -45,7 +45,7 @@ data:
   "Καλημέα", "abc" ;
 
  vo =
-  {1, 35, 69, 103, 137, 171, 205, 239}, {171, 205, 239, 0, 0, 0, 0, 0} ;
+  0X0123456789ABCDEF0000000000000000, 0XABCDEF00000000000000000000000000 ;
 
  primary_cloud = Clear, Stratus, Clear, Cumulonimbus, _ ;
 }
diff --git a/dap4_test/baseline/test_atomic_array.syn.d4d b/dap4_test/baseline/test_atomic_array.syn.d4d
@@ -4,7 +4,7 @@ types:
       Stratocumulus = 3, Cumulus = 4, Altostratus = 5, Nimbostratus = 6, 
       Altocumulus = 7, Cirrostratus = 8, Cirrocumulus = 9, Cirrus = 10, 
       Missing = 127} ;
-  ubyte(*) _bytestring ;
+  opaque(16) opaque16_t ;
 dimensions:
 	d1 = 1 ;
 	d2 = 2 ;
@@ -18,7 +18,7 @@ variables:
 	double vd(d2) ;
 	char vc(d2) ;
 	string vs(d2, d2) ;
-	_bytestring vo(d1, d2) ;
+	opaque16_t vo(d1, d2) ;
 	cloud_class_t primary_cloud(d5) ;
 		cloud_class_t primary_cloud:_FillValue = Missing ;
 
@@ -46,8 +46,7 @@ data:
 
  vo =
 
-    {162, 23, 122, 167, 40, 124, 4, 250, 139, 181, 123, 205, 247, 110, 200, 15}, 
-    {52, 250, 71, 42, 169, 64, 77, 213, 67, 20, 60, 173, 237, 48, 58, 117} ;
+    0XA2177AA7287C04FA8BB57BCDF76EC80F, 0X34FA472AA9404DD543143CADED303A75 ;
 
  primary_cloud = Stratus, Cirrocumulus, Nimbostratus, Cirrostratus, 
     Stratocumulus ;

diff --git a/dap4_test/baseline/test_atomic_array.syn.d4m b/dap4_test/baseline/test_atomic_array.syn.d4m
@@ -4,7 +4,7 @@ types:
       Stratocumulus = 3, Cumulus = 4, Altostratus = 5, Nimbostratus = 6, 
       Altocumulus = 7, Cirrostratus = 8, Cirrocumulus = 9, Cirrus = 10, 
       Missing = 127} ;
-  ubyte(*) _bytestring ;
+  opaque(16) opaque16_t ;
 dimensions:
 	d1 = 1 ;
 	d2 = 2 ;
@@ -18,7 +18,7 @@ variables:
 	double vd(d2) ;
 	char vc(d2) ;
 	string vs(d2, d2) ;
-	_bytestring vo(d1, d2) ;
+	opaque16_t vo(d1, d2) ;
 	cloud_class_t primary_cloud(d5) ;
 		cloud_class_t primary_cloud:_FillValue = Missing ;
 

diff --git a/dap4_test/baseline/test_atomic_array.syn.d4p b/dap4_test/baseline/test_atomic_array.syn.d4p
@@ -26,7 +26,6 @@
       <EnumConst name="Cirrus" value="10"/>
       <EnumConst name="Missing" value="127"/>
     </Enumeration>
-    <Opaque name="_bytestring"/>
   </Types>
   <Variables>
     <UInt8 name="vu8">
@@ -50,7 +49,7 @@
       <Dim name="/d2"/>
       <Dim name="/d2"/>
     </String>
-    <Opaque name="vo" type="/_bytestring">
+    <Opaque name="vo" type="/opaque16_t">
       <Dim name="/d1"/>
       <Dim name="/d2"/>
     </Opaque>

diff --git a/dap4_test/baseline/test_atomic_types.nc.d4d b/dap4_test/baseline/test_atomic_types.nc.d4d
@@ -4,7 +4,7 @@ types:
       Stratocumulus = 3, Cumulus = 4, Altostratus = 5, Nimbostratus = 6, 
       Altocumulus = 7, Cirrostratus = 8, Cirrocumulus = 9, Cirrus = 10, 
       Missing = 127} ;
-  ubyte(*) _bytestring ;
+  opaque(16) opaque16_t ;
 variables:
 	byte v8 ;
 	ubyte vu8 ;
@@ -18,7 +18,7 @@ variables:
 	double vd ;
 	char vc ;
 	string vs ;
-	_bytestring vo ;
+	opaque16_t vo ;
 	cloud_class_t primary_cloud ;
 		cloud_class_t primary_cloud:_FillValue = Missing ;
 	cloud_class_t secondary_cloud ;
@@ -52,7 +52,7 @@ data:
 
  vs = "hello\tworld" ;
 
- vo = {1, 35, 69, 103, 137, 171, 205, 239} ;
+ vo = 0X0123456789ABCDEF0000000000000000 ;
 
  primary_cloud = Stratus ;
 

diff --git a/dap4_test/baseline/test_atomic_types.syn.d4d b/dap4_test/baseline/test_atomic_types.syn.d4d
@@ -4,7 +4,7 @@ types:
       Stratocumulus = 3, Cumulus = 4, Altostratus = 5, Nimbostratus = 6, 
       Altocumulus = 7, Cirrostratus = 8, Cirrocumulus = 9, Cirrus = 10, 
       Missing = 127} ;
-  ubyte(*) _bytestring ;
+  opaque(16) opaque16_t ;
 variables:
 	byte v8 ;
 	ubyte vu8 ;
@@ -18,7 +18,7 @@ variables:
 	double vd ;
 	char vc ;
 	string vs ;
-	_bytestring vo ;
+	opaque16_t vo ;
 	cloud_class_t primary_cloud ;
 		cloud_class_t primary_cloud:_FillValue = Missing ;
 	cloud_class_t secondary_cloud ;
@@ -52,8 +52,7 @@ data:
 
  vs = "O,L?c8A%V" ;
 
- vo = 
-    {70, 241, 105, 239, 35, 203, 175, 155, 31, 235, 217, 158, 78, 22, 206, 201} ;
+ vo = 0X46F169EF23CBAF9B1FEBD99E4E16CEC9 ;
 
  primary_cloud = Altocumulus ;
 

diff --git a/dap4_test/baseline/test_atomic_types.syn.d4m b/dap4_test/baseline/test_atomic_types.syn.d4m
@@ -4,7 +4,7 @@ types:
       Stratocumulus = 3, Cumulus = 4, Altostratus = 5, Nimbostratus = 6, 
       Altocumulus = 7, Cirrostratus = 8, Cirrocumulus = 9, Cirrus = 10, 
       Missing = 127} ;
-  ubyte(*) _bytestring ;
+  opaque(16) opaque16_t ;
 variables:
 	byte v8 ;
 	ubyte vu8 ;
@@ -18,7 +18,7 @@ variables:
 	double vd ;
 	char vc ;
 	string vs ;
-	_bytestring vo ;
+	opaque16_t vo ;
 	cloud_class_t primary_cloud ;
 		cloud_class_t primary_cloud:_FillValue = Missing ;
 	cloud_class_t secondary_cloud ;

diff --git a/dap4_test/baseline/test_atomic_types.syn.d4p b/dap4_test/baseline/test_atomic_types.syn.d4p
@@ -19,7 +19,6 @@
       <EnumConst name="Cirrus" value="10"/>
       <EnumConst name="Missing" value="127"/>
     </Enumeration>
-    <Opaque name="_bytestring"/>
   </Types>
   <Variables>
     <Int8 name="v8"/>
@@ -34,7 +33,7 @@
     <Float64 name="vd"/>
     <Char name="vc"/>
     <String name="vs"/>
-    <Opaque name="vo" type="/_bytestring"/>
+    <Opaque name="vo" type="/opaque16_t"/>
     <Enum name="primary_cloud" enum="/cloud_class_t">
       <Attribute name="_FillValue" type="/cloud_class_t">
         <Value value="Missing"/>

diff --git a/dap4_test/baseline/test_opaque.nc.d4d b/dap4_test/baseline/test_opaque.nc.d4d
@@ -1,12 +1,12 @@
 netcdf test_opaque.nc {
 types:
-  ubyte(*) _bytestring ;
+  opaque(16) opaque16_t ;
 variables:
-	_bytestring vo1 ;
+	opaque16_t vo1 ;
 
 // global attributes:
 		:_DAP4_Little_Endian = 1UB ;
 data:
 
- vo1 = {1, 35, 69, 103, 137, 171, 205, 239} ;
+ vo1 = 0X0123456789ABCDEF0000000000000000 ;
 }
diff --git a/dap4_test/baseline/test_opaque_array.7.nc.d4d b/dap4_test/baseline/test_opaque_array.7.nc.d4d
@@ -1,18 +1,17 @@
 netcdf test_opaque_array.7.nc {
 types:
-  ubyte(*) _bytestring ;
+  opaque(16) opaque16_t ;
 dimensions:
 	_Anonymous1 = 1 ;
 	_Anonymous2 = 2 ;
 variables:
-	_bytestring vo2(_Anonymous1, _Anonymous2) ;
+	opaque16_t vo2(_Anonymous1, _Anonymous2) ;
 
 // global attributes:
 		string :_dap4.ce = "/vo2[1][0:1]" ;
 		:_DAP4_Little_Endian = 1UB ;
 data:
 
  vo2 =
-  {254, 220, 186, 152, 118, 84, 50, 16}, 
-    {254, 220, 186, 153, 153, 153, 153, 153} ;
+  0XFEDCBA98765432100000000000000000, 0XFEDCBA99999999990000000000000000 ;
 }
diff --git a/dap4_test/baseline/test_opaque_array.nc.d4d b/dap4_test/baseline/test_opaque_array.nc.d4d
@@ -1,17 +1,16 @@
 netcdf test_opaque_array.nc {
 types:
-  ubyte(*) _bytestring ;
+  opaque(16) opaque16_t ;
 dimensions:
 	d2 = 2 ;
 variables:
-	_bytestring vo2(d2, d2) ;
+	opaque16_t vo2(d2, d2) ;
 
 // global attributes:
 		:_DAP4_Little_Endian = 1UB ;
 data:
 
  vo2 =
-  {1, 35, 69, 103, 137, 171, 205, 239}, {171, 205, 239, 0, 0, 0, 0, 0},
-  {254, 220, 186, 152, 118, 84, 50, 16}, 
-    {254, 220, 186, 153, 153, 153, 153, 153} ;
+  0X0123456789ABCDEF0000000000000000, 0XABCDEF00000000000000000000000000,
+  0XFEDCBA98765432100000000000000000, 0XFEDCBA99999999990000000000000000 ;
 }
diff --git a/dap4_test/baselineraw/test_atomic_array.5.nc.dmp b/dap4_test/baselineraw/test_atomic_array.5.nc.dmp
@@ -1,14 +1,14 @@
 netcdf test_atomic_array.5 {
 types:
-  ubyte(*) _bytestring ;
+  opaque(16) opaque16_t ;
 dimensions:
 	_Anonymous1 = 1 ;
 	_Anonymous2 = 2 ;
 variables:
 	ubyte vu8(_Anonymous1, _Anonymous2) ;
 	double vd(_Anonymous1) ;
 	string vs(_Anonymous1, _Anonymous1) ;
-	_bytestring vo(_Anonymous1, _Anonymous1) ;
+	opaque16_t vo(_Anonymous1, _Anonymous1) ;
 
 // global attributes:
 		string :_dap4.ce = "/vu8[1][0:2:2];/vd[1];/vs[1][0];/vo[0][1]" ;
@@ -24,5 +24,5 @@ data:
   "Καλημέα" ;
 
  vo =
-  {171, 205, 239, 0, 0, 0, 0, 0} ;
+  0XABCDEF00000000000000000000000000 ;
 }
diff --git a/dap4_test/baselineraw/test_atomic_array.nc.dmp b/dap4_test/baselineraw/test_atomic_array.nc.dmp
@@ -4,7 +4,7 @@ types:
       Stratocumulus = 3, Cumulus = 4, Altostratus = 5, Nimbostratus = 6, 
       Altocumulus = 7, Cirrostratus = 8, Cirrocumulus = 9, Cirrus = 10, 
       Missing = 127} ;
-  ubyte(*) _bytestring ;
+  opaque(16) opaque16_t ;
 dimensions:
 	d1 = 1 ;
 	d2 = 2 ;
@@ -18,7 +18,7 @@ variables:
 	double vd(d2) ;
 	char vc(d2) ;
 	string vs(d2, d2) ;
-	_bytestring vo(d1, d2) ;
+	opaque16_t vo(d1, d2) ;
 	cloud_class_t primary_cloud(d5) ;
 		cloud_class_t primary_cloud:_FillValue = Missing ;
 
@@ -45,7 +45,7 @@ data:
   "Καλημέα", "abc" ;
 
  vo =
-  {1, 35, 69, 103, 137, 171, 205, 239}, {171, 205, 239, 0, 0, 0, 0, 0} ;
+  0X0123456789ABCDEF0000000000000000, 0XABCDEF00000000000000000000000000 ;
 
  primary_cloud = Clear, Stratus, Clear, Cumulonimbus, _ ;
 }
diff --git a/dap4_test/baselineraw/test_atomic_array.syn.dmp b/dap4_test/baselineraw/test_atomic_array.syn.dmp
@@ -4,7 +4,7 @@ types:
       Stratocumulus = 3, Cumulus = 4, Altostratus = 5, Nimbostratus = 6, 
       Altocumulus = 7, Cirrostratus = 8, Cirrocumulus = 9, Cirrus = 10, 
       Missing = 127} ;
-  ubyte(*) _bytestring ;
+  opaque(16) opaque16_t ;
 dimensions:
 	d1 = 1 ;
 	d2 = 2 ;
@@ -18,7 +18,7 @@ variables:
 	double vd(d2) ;
 	char vc(d2) ;
 	string vs(d2, d2) ;
-	_bytestring vo(d1, d2) ;
+	opaque16_t vo(d1, d2) ;
 	cloud_class_t primary_cloud(d5) ;
 		cloud_class_t primary_cloud:_FillValue = Missing ;
 
@@ -45,9 +45,7 @@ data:
   "4a/q%n9;5Y", "{fIl?T\"\\A[" ;
 
  vo =
-
-    {162, 23, 122, 167, 40, 124, 4, 250, 139, 181, 123, 205, 247, 110, 200, 15}, 
-    {52, 250, 71, 42, 169, 64, 77, 213, 67, 20, 60, 173, 237, 48, 58, 117} ;
+  0XA2177AA7287C04FA8BB57BCDF76EC80F, 0X34FA472AA9404DD543143CADED303A75 ;  
 
  primary_cloud = Stratus, Cirrocumulus, Nimbostratus, Cirrostratus, 
     Stratocumulus ;

diff --git a/dap4_test/baselineraw/test_atomic_types.nc.dmp b/dap4_test/baselineraw/test_atomic_types.nc.dmp
@@ -4,7 +4,7 @@ types:
       Stratocumulus = 3, Cumulus = 4, Altostratus = 5, Nimbostratus = 6, 
       Altocumulus = 7, Cirrostratus = 8, Cirrocumulus = 9, Cirrus = 10, 
       Missing = 127} ;
-  ubyte(*) _bytestring ;
+  opaque(16) opaque16_t ;
 variables:
 	byte v8 ;
 	ubyte vu8 ;
@@ -18,7 +18,7 @@ variables:
 	double vd ;
 	char vc ;
 	string vs ;
-	_bytestring vo ;
+	opaque16_t vo ;
 	cloud_class_t primary_cloud ;
 		cloud_class_t primary_cloud:_FillValue = Missing ;
 	cloud_class_t secondary_cloud ;
@@ -52,7 +52,7 @@ data:
 
  vs = "hello\tworld" ;
 
- vo = {1, 35, 69, 103, 137, 171, 205, 239} ;
+ vo = 0X0123456789ABCDEF0000000000000000 ;
 
  primary_cloud = Stratus ;