[gompi/2022.05] in-place update to netCDF v4.9.0

easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2022.05.eb → easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb

@@ -1,5 +1,5 @@
 name = 'netCDF'
-version = '4.8.1'
+version = '4.9.0'
 
 homepage = 'https://www.unidata.ucar.edu/software/netcdf/'
 description = """NetCDF (network Common Data Form) is a set of software libraries
@@ -11,7 +11,15 @@ toolchainopts = {'pic': True, 'usempi': True}
 
 source_urls = ['https://github.com/Unidata/netcdf-c/archive/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['bc018cc30d5da402622bf76462480664c6668b55eb16ba205a0dfb8647161dd0']
+patches = [
+    'netCDF-%(version)s_fix-lib-name.patch',
+    'netCDF-%(version)s_fix-linking-errors.patch',
+]
+checksums = [
+    '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6',  # v4.9.0.tar.gz
+    'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a',  # netCDF-4.9.0_fix-lib-name.patch
+    '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15',  # netCDF-4.9.0_fix-linking-errors.patch
+]
 
 builddependencies = [
     ('Autotools', '20220317'),
@@ -23,15 +31,18 @@ dependencies = [
     ('HDF5', '1.13.1'),
     ('cURL', '7.83.0'),
     ('Szip', '2.1.1'),
+    ('zstd', '1.5.2'),
 ]
 
-# HDF5 version detection is missed in netCDF 4.8.1 when HDF5_C_LIBRARY, HDF5_INCLUDE_DIR, and HDF5_HL_LIBRARY are set
-local_hdf5_version_fix = '-DHDF5_VERSION=$EBVERSIONHDF5'
-
 # make sure both static and shared libs are built
 configopts = [
-    "-DBUILD_SHARED_LIBS=OFF %s " % local_hdf5_version_fix,
-    "-DBUILD_SHARED_LIBS=ON %s " % local_hdf5_version_fix,
+    "-DBUILD_SHARED_LIBS=OFF",
+    "-DBUILD_SHARED_LIBS=ON",
 ]
 
+# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests
+pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 "
+
+runtest = 'test'
+
 moduleclass = 'data'

easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_fix-lib-name.patch

@@ -0,0 +1,23 @@
+From 80a6611cfca98a5979c5ac69cba56a49af8c1e48 Mon Sep 17 00:00:00 2001
+From: Yuriy Chernyshov <[email protected]>
+Date: Sun, 19 Jun 2022 19:29:20 +0300
+Subject: [PATCH] Fix typo in CMakeLists.txt
+
+At the time generated dynamic library is named `libnetcdf.so.19}` which looks like a typo.
+---
+ CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 7bf8641bec..18366d24ad 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -39,7 +39,7 @@ SET(NC_VERSION ${netCDF_VERSION})
+ SET(PACKAGE_VERSION ${VERSION})
+
+ # These values should match those in configure.ac
+-SET(netCDF_LIB_VERSION 19})
++SET(netCDF_LIB_VERSION 19)
+ SET(netCDF_SO_VERSION 19)
+
+ # Version of the dispatch table. This must match the value in

easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_fix-linking-errors.patch

@@ -0,0 +1,99 @@
+fix "multiple definition" linking errors,
+see also https://github.com/Unidata/netcdf-c/issues/2419
+author: Kenneth Hoste (HPC-UGent) + Lars Viklund (Umeå University)
+--- netcdf-c-4.9.0/include/netcdf_json.h.orig	2022-06-23 08:35:33.345891769 +0200
++++ netcdf-c-4.9.0/include/netcdf_json.h	2022-06-23 08:37:38.626339409 +0200
+@@ -57,25 +57,25 @@
+ #endif
+
+ /* Parse a JSON string */
+-DLLEXPORT int NCJparse(const char* text, unsigned flags, NCjson** jsonp);
++DLLEXPORT static int NCJparse(const char* text, unsigned flags, NCjson** jsonp);
+
+ /* Reclaim a JSON tree */
+-DLLEXPORT extern void NCJreclaim(NCjson* json);
++DLLEXPORT static void NCJreclaim(NCjson* json);
+
+ /* Create a new JSON node of a given sort */
+-DLLEXPORT extern int NCJnew(int sort, NCjson** objectp);
++DLLEXPORT static int NCJnew(int sort, NCjson** objectp);
+
+ /* Create new json object with given string content */
+-DLLEXPORT extern int NCJnewstring(int sort, const char* value, NCjson** jsonp);
++DLLEXPORT static int NCJnewstring(int sort, const char* value, NCjson** jsonp);
+
+ /* Create new json object with given counted string content */
+-DLLEXPORT extern int NCJnewstringn(int sort, size_t len, const char* value, NCjson** jsonp);
++DLLEXPORT static int NCJnewstringn(int sort, size_t len, const char* value, NCjson** jsonp);
+
+ /* Get dict key value by name */
+-DLLEXPORT extern int NCJdictget(const NCjson* dict, const char* key, NCjson** valuep);
++DLLEXPORT static int NCJdictget(const NCjson* dict, const char* key, NCjson** valuep);
+
+ /* Convert one json sort to  value of another type; don't use union so we can know when to reclaim sval */
+-DLLEXPORT extern int NCJcvt(const NCjson* value, int outsort, struct NCJconst* output);
++DLLEXPORT static int NCJcvt(const NCjson* value, int outsort, struct NCJconst* output);
+
+ #ifndef NETCDF_JSON_H
+
+@@ -230,7 +230,7 @@
+
+ /**************************************************/
+
+-int
++static int
+ NCJparse(const char* text, unsigned flags, NCjson** jsonp)
+ {
+     int stat = NCJ_OK;
+@@ -579,7 +579,7 @@
+
+ /**************************************************/
+
+-void
++static void
+ NCJreclaim(NCjson* json)
+ {
+     if(json == NULL) return;
+@@ -621,7 +621,7 @@
+ /**************************************************/
+ /* Build Functions */
+
+-int
++static int
+ NCJnew(int sort, NCjson** objectp)
+ {
+     int stat = NCJ_OK;
+@@ -651,13 +651,13 @@
+     return NCJTHROW(stat);
+ }
+
+-int
++static int
+ NCJnewstring(int sort, const char* value, NCjson** jsonp)
+ {
+     return NCJTHROW(NCJnewstringn(sort,strlen(value),value,jsonp));
+ }
+
+-int
++static int
+ NCJnewstringn(int sort, size_t len, const char* value, NCjson** jsonp)
+ {
+     int stat = NCJ_OK;
+@@ -679,7 +679,7 @@
+     return NCJTHROW(stat);
+ }
+
+-int
++static int
+ NCJdictget(const NCjson* dict, const char* key, NCjson** valuep)
+ {
+     int i,stat = NCJ_OK;
+@@ -755,7 +755,7 @@
+ #endif
+
+ /* Convert a JSON value to an equivalent value of a specified sort */
+-int
++static int
+ NCJcvt(const NCjson* jvalue, int outsort, struct NCJconst* output)
+ {
+     int stat = NCJ_OK;