add debug flags to GNU CI and fix remaining failures #990

Job	Run time
build (-DOPENMP=on, -DCMAKE_BUILD_TYPE=Release)	11m 10s
build (-DOPENMP=on, -DCMAKE_BUILD_TYPE=Debug)	3m 23s
build (-DOPENMP=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Release)	12m 27s
build (-DOPENMP=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Debug)	3m 42s
build (-DOPENMP=on, -DWITH_YAML=on, -DCMAKE_BUILD_TYPE=Release)	11m 43s
build (-DOPENMP=on, -DWITH_YAML=on, -DCMAKE_BUILD_TYPE=Debug)	3m 33s
build (-DOPENMP=on, -DWITH_YAML=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Release)	12m 44s
build (-DOPENMP=on, -DWITH_YAML=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Debug)	3m 56s
build (-DOPENMP=off, -DCMAKE_BUILD_TYPE=Release)	11m 30s
build (-DOPENMP=off, -DCMAKE_BUILD_TYPE=Debug)	3m 24s
build (-DOPENMP=off, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Release)	12m 31s
build (-DOPENMP=off, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Debug)	3m 40s
build (-DOPENMP=off, -DWITH_YAML=on, -DCMAKE_BUILD_TYPE=Release)	11m 35s
build (-DOPENMP=off, -DWITH_YAML=on, -DCMAKE_BUILD_TYPE=Debug)	3m 34s
build (-DOPENMP=off, -DWITH_YAML=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Release)	12m 49s
build (-DOPENMP=off, -DWITH_YAML=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Debug)	3m 51s
	2h 5m 32s

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