add debug flags to GNU CI and fix remaining failures #984

Job	Run time
build (-DOPENMP=on, -DCMAKE_BUILD_TYPE=Release)	11m 29s
build (-DOPENMP=on, -DCMAKE_BUILD_TYPE=Debug)	3m 21s
build (-DOPENMP=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Release)	12m 24s
build (-DOPENMP=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Debug)	3m 35s
build (-DOPENMP=on, -DWITH_YAML=on, -DCMAKE_BUILD_TYPE=Release)	12m 6s
build (-DOPENMP=on, -DWITH_YAML=on, -DCMAKE_BUILD_TYPE=Debug)	3m 46s
build (-DOPENMP=on, -DWITH_YAML=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Release)	12m 47s
build (-DOPENMP=on, -DWITH_YAML=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Debug)	3m 56s
build (-DOPENMP=off, -DCMAKE_BUILD_TYPE=Release)	11m 23s
build (-DOPENMP=off, -DCMAKE_BUILD_TYPE=Debug)	3m 24s
build (-DOPENMP=off, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Release)	12m 17s
build (-DOPENMP=off, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Debug)	3m 43s
build (-DOPENMP=off, -DWITH_YAML=on, -DCMAKE_BUILD_TYPE=Release)	11m 44s
build (-DOPENMP=off, -DWITH_YAML=on, -DCMAKE_BUILD_TYPE=Debug)	3m 32s
build (-DOPENMP=off, -DWITH_YAML=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Release)	12m 50s
build (-DOPENMP=off, -DWITH_YAML=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Debug)	3m 46s
	2h 6m 3s

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