add debug flags to GNU CI and fix remaining failures #985

Job	Run time
build (-DOPENMP=on, -DCMAKE_BUILD_TYPE=Release)	11m 23s
build (-DOPENMP=on, -DCMAKE_BUILD_TYPE=Debug)	3m 21s
build (-DOPENMP=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Release)	12m 19s
build (-DOPENMP=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Debug)	3m 38s
build (-DOPENMP=on, -DWITH_YAML=on, -DCMAKE_BUILD_TYPE=Release)	11m 41s
build (-DOPENMP=on, -DWITH_YAML=on, -DCMAKE_BUILD_TYPE=Debug)	3m 31s
build (-DOPENMP=on, -DWITH_YAML=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Release)	13m 14s
build (-DOPENMP=on, -DWITH_YAML=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Debug)	3m 51s
build (-DOPENMP=off, -DCMAKE_BUILD_TYPE=Release)	11m 8s
build (-DOPENMP=off, -DCMAKE_BUILD_TYPE=Debug)	3m 20s
build (-DOPENMP=off, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Release)	12m 3s
build (-DOPENMP=off, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Debug)	3m 36s
build (-DOPENMP=off, -DWITH_YAML=on, -DCMAKE_BUILD_TYPE=Release)	11m 50s
build (-DOPENMP=off, -DWITH_YAML=on, -DCMAKE_BUILD_TYPE=Debug)	3m 29s
build (-DOPENMP=off, -DWITH_YAML=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Release)	12m 35s
build (-DOPENMP=off, -DWITH_YAML=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Debug)	3m 56s
	2h 4m 55s

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