add debug flags to GNU CI and fix remaining failures #989

Job	Run time
build (-DOPENMP=on, -DCMAKE_BUILD_TYPE=Release)	7m 8s
build (-DOPENMP=on, -DCMAKE_BUILD_TYPE=Debug)	3m 22s
build (-DOPENMP=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Release)	7m 7s
build (-DOPENMP=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Debug)	3m 43s
build (-DOPENMP=on, -DWITH_YAML=on, -DCMAKE_BUILD_TYPE=Release)	5m 2s
build (-DOPENMP=on, -DWITH_YAML=on, -DCMAKE_BUILD_TYPE=Debug)	3m 41s
build (-DOPENMP=on, -DWITH_YAML=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Release)	7m 8s
build (-DOPENMP=on, -DWITH_YAML=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Debug)	3m 55s
build (-DOPENMP=off, -DCMAKE_BUILD_TYPE=Release)	7m 9s
build (-DOPENMP=off, -DCMAKE_BUILD_TYPE=Debug)	3m 19s
build (-DOPENMP=off, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Release)	7m 4s
build (-DOPENMP=off, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Debug)	3m 46s
build (-DOPENMP=off, -DWITH_YAML=on, -DCMAKE_BUILD_TYPE=Release)	7m 8s
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)	7m 10s
build (-DOPENMP=off, -DWITH_YAML=on, -DUSE_DEPRECATED_IO=on, -DCMAKE_BUILD_TYPE=Debug)	3m 46s
	1h 24m 0s

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