Fix cmake build

[dtmoodie]

There are several runtime issues that exist in a cmake build but not a make build:
#6592
#6204
#6775

All the above are resolved using the makefile build on ubuntu 16.04.

[piiswrong]

@cjolivier01

[chinakook]

#6685

[szha]

This issue is closed due to lack of activity in the last 90 days. Feel free to ping me to reopen if this is still an active issue. Thanks!