1) I assume you are trying with CodeXL's CPU Profiling functionality on a system with AMD processor.
2) Currently CodeXL does not support any command line tools. In future, we plan to provide command line tools to collect & analyze the profile data.
3) CodeXL successfully profiles an application invoked through a shell script. When you create a project, if you specify the shell script in the "Executable Path", then codexl will profile the programs launched through that script.