Issue with installation of PAML on a red-hat computer

[Tina Lan]

Our group has recently installed PAML in a red hat computer. The installation
process seemed OK. But when we run codeml program, we got an error message
complaining about "error when opening file rub". Other error messages, such as
"outfile creation error" or "ctl file open error", were showing with baseml,
basemlg etc. Only chi2 module worked well. 

And our IT department has confirmed that the space on the computer is enough and the administrator tried to run several times as root. 

I really appreciate if anyone could help me on this issue.

[Ziheng]

I am not sure.  The error message sounds like you have an issue with file permissions (that is, you may not have the permission to create a new file in the directory you are working in).  However, if your administrator confirmed that is not the case, I am at a loss.
The "ctl file open error" is probably because you are in the wrong folder when you run the program.
I suggest you do a few simple tests.

After you have compiled the programs in the paml4.7/src/ folder, move the executables into the paml4.7/bin/ folder.
Then cd to paml4.7/ folder.  Then type

bin/baseml

to run the program. 
If you get the same error message, I suggest that you first try to create a new file in that folder using whatever program you use, emacs, vi, etc.
ziheng yang

[Sakshi Bharti]

I am also facing this problem. Ziheng kindly help me.

[Ziheng]

But did my suggestions above work?
Ziheng