On Nov 11, 2010, at 10:19 AM, Dean Cuebas wrote:
> <snip>
> 4) I cd to the src directory of Ambertools and type
> ./configure -macAccelerate gnu
>
> +++++++++++++++++++++++++++++++++++++++++++++
> Your AMBERHOME environment variable should be set to /usr/local/amber11
>
>
You may want to try compiling as root, if you are going to compile to /usr/local/amber11
Here's what I do when compiling amber:
sudo -E -s
You will now be root, and hopefully your environmental variables will be preserved; use plenty of caution.
Follow the remaining instructions regarding installation of AMBER.
When it comes time to run the tests, you may want to perform the following (as root):
chown -R dean:staff /usr/local/amber11/test
Note: change dean to whatever your short username is.
Then when you go to run the tests, either exit the "root" session, or start a fresh terminal and change to the correct directory for performing the tests. It's a lot easier and safer to set up mpi as a normal user than to try to configure passwordless ssh as root.
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Received on Thu Nov 11 2010 - 09:00:06 PST
