Re: [AMBER] mac hangs when compile ambertools15 on El capitan

From: Yong Yao <>
Date: Wed, 2 Dec 2015 04:10:45 +0000

I did run "sudo xcodebuild -license" and type accept. if I go to src/netcdf-4.3.0 directory and run ./configure there, the computer hangs at "checking whether make sets $(MAKE)..."
From: Jason Swails []
Sent: Tuesday, December 01, 2015 5:07 AM
To: AMBER Mailing List
Subject: Re: [AMBER] mac hangs when compile ambertools15 on El capitan

On Mon, Nov 30, 2015 at 11:54 PM, Yong Yao <> wrote:

> I have waited for more than 10 hours.

​Holy cow! I applaud your patience. Even on the slowest filesystem it
should take well less than 10 minutes to configure (usually less than 1 or

> ​​
> I think it hangs at building Netcdf because the log file shows it does not
> pass the check make sets step.
> ​​
​I do not currently have or use El Capitan (I may upgrade one of my Macs
soon), but others use it just fine. I *suspect* what is happening is that
the XCode license has not yet been accepted. This typically happens the
first time you run "make" or a related command. A prompt pops up on the
command-line and asks if you accept Apple's EULA.

If you hadn't done this before, it probably did that while running the
NetCDF configure script. Which meant for the past 10 hours, your Mac was
waiting for the NetCDF configure script to accept Apple's EULA... It's an
incredibly irritating "feature" in Apple's newer development tools.

The solution is to run "make" by itself somewhere in the terminal. That
should pop up with a dialog in the terminal where you "read" the EULA and
accept it. Once you do this, it should not happen again (try reconfiguring
AmberTools and see if it works).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
AMBER mailing list
Received on Tue Dec 01 2015 - 20:30:03 PST
Custom Search