Re: [AMBER] Word of caution for Xcode 5, Mac OS X

From: M. L. Dodson <>
Date: Mon, 23 Sep 2013 09:00:19 -0500

On Sep 23, 2013, at 8:26 AM, Jason Swails <> wrote:

> On Mon, Sep 23, 2013 at 9:13 AM, Julio Dominguez <>wrote:
>> Re: Word of caution for Xcode 5, Mac OS X (M. L. Dodson)
>> Thanks for the instructions Bud. I think I was missing something along the
>> lines of your suggestion. At any rate, you instructions will be be useful
>> for far more users than just me.
>> However, I do have the intel compilers installed and those worked
>> perfectly.
>> Today I'll try to double check if the Apple provided gcc works with AMBER
> It will not work with Amber. I put together a Wiki describing how to set
> up a Mac for use with Amber (which
> includes instructions regarding the command-line tools as well, in addition
> to activating the correct xcode versions and using MacPorts).
> You will need to use the MacPorts-generated compilers. It may be that
> upgrading Xcode tools will necessitate recompiling all of your ports, but
> that has not been true in my experience.
> HTH,
> Jason

But the point is that when I upgraded to 10.8.5 (probably true of 10.8.*,
as well), the upgrade removed Xcode (which is required for MacPorts.)
And I doubt a fresh install of 10.[89].x would ever install Xcode,
since the move is toward App Store distribution for that kind of s/w. So
you need Xcode to use MacPorts to get an appropriate compiler for AMBER.
Other package managers may behave differently.

Under these conditions, MacPorts also needs a new XQuartz version of
X11. I can't remember exactly when I was prompted to install it, but the
site was presented to me automatically as I proceeded along the route
outlined. I am guessing the OS upgrade removed the X11 install, as well,
but am not sure.


PS, my upgrade was 10.7.x to 10.8.5, not a minor version upgrade, which
may well preserve any Xcode installation you may have done earlier. In
any case, there are upgrade paths that result in having no base of
development software. The test is to just type "make" in a terminal
window. If it returns "make: Command not found." then the scenario
I outlined is active.

PPS, App Store distribution of Xcode is free as was XQuartz, although
you will have to register as a developer before you can use Xcode.
There is no developer category for people who just want to install
professional software distributed as source. (If it were possible,
Jobs would probably spin in his grave at the very idea of distributing
s/w as source code :-) So, you will have to pick a developer category
that comes close. I picked "non-App Store App developer," or some
such. Your mileage may vary.
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Mon Sep 23 2013 - 07:30:02 PDT
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