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

From: M. L. Dodson <>
Date: Mon, 23 Sep 2013 13:33:41 -0500

On Sep 23, 2013, at 1:06 PM, Jason Swails <> wrote:

> On Mon, Sep 23, 2013 at 10:00 AM, M. L. Dodson <> wrote:
>> 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
>>> 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.
> Yes, of course. I had taken the installation of Xcode for granted. Every
> package manager designed to build "Linux" packages on the Mac that I'm
> aware of (fink, MacPorts, Homebrew, etc.) requires not only Xcode tools,
> but also the command-line tools option. That said, the Apple-modified
> compilers included with Xcode's command-line tools will not build Amber, if
> for no other reason than there's no Fortran compiler.
> Once you have Xcode, you need to use that to build a suitable compiler (or,
> as the OP has done, just use the Intel compilers if you pay for them).
> 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.
> This is a somewhat involved discussion, but the punchline is that Apple
> split off development of its X11 port from the development of the core OS.
> Ergo, XQuartz stopped shipping as part of Mac OS X, thereby allowing
> XQuartz development to progress at its own pace.
> That said, discussions that I've seen on the MacPorts list (as well as
> their list of available ports) suggest that XQuartz is not required -- you
> can build MacPorts' X11 server instead (xorg-server? xorg? I can't remember
> the name of the port exactly. "port search xorg" should provide hits).
> I've always opted for XQuartz, myself.

I was influenced by the statement on the main MacPorts site that X11 was
required, but when I tried to install X11 (don't remember the details now) I was
directed to XQuartz. So I have no experience differing from what you said.

> Alas, development proceeds too quickly in Apple's universe for me to keep
> my Wiki completely up-to-date for every Xcode/OS/blah update they release.
> As a result, I try to keep specific dates and version numbers on my Wiki.
> All the best,
> Jason

Maybe you could point Your Wiki to this thread? I just want people new to
AMBER/Mac OSX to know how to get started.

Sorry, I have not read your Wiki as I never had any problem unless the solution
was obvious. Then I don't remember ever trying to compile regular AMBER on a Mac
(i.e., sander, etc,) only AmberTools. I don't see the point, I guess. Why
hamstring your computational work by running it on a workstation a large
fraction of whose resources are devoted to running a very complex GUI? Maybe for
one shot quick tests, I guess, but then I always had a terminal login to the
computational box going, so it was as convenient as my local machine.

But this is getting far beyond the set of original points, so I'll quit posting

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 - 12:30:03 PDT
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