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

From: Jason Swails <>
Date: Mon, 23 Sep 2013 14:06:07 -0400

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.

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 M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Sep 23 2013 - 12:00:03 PDT
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