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

From: Jason Swails <>
Date: Tue, 24 Sep 2013 08:24:29 -0400

On Mon, Sep 23, 2013 at 2:33 PM, M. L. Dodson <> wrote:

> [snip]
> >>> 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
> [snip]
> 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.

I have no experience, either (having installed XQuartz myself). A reliable
member of the MacPorts team insists you can do it and that he has done it,
so I tend to trust him. (Ryan Schmidt: -- second
post; it appears to be the source code for XQuartz).

> 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.

Sure. I had posted it earlier, but I have no objection to peppering my
wiki links everywhere :)

The link is also on the main Amber website under the "Mac" instructions.

> 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?

In my experience, running Amber on a Mac is comparable to running it on a
Linux box with comparable hardware. The Intel CPUs they use also do a
fantastically better job of multitasking than their AMD counterparts. If I
run a 4-threaded pmemd.MPI job on my dual-core (Core 2 duo) MBP, it's maybe
25% slower than running only 2-threaded pmemd.MPI. In fact, I see less of
a slow-down running an 8-thread job on my Core 2 Duo MBP than I do running
an 8-thread job on my (much newer) AMD FX-6100 Hex-core. But again, YMMV.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 24 2013 - 05:30:03 PDT
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