Figure: An early test of our new 3-D agent-based cell model, growing from 10 to 80,000 agents in about 25 days (24-threaded simulation required about 5 hours). Rendered in 3D using POVRAY (with a cutaway view). [Read more ...]

Monday, January 18, 2016

Setting up gcc / OpenMP on OSX (MacPorts edition)

Note: This is the second in a series of "how-to" blog posts to help new users and developers of BioFVM and PhysiCell. This guide is for OSX users. Windows users should use this guide instead. A Linux guide is expected soon.

These instructions should get you up and running with a minimal environment for compiling 64-bit C++ projects with OpenMP (e.g., BioFVM and PhysiCell) using gcc. These instructions were tested with OSX 10.11 (El Capitan), but they should work on any reasonably recent version of OSX.

In the end result, you'll have a compiler and key makefile capabilities. The entire toolchain is free and open source.

Of course, you can use other compilers and more sophisticated integrated desktop environments, but these instructions will get you a good baseline system with support for 64-bit binaries and OpenMP parallelization.

Note 1: OSX / Xcode appears to have gcc out of the box (you can type "gcc" in a Terminal window), but this really just maps back onto Apple's build of clang. Alas, this will not support OpenMP for parallelization.

Note 2: This process is somewhat painful because MacPorts compiles everything from source, rather than using pre-compiled binaries. This tutorial uses Homebrew: a newer package manager that uses pre-compiled binaries to dramatically speed up the process. I highly recommend using the Homebrew version of this tutorial.

What you'll need:

  • XCode: This includes command line development tools. Evidently, it is required for both Macports and its competitors (e.g., Homebrew). Download the latest version in the App Store. (Search for xcode.) As of January 15, 2016, the App Store will install Version 7.2. Please note that this is a 4.41 GB download!
  • MacPorts: This is a package manager for OSX, which will let you easily download, build and install many linux utilities. You'll particularly need it for getting gcc. Download the latest installer (MacPorts-2.3.4-10.11-ElCapitan.pkg) here. As of January 15, 2016, this will download Version 2.3.4. 
  • gcc5 (from MacPorts): This will be an up-to-date 64-bit version of gcc, with support for OpenMP. As of January 15, 2016, this will download Version 5.3.0.

Main steps:

1) Download, install, and prepare XCode

As mentioned above, open the App Store, search for Xcode, and start the download / install. Go ahead and grab a coffee while it's downloading and installing 4+ GB. Once it has installed, open Xcode, agree to the license, and let it install whatever components it needs. 

Now, you need to get the command line tools. Go to the Xcode menu, select "Open Developer Tool", and choose "More Developer Tools ...". This will open up a site in Safari and prompt you to log in. 

Sign on with your AppleID, agree to yet more licensing terms, and then search for "command line tools" for your version of Xcode and OSX. (In my case, this is OSX 10.11 with Xcode 7.2) Click the + next to the correct version, and then the link for the dmg file. (Command_Line_Tools_OS_X_10.11_for_Xcode_7.2.dmg).  

Double-click the dmg file. Double-click pkg file it contains. Click "continue", "OK", and "agree" as much as it takes to install. Once done, go ahead and exit the installer and close the dmg file. 

2) Install Macports

Double-click the MacPorts pkg file you downloaded above. OSX may complain with a message like this:
"MacPorts-2.3.4-10.11-ElCapitan.pkg" can't be opened because it is from an unidentified developer.
If so, follow the directions here.

Leave all the default choices as they are in the installer. Click OK a bunch of times. The package scripts might take awhile.

Open a terminal window (Open Launchpad, then "Other", then "Terminal"), and run:

> sudo port -v selfupdate

to make sure that everything is up-to-date. 

3) Get, install, and prepare gcc

Open a terminal window (see above), and search for gcc, version 5.x or above

> port search gcc5

You should see a list of packages, including gcc5.

Then, download, build and install gcc5:

> sudo port install gcc5

You should see a list of packages, including gcc5.

This will download, build, and install any dependencies necessary for gcc5, including llvm and many, many other things. This takes even longer than the 4.4 GB download of Xcode. Go get dinner and a coffee. You may well need to let this run overnight. (On my 2012 Macbook Air, it required 16 hours to fully build gcc5 and its dependencies. We'll discuss this point further below.)

Lastly, you need to get the exact name of your compiler. In your terminal window, type g++, and then hit tab twice to see a list. On my system, I see this:

Pauls-MBA:~ pmacklin$ g++

g++       g++-mp-5 

Look for the version of g++ with an "mp" in its name. In my case, it's g++-mp-5. Double-check that you have the right one by checking its version. It should look something like this: 

Pauls-MBA:~ pmacklin$ g++-mp-5 --version
g++-mp-5 (MacPorts gcc5 5.3.0_0) 5.3.0
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Notice that MacPorts shows up in the information. The correct compiler is g++-mp-5. 

5) Test the compiler

Write a basic parallelized program:

Open Terminal (see above). You should be in your user profile's root directory. Make a new subdirectory, enter it, and create a new file:  

> mkdir omp_test
> cd omp_test
> nano omp_test.cpp

Then, write your basic OpenMP test: 

#include <iostream>
#include <cmath> 
#include <vector>
#include <omp.h>

int main( int argc, char* argv[] ) 
 omp_set_num_threads( 8 ); 

 double pi = acos( -1.0 ); 

 std::cout << "Allocating memory ..." << std::endl; 
 std::vector<double> my_vector( 128000000, 0.0 ); 
 std::cout << "Done!" << std::endl << std::endl; 

 std::cout << "Entering main loop ... " << std::endl; 

 #pragma omp parallel for
 for( int i=0; i < my_vector.size(); i++ )
  my_vector[i] = exp( -sin( i*i + pi*log(i+1) ) ); 
 std::cout << "Done!" << std::endl; 

 return 0; 

Save the file (as omp_test.cpp). (In nano, use [Control]-X, Y, and then confirm the choice of filename.)

In the omp_set_num_threads() line above, replace 8 with the maximum number of virtual processors on your CPU. (For a quad-core CPU with hyperthreading, this number is 8. On a hex-core CPU without hyperthreading, this number is 6.) If in doubt, leave it alone for now, or set it at a relatively safe value of 4. 

Write a makefile:

Next,  create a Makefile to start editing:

> nano Makefile 

Add the following contents: 

CC := g++-mp-5
# replace this with your correct compiler as identified above

ARCH := core2 # Replace this with your CPU architecture.
# core2 is pretty safe for most modern machines. 

CFLAGS := -march=$(ARCH) -O3 -fopenmp -m64 -std=c++11


OUTPUT := my_test

all: omp_test.cpp
 $(COMPILE_COMMAND) -o $(OUTPUT) omp_test.cpp

 rm -f *.o $(OUTPUT).*

Go ahead and save this (as Makefile). ([Control]-X, Y, confirm the filename.)

Compile and run the test:

Go back to your (still open) command prompt. Compile and run the program: 

> make
> ./my_test

The output should look something like this: 

Allocating memory ...

Entering main loop ... 

Note 1: If the make command gives errors like "**** missing separator", then you need to replace the white space (e.g., one or more spaces) at the start of the "$(COMPILE_COMMAND)" and "rm -f" lines with a single tab character. 

Note 2: If the compiler gives an error like "fatal error: 'omp.h' not found", you probably used Apple's build of clang, which does not include OpenMP support. You'll need to make sure that you specify your compiler on the CC line of your makefile. 

Now, let's verify that the code is using OpenMP.

Open another Terminal window. While the code is running, run top. Take a look at the performance, particularly CPU usage. While your program is running, you should see CPU usage fairly close to '100% user'. (This is a good indication that your code is running the OpenMP parallelization as expected.)

MacPorts and Pain

MacPorts builds all the tools from source. While this ensures that you get very up-to-date binaries, it is very, very slow!

However, all hope is not lost. It turns out that Homebrew will install pre-compiled binaries, so the 16-hour process of installing gcc is reduced to about 5-10 minutes. Check back tomorrow for a follow-up tutorial on how to use Homebrew to set up gcc.

What's next?

Download a copy of BioFVM and try out the included examples!
  1. BioFVM announcement on Blogspot: [click here
  2. BioFVM on 
  3. BioFVM on SourceForge: 
  4. BioFVM Method Paper in BioInformatics: 

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  1. Note that MacPorts actually supports and offers precompiled binaries as well, but those are only available if license permits and default variants are used. Additionally, the buildbot for El Capitan has only recently been set up, so El Capitan binaries will appear over the next few weeks.

  2. Thanks a lot , was really useful!