Category: PhysiCell

Setting up gcc / OpenMP on OSX (MacPorts edition)

Note: This is the part of 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:

  1. 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!
  2. 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 August 2, 2017, this will download Version 2.4.1.
  3. gcc7 (from MacPorts): This will be an up-to-date 64-bit version of gcc, with support for OpenMP. As of August 2, 2017, this will download Version 7.1.1.

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-2.4.1-10.11-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 7.x or above

port search gcc7

You should see a list of packages, including gcc7.

Then, download, build and install gcc7:

sudo port install gcc7

You should see a list of packages, including gcc7.

This will download, build, and install any dependencies necessary for gcc7, 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 gcc7 and its dependencies in a prior tutorial. 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-7 

Look for the version of g++ with an “mp” in its name. In my case, it’s g++-mp-7. Double-check that you have the right one by checking its version. It should look something like this:

Pauls-MBA:~ pmacklin$ g++-mp-7 --version

g++-mp-7 (MacPorts gcc7 7-20170622_0) 7.1.1 20170622
Copyright (C) 2017 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-7.

PhysiCell Version 1.2.2 and greater use a system variable to record your compiler version, so that you don’t need to modify the CC line in PhysiCell Makefiles. Set the PHYSICELL_CPP variable to record the compiler you just found above. For example, on the bash shell:

export PHYSICELL_CPP=g++-mp-7
echo export PHYSICELL_CPP=g++-mp-7 >> ~/.bash_profile

4) Test your setup

I wrote a sample C++ program that tests OpenMP parallelization (32 threads). If you can compile and run it, it means that everything (including make) is working! :-)

Make a new directory, and enter it

Open Terminal (see above). You should be in your user profile’s root directory. Make a new subdirectory called GCC_test, and enter it.

mkdir GCC_test
cd GCC_test
Grab a sample parallelized program:

Download a Makefile and C++ source file, and save them to the GCC_test directory. Here are the links:

  1. Makefile: [click here]
  2. C++ source: [click here]

Note: The Makefiles in PhysiCell (versions > 1.2.1) can use an environment variable to specify an OpenMP-capable g++ compiler. If you have not yet done so, you should go ahead and set that now, e.g., for the bash shell:

export PHYSICELL_CPP=g++-mp-7
echo export PHYSICELL_CPP=g++-mp-7 >> ~/.bash_profile
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 4096 MB of memory ...
Done!

Entering main loop ...
Done!

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 set the environment variable PHYSICELL_CPP as above (for PhysiCell 1.2.2 or later), or specify your compiler on the CC line of your makefile (for PhysiCell 1.2.1 or earlier). 

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 PhysiCell and try out the included examples! Visit BioFVM at MathCancer.org.

  1. PhysiCell links:
    1. PhysiCell Method Paper at bioRxiv: https://doi.org/10.1101/088773
    2. PhysiCell on MathCancer: http://PhysiCell.MathCancer.org
    3. PhysiCell on SourceForge: http://PhysiCell.sf.net
    4. PhysiCell on github: http://github.com/MathCancer/PhysiCell
    5. PhysiCell tutorials: [click here]
  2. BioFVM links:
    1. BioFVM announcement on this blog: [click here]
    2. BioFVM on MathCancer.org: http://BioFVM.MathCancer.org
    3. BioFVM on SourceForge: http://BioFVM.sf.net
    4. BioFVM Method Paper in BioInformatics: http://dx.doi.org/10.1093/bioinformatics/btv730
    5. BioFVM tutorials: [click here]

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Setting up a 64-bit gcc/OpenMP environment on Windows

Note: This is the part of a series of “how-to” blog posts to help new users and developers of BioFVM and PhysiCell. This guide is for Windows users. OSX users should use this guide for Homebrew (preferred method) or this guide for MacPorts (much slower but reliable). 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 a 64-bit Windows port of gcc. These instructions should work for any modern Windows installation, say Windows 7 or above. This tutorial assumes you have a 64-bit CPU running on a 64-bit operating system.

In the end result, you’ll have a compiler, key makefile capabilities, and a decent text editor. 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.

What you’ll need:

  1. MinGW-w64 compiler: This is a native port of the venerable gcc compiler for windows, with support for 64-bit executables. Download the latest installer (mingw-w64-install.exe) here. As of January 8, 2016, this installer will download gcc 5.3.0.
  2. MSYS tools: This gets you some of the common command-line utilities from Linux, Unix, and BSD systems (make, touch, etc.). Download the latest installer (mingw-get-setup.exe) here.
  3. Notepad++ text editor: This is a full-featured text editor for Windows, including syntax highlighting, easy commenting, tabbed editing, etc. Download the latest version here.  As of January 8, 2016, this will download Version 6.8.8.

Main steps:

1) Install the compiler

Run the mingw-w64-install.exe. When asked, select:

Version: 5.3.0 (or later)
Architecture: x86_64
Threads: posix (to posix to support PhysiBoSS)
Exception: seh (While sjlj works and should be more compatible with various GNU tools, the native SEH should be faster.)
Build version: 0 (or the default)

Leave the destination folder wherever the installer wants to put it. In my case, it is:

c:\Program Files\mingw-w64\x86_64-5.3.0-posix-seh-rt_v4_rev0

Let MinGW-w64 download and install whatever it needs.

2) Install the MSYS tools

Run mingw-get-setup.exe. Leave the default installation directory and any other defaults on the initial screen. Click “continue” and let it download what it needs to get started. (a bunch of XML files, for the most part.) Click “Continue” when it’s done.

This will open up a new package manager. Our goal here is just to grab MSYS, rather than the full (but merely 32-bit) compiler. Scroll through and select (“mark for installation”) the following:

  • mingw-developer-toolkit. (Note: This should automatically select msys-base.)

Next, click “Apply Changes” in the “Installation” menu. When prompted, click “Apply.” Let the package manager download and install what it needs (on the order of 95 packages). Go ahead and close things once the installation is done, including the package manager.

3) Install the text editor

Run the Notepad++ installer. You can stick with the defaults.

4) Add these tools to your system path

Adding the compiler, text editor, and MSYS tools to your path helps you to run make files from the compiler. First, get the path of your compiler:

  1. Open Windows Explorer ( [Windows]+E )
  2. Browse through C:\, then Program Files, mingw-w64, then a messy path name corresponding to our installation choices (in my case, x86_64-5.3.0-posix-seh_rt_v4-rev0), then mingw64, and finally bin.
  3. Record your answer. For me, it’s
    c:\Program Files\mingw-w64\x86_64-5.3.0-posix-seh-rt_v4_rev0\mingw64\bin\

Then, get the path to Notepad++.

  1. Go back to Explorer, and choose “This PC” or “My Computer” from the left column.
  2. Browse through C:\, then Program Files (x86), then Notepad++.
  3. Copy the path from the Explorer address bar.
  4. Record your answer. For me, it’s
    c:\Program Files (x86)\Notepad++\

Then, get the path for MSYS:

  1. Go back to Explorer, and choose “This PC” or “My Computer” from the left column.
  2. Browse through C:\, then MinGW, then msys, then 1.0, and finally bin.
  3. Copy the path from the Explorer address bar.
  4. Record your answer. For me, it’s
    C:\MinGW\msys\1.0\bin\

Lastly, add these paths to the system path, as in this tutorial.

5) Test your setup

I wrote a sample C++ program that tests OpenMP parallelization (32 threads). If you can compile and run it, it means that everything (including make) is working! :-)

Make a new directory, and enter it

Enter a command prompt ( [windows]+R, then cmd ). You should be in your user profile’s root directory. Make a new subdirectory, called GCC_test, and enter it.

mkdir GCC_test
cd GCC_test
Grab a sample parallelized program:

Download a Makefile and C++ source file, and save them to the GCC_test directory. Here are the links:

  1. Makefile: [click here]
  2. C++ source: [click here]
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 4096 MB of memory ...
Done!

Entering main loop ...
Done!

Open up the Windows task manager ([windows]+R, taskmgr) while the code is running.  Take a look at the performance tab, particularly the graphs of the CPU usage history. While your program is running, you should see all your virtual processes 100% utilized, unless you have more than 32 virtual CPUs. (This is a good indication that your code is running the OpenMP parallelization as expected.)

Note: 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.

What’s next?

Download a copy of PhysiCell and try out the included examples! Visit BioFVM at MathCancer.org.

  1. PhysiCell links:
    1. PhysiCell Method Paper at bioRxiv: https://doi.org/10.1101/088773
    2. PhysiCell on MathCancer: http://PhysiCell.MathCancer.org
    3. PhysiCell on SourceForge: http://PhysiCell.sf.net
    4. PhysiCell on github: http://github.com/MathCancer/PhysiCell
    5. PhysiCell tutorials: [click here]
  2. BioFVM links:
    1. BioFVM announcement on this blog: [click here]
    2. BioFVM on MathCancer.org: http://BioFVM.MathCancer.org
    3. BioFVM on SourceForge: http://BioFVM.sf.net
    4. BioFVM Method Paper in BioInformatics: http://dx.doi.org/10.1093/bioinformatics/btv730
    5. BioFVM tutorials: [click here]

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