On Mac OS X, you use wxMac-x.y.z.tar.gz instead; the other instructions are the same. Once you have built the library, compiling applications is fairly simple, thanks to the handy wx-config utility. G -o executablename `wx-config -cflags` sourcefile `wx-config -libs` For example. This project presents clone of the Borland Turbo C/C or Embarcadero C 10.1 ‘Berlin’ library 'conio' for the GCC compiler, more precisely for the C language in Windows, Linux and Mac OS operating systems. Because all functions are defined within the header file itself, the installation is simple.
- G++ Compiler Install
- Gcc Compiler Mac
- G++ Compiler On Mac
- G++ Compiler For Windows 10
- G++ Compiler Mac Os X Download Windows 10
Installing G on a Mac. This section is intended to get you quickly started with C programming on your Mac. We'll be installing GCC 4.8.1 and GDB through a tool called Homebrew. If you want an additional guide on all of the following steps (except for installing GCC), the one by Moncef Belyamani is quite helpful. When you follow it, ignore. Click on Settings, pull down to Compiler Settings, and pull down to Workspace. Change the language to C. Select 'c (g) - Mac OS X' or 'g - generic', click on Use, and click on OK. You are now ready to start developing in C/C and you have two ways to proceed, depending on your personal preferences. Instructions for older versions of Mac OS X (10.6 - 10.10) Instructions for installing the GNU compilers for older versions of Mac OS X (10.6 - 10.10) have been moved and are available on another page. Tips & Warnings. I mention all but the last of these tips and warnings in the text above, but it doesn't hurt to list them a second time.
The following sections describe the installation procedures on UNIX/Linux, Mac OS X, and Windows systems.
The configuration script and Makefiles in the
Ipopt distribution have been created using GNU's autoconf and automake. In general, you can see the list of options and variables that can be set for the configure script by typing
Many Linux distributions will come with all necessary tools. All you should need to do is check the compiler versions. On a Debian-based distribution, you can obtain all necessary tools with the following command:
Replace apt-get with your relevant package manager, e.g.
dnf for RedHat-based distributions,
pacman for Arch, etc. The g++ and gfortran compilers may need to be specified respectively as
gcc-gfortran with some package managers.
Mac OS X
You need either the Xcode Command Line Tools or a community alternative such as Homebrew to install the GNU compilers:
Further, pkg-config is required, which can be installed via Homebrew by
If you have Xcode installed, the Command Line Tools are available under Preferences, Downloads. These items unfortunately do not come with a Fortran compiler, but you can get gfortran from http://gcc.gnu.org/wiki/GFortranBinaries#MacOS. In the past, we have been able to compile
Ipopt using default Xcode versions of gcc and g++ and a newer version of gfortran from this link, but consistent version numbers may be an issue in future cases.
If you intend to use MUMPS or one of the DOWNLOAD_HSL 'HSL linear solvers', then they may profit from an installation of METIS. This can be accomplished via
Windows with MSYS2/MinGW
For Windows, one can compile
Ipopt under MSYS2/MinGW, which is a light-weight UNIX-like environment for Windows.
MSYS2/MinGW can be obtained from https://www.msys2.org/. After installation, a number of additional packages need to be installed:
(I might have forgotten something.) If you also want to use GNU compilers, then install them, too:
When using MinGW, it is convenient to install MinGW's Lapack and METIS as well:
To use MSYS2/MinGW to compile
Ipopt with native MSVC/Intel compilers, the basic version MSYS2 version without MinGW is sufficient. To use the GNU compilers, MinGW is required.
If you want to use the native MSVC or Intel compiler, you need to make sure that environment variables are setup for the compilers. One way is to create a shell script that executes the batch files that are provided by Microsoft and Intel for this purpose before starting MSYS2. For using MSVC, this script may have a form similar to
For using Intel C/C++ and Fortran compilers, the 2nd line may be replaced by something like
You might have to search around a bit. The important thing is that, after your change, you can type
cl and it finds the Microsoft C++ compiler and, if installed, you can type
ifort and it finds the Intel Fortran compiler.
- The build systems of
Ipoptby default first looks for GCC and Clang before the Intel and MS compilers. To disable this, specify the flag
--enable-msvcas argument to configure below.
Ipopt uses a few external packages that are not included in the
Ipopt source code distribution, for example ASL (the AMPL Solver Library if you want to compile the
Ipopt AMPL solver executable), Blas, Lapack.
Ipopt also requires at least one linear solver for sparse symmetric indefinite matrices. There are different possibilities, see below. It is important to keep in mind that usually the largest fraction of computation time in the optimizer is spent for solving the linear system, and that your choice of the linear solver impacts
Ipopt's speed and robustness. It might be worthwhile to try different linear solver to experiment with what is best for your application.
Since this third party software is released under different licenses than
Ipopt, we cannot distribute their code together with the
Ipopt packages and have to ask you to go through the hassle of obtaining it yourself. Keep in mind that it is still your responsibility to ensure that your downloading and usage of the third party components conforms with their licenses.
For ASL, HSL, and MUMPS, COIN-OR provides specialized build systems that produce libraries which are easy to use with the build system of
Ipopt. Some of the specialized build systems also come with a script that makes it easy to download the code using
ASL (Ampl Solver Library)
Note that you only need to obtain the ASL if you intend to use
Ipopt from AMPL. It is not required if you want to specify your optimization problem in a programming language (e.g., C++, C, or Fortran).
The COIN-OR Tools project ThirdParty-ASL can be used to download the ASL code and build an ASL library that is recognized by Ipopt. To do so, execute
BLAS and LAPACK
Ipopt's build system tries to find an installation of BLAS and LAPACK in your system. On Ubuntu, such libraries can be made available by installing liblapack-dev. Other Linux distributions typically also offer a way to install Blas and Lapack via its package manager. On Mac OS X,
Ipopt's build system should pick up the Blas and Lapack from the Accelerate framework.
- It is highly recommended that you obtain an efficient implementation of the BLAS and LAPACK library, tailored to your hardware; Section Prerequisites lists a few options. For instance, to have configure pick up a local installation of ATLAS in $HOME/lib, one would use the
--with-lapackflag when running
configure(see Compiling and Installing Ipopt): The configure script already tries to find Intel MKL libraries on some systems. If that fails, e.g., because the libraries are not available in a standard search path, then also use the
--with-lapackflag to explictly state what flags are necessary to use MKL, e.g.,
HSL (Harwell Subroutines Library)
There are two versions of HSL available:
- HSL Archive: contains outdated codes that are freely available for personal commercial or non-commercial usage. Note that you may not redistribute these codes in either source or binary form without purchasing a licence from the authors. This version includes MA27, MA28, and MC19.
- HSL Full: contains more modern codes that are freely available for academic use only. This version includes the codes from the HSL Archive and additionally MA57, HSL_MA77, HSL_MA86, and HSL_MA97.
Ipoptsupports the HSL Full codes from 2013 and later.
To obtain the HSL code, you can follow the following steps:
- Go to http://hsl.rl.ac.uk/ipopt.
- Choose whether to download either the Archive code or the HSL Full code. To download, select the relevant 'source' link.
- Follow the instructions on the website, read the license, and submit the registration form.
- Wait for an email containing a download link (this should take no more than one working day).
You may either:
- Compile the HSL code via the COIN-OR Tools project ThirdParty-HSL. See the instructions below.
- Compile the HSL code separately either before or after the
Ipoptcode and use the shared library loading mechanism. See the documentation distributed with the HSL package for information on how to do so.
To compile the HSL code via the COIN-OR Tools project ThirdParty-HSL, run
Now unpack the HSL sources archive, move and rename the resulting directory so that it becomes
ThirdParty-HSL/coinhsl. Then, in
ThirdParty-HSL, configure, build, and install the HSL sources:
- The build system of Ipopt currently requires that MA27 is part of a HSL library, if a HSL library is provided.
- Whereas it is essential to have at least one linear solver, the package MC19 could be omitted (with the consequence that you cannot use this method for scaling the linear systems arising inside the
Ipoptalgorithm). By default, MC19 is only used to scale the linear system when using one of the HSL solvers, but it can also be switched on for other linear solvers (which usually have internal scaling mechanisms). Further, also the package MA28 can be omitted, since it is used only in the experimental dependency detector, which is not used by default.
- If you are an academic or a student, we recommend you download the HSL Full package as this ensures you have access to the full range of solvers. MA57 can be considerably faster than MA27 on some problems.
- If you have a precompiled library containing the HSL codes, you can specify the directory containing the
CoinHslConfig.hheader file and the linker flags for this library with the flags
--with-hsl-lflagsflags, respectively, when running
Ipopt(see Compiling and Installing Ipopt).
- The linear solvers MA57, HSL_MA77, HSL_MA86, HSL_MA97 can make use of the matrix ordering algorithms implemented in METIS. ThirdParty-HSL will look automatically for a METIS installation in your system and should work with both METIS 4 and METIS 5.
MUMPS Linear Solver
You can also use the (public domain) sparse linear solver MUMPS. Please visit the MUMPS home page for more information about the solver. MUMPS is provided as Fortran 90 and C source code. You need to have a Fortran 90 compiler (e.g., the GNU compiler gfortran) to be able to use it.
The COIN-OR Tools project ThirdParty-Mumps can be used to download the MUMPS 4.10.0 code and build a MUMPS library that is recognized by Ipopt. To do so, execute
- MUMPS will perform better if the matrix ordering algorithms implemented in METIS are available on the system.
- MUMPS uses internally a fake implementation of MPI. If you are using
Ipoptwithin an MPI program together with MUMPS, the code will not run. You will have to modify the MUMPS sources so that the MPI symbols inside the MUMPS code are renamed.
- Branch mumps5 of project ThirdParty-Mumps can be used to build a a library of MUMPS 5.2.x that is usable with
Ipopt. However, initial experiments on the CUTEst testset have shown that performance with MUMPS 5.2.x is worse than with Mumps 4.10.0 on average.
Ipopt with a precompiled MUMPS library, you need to specify the
-I flag to have the compiler find the directory containing the MUMPS header files with the
--with-mumps-cflags flag of
Ipopt's configure, e.g.,
and you also need to provide the linker flags for MUMPS with the
Pardiso (Parallel Sparse Direct Linear Solver)
If you would like to compile
Ipopt with Pardiso, you need to obtain either Intel's MKL library or the Pardiso library from http://www.pardiso-project.org for your operating system.
From http://www.pardiso-project.org, you can obtain a limited time license of Pardiso for academic or evaluation purposes or buy a non-profit or commercial license. Make sure you read the license agreement before filling out the download form.
Ipopt with the linear solver Pardiso from the Pardiso project website, you need to specify the link flags for the library with the
--with-pardiso flag, including required additional libraries (except for Lapack) and flags. For example, if you want to compile
Ipopt with the parallel version of Pardiso (located in
$HOME/lib) on a GNU/Linux system, you should add the flag
For best performance on Linux, use Pardiso from the Pardiso project website together with linear algebra routines from Intel MKL (see BLAS and LAPACK).
If you are using the parallel version of Pardiso, you need to specify the number of processors it should run on with the environment variable
OMP_NUM_THREADS, as described in the Pardiso manual.
If you want to compile
Ipopt with the Pardiso library that is included in Intel MKL, it is sufficient to ensure that MKL is used for the linear algebra routines (Blas/Lapack), see BLAS and LAPACK.
WSMP (Watson Sparse Matrix Package)
If you would like to compile
Ipopt with WSMP, you need to obtain the WSMP library for your operating system. Information about WSMP can be found at http://www.research.ibm.com/projects/wsmp.
At this website you can download the library for several operating systems including a trial license key for 90 days that allows you to use WSMP for 'educational, research, and benchmarking purposes by non-profitacademic institutions' or evaluation purposes by commercial organizations; make sure you read the license agreement before using the library. Once you obtained the library and license, please check if the version number of the library matches the one on the WSMP website.
If a newer version is announced on that website, you can (and probably should) request the current version by sending a message to
[email protected]. Please include the operating system and other details to describe which particular version of WSMP you need.
- Only the interface to the shared-memory version of WSMP is currently supported.
Ipopt with the linear solver WSMP, you need to specify the linker flags for the library with the
--with-wsmp flag, including required additional libraries and flags. For example, if you want to compile
Ipopt with WSMP (located in
$HOME/lib) on an Intel IA32 Linux system, you should use the
Using the Linear Solver Loader
Ipopt will be compiled with a mechanism, the Linear Solver Loader, which can dynamically load shared libraries with MA27, MA57, HSL_MA77, HSL_MA86, HSL_MA97, or the Pardiso linear solver at runtime.
This means, if you obtain one of those solvers after you compiled
Ipopt, you don't need to recompile to use it. Instead, you can just put a shared library called
libpardiso.so into the shared library search path,
LD_LIBRARY_PATH. These are the names on most UNIX platforms, including Linux. On Mac OS X, the names are
DYLD_LIBRARY_PATH. On Windows, the names are
The Pardiso shared library can be downloaded from the Pardiso website. To create a shared library containing the HSL linear solvers, follow the instructions from HSL (Harwell Subroutines Library), but rename the resulting library to
If you have problems compiling this feature, you can disable this by specifying
--disable-linear-solver-loader for the
Ipopt is available from the COIN-OR group at GitHub. You can either download the code using
git or simply retrieve a tarball (compressed archive file). While the tarball is an easy method to retrieve the code, using the git system allows users the benefits of the version control system, including easy updates and revision control.
Getting the Ipopt code via git
Of course, the git client must be installed on your system if you want to obtain the code this way (the executable is called
git). Information about git and how to download it can be found at http://git-scm.com.
To obtain the
Ipopt source code via git, change into the directory in which you want to create a subdirectory
Ipopt with the
Ipopt source code. Then follow the steps below:
- Download the code from the repository:
- Change into the root directory of the
G++ Compiler Install
In the following,
$IPOPTDIR will refer to the directory in which you are right now (output of
Getting the Ipopt code as a tarball
To use the tarball, follow the steps below:
- Download the desired tarball from http://www.coin-or.org/download/source/Ipopt, it has the form
x.y.zis the version number, such as 3.12.0.
- Issue the following commands to unpack the archive file:
- Rename the directory you just extracted:
- Change into the root directory of the
In the following,
$IPOPTDIR will refer to the directory in which you are right now (output of
Ipopt can be easily compiled and installed with the usual configure, make, make install commands. We follow the procedure that is used for most of the COIN-OR projects, based on the GNU autotools.
Below are the basic steps for the
Ipopt compilation that should work on most systems. For special compilations and for some troubleshooting see Flags to configure before creating an issue or sending a message to the mailing list.
Create a directory where you want to compile
Ipopt, for example
and change into this directory
- You can choose any location, including $IPOPTDIR itself, as the location of your compilation. However, on COIN-OR we recommend to keep the source and compiled files separate as this comes in handy when you want to compile the code with different compilers, compiler options, or different operating system that share a common file system. For this to work, the directories with the
Ipoptsource must not have any configuration and compiled code.
Run the configure script:
One might have to give options to the configure script, e.g., in order to choose a non-default compiler, or to tell it where to install Ipopt eventually, see Flags to configure.
If the last output line reads
configure: Main configuration of Ipopt successfulthen everything worked fine. Otherwise, look at the screen output, have a look at the
config.logoutput file and/or consult Flags to configure.
The default configure (without any options) is sufficient for most users that downloaded and installed the source code for the linear solver and other dependencies. If you want to see the configure options, consult Flags to configure.
Build the code:
Note: If you are using GNU make, you can also try to speed up the compilation by using the
make -j3), where
Nis the number of parallel compilation jobs. A good number for
Nis the number of available processors plus one. Under some circumstances, this fails, and you might have to re-issue the command, or omit the
If you want, you can run a short test to verify that the compilation was successful. For this, you just enter
This will test if the AMPL solver executable works (if you got the ASL code) and if the included C++, C, Java, and Fortran examples work.
- The configure script is not able to automatically determine the C++ runtime libraries for the C++ compiler. For certain compilers we enabled default values for this, but those might not exist or be wrong for your compiler. In that case, the C and Fortran example in the test will most probably fail to compile. If you don't want to hook up the compiled
Ipoptlibrary to some Fortran or C code that you wrote you don't need to worry about this. If you do want to link the
Ipoptlibrary with a C or Fortran compiler, you need to find out the C++ runtime libraries (e.g., by running the C++ compiler in verbose mode for a simple example program) and run
configureagain, and this time specify all C++ runtime libraries with the
CXXLIBSvariable (see also Flags to configure).
sudohas been added here as
make installinstalls files into
/usr/local, where only system administrators have write permissions. This installs
sIpoptAMPL solver executables (if ASL source was downloaded) in
libipopt.aor similar) in
- pkg-config files for use of the
You can change the default installation directory (here
/usr/local) by using the
configure. If this is a directory that you have write permissions for,
sudocan be omitted for
Flags to configure
In general, you can see the list of options and variables that can be set for the configure script by typing
Below a few particular options are discussed:
If you want to specify that you want to use particular compilers, you can do so by adding the variables definitions for CXX, CC, and F77 to the
./configurecommand line, to specify the C++, C, and Fortran 77 compiler, respectively. For example,
In order to set the compiler flags, you should use the variables
FFLAGS. Note, that the
dynamic_cast. Therefore it is necessary that the C++ code is compiled including RTTI (Run-Time Type Information). Some compilers need to be given special flags to do that (e.g.,
-qrtti=dynafor the AIX
- By default, the
Ipoptlibrary is compiled as a shared library, on systems where this is supported. If you want to generate a static library, you need to specify the
--disable-sharedflag. If you want to compile both shared and static libraries, you should specify the
--enable-staticflag. This is no possible on Windows.
It is possible to compile the
Ipoptlibrary in a debug configuration, by specifying
--enable-debug. This switches the default compiler flags (CFLAGS, CXXFLAGS, FFLAGS) to instruct the compiler to include debug information into object files and disables compiler optimization.
Also, you can tell
Ipoptto do some additional runtime sanity checks, by specifying the flag
This usually leads to a significant slowdown of the code, but might be helpful when debugging something.
If you want to link the
Ipoptlibrary with a main program written in C or Fortran, the C and Fortran compiler doing the linking of the executable needs to be told about the C++ runtime libraries. Unfortunately, the current version of autoconf does not provide the automatic detection of those libraries. We have hard-coded some default values for some systems and compilers, but this might not work all the time.
If you have problems linking your Fortran or C code with the
Ipoptlibrary libipopt.a and the linker complains about missing symbols from C++ (e.g., the standard template library), you should specify the C++ libraries with the
CXXLIBSvariable. To find out what those libraries are, it is probably helpful to link a simple C++ program with verbose compiler output.
For example, for the Intel compilers on a Linux system, you might need to specify something like
- Compilation on an AIX 64bit system sometimes requires some special consideration. We recommend the following configuration (Alternatively, a simpler solution for AIX is to set the environment variable
Ipopt's Java interface
JIpoptuses the Java Native Interface (JNI), which is a programming framework that allows Java code running in the Java Virtual Machine (JVM) to call and be called by native applications and libraries written in languages such as C and C++.
configure tries to find a Java compiler and the necessary compiler flags to locate the JNI header files automatically. You can influence this automated check by setting the environment variable
JAVA_HOMEto the directory that contains your JDK.
- The build procedure currently cannot deal with spaces in the path to the JDK. If you are on Windows and have Java in a path like
C:Program FilesJava, try setting
JAVA_HOMEto the DOS equivalent
You can disable the checks for Java and build of the Java interface by specifying the configure flag
--disable-java. This is also the default if
JAVA_HOMEcontains a space or the build of shared libraries has been disabled as
JIpoptneeds to be able to load the
Ipoptlibrary dynamically at runtime.
- sIpopt is build and installed together with Ipopt. If you do not need sIpopt, you can disable it via
Configure flags specific to the use of
Ipopt's dependencies were discussed in the corresponding sections of Download, build, and install dependencies.
On sufficiently prepared systems, an alternative way to download, build, and install
Ipopt with dependencies ASL, HSL, and MUMPS is to use the coinbrew script from https://coin-or.github.io/coinbrew/
After obtaining the script, run
The coinbrew script will take care of building and installing the dependencies ASL and Mumps before building
Ipopt. To use HSL sources, change to the
ThirdParty/HSL directory created by
coinbrew fetch and follow the download instructions (i.e., skip the build step) from HSL (Harwell Subroutines Library). Then proceed with the
coinbrew build step.
More details on using coinbrew can be found at the instructions on Getting Started with the COIN-OR Optimization Suite.
ipoptr interface can be build after
Ipopt has been build and installed. In the best case, it is sufficient to execute the following command in R:
After installation of the
ipoptr package, it should be possible to load the package in R and to view the help page:
Setting up gcc / OpenMP on OSX (Homebrew edition)
Note: This is 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) and 10.12 (Sierra), 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.
Gcc Compiler Mac
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: In this post, we showed how to set up gcc using the popular MacPorts package manager. Because MacPorts builds gcc (and all its dependencies!) from source, it takes a very, very long time. On my 2012 Macbook Air, this step took 16 hours. This tutorial uses Homebrew to dramatically speed up the process!
Note 3: This is an update over the previous version. It incorporates new information that Xcode command line tools can be installed without the full 4.41 GB download / installation of Xcode. Many thanks to Walter de Back and Tim at the Homebrew project for their help!
What you’ll need:
- XCode Command Line Tools: These command line tools are needed for Homebrew and related package managers. Installation instructions are now very simple and included below. As of January 18, 2016, this will install Version 2343.
- Homebrew: This is a package manager for OSX, which will let you easily download and install many linux utilities without building them from source. You’ll particularly need it for getting gcc. Installation is a simple command-line script, as detailed below. As of August 2, 2017, this will download Version 1.3.0.
- gcc (from Homebrew): 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 7.1.0.
1) Install the XCode Command Line Tools
Open a terminal window (Open Launchpad, then “Other”, then “Terminal”), and run:
A window should pop up asking you to either get Xcode or install. Choose the “install” option to avoid the huge 4+ GB Xcode download. It should only take a few minutes to complete.
2) Install Homebrew
Open a terminal window (Open Launchpad, then “Other”, then “Terminal”), and run:
Let the script run, and answer “y” whenever asked. This will not take very long.
3) Get, install, and prepare gcc
Open a terminal window (see above), and search for gcc, version 7.x or above
You should see a list of packages, including gcc7. (In 2015, this looked like “gcc5”. In 2017, this looks like “[email protected]”.)
Then, download and install gcc:
G++ Compiler On Mac
This will download whatever dependencies are needed, generally already pre-compiled. The whole process should only take five or ten minutes.
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:
Look for the version of g++ without an “mp” (from MacPorts) in its name. In my case, it’s g++-7. Double-check that you have the right one by checking its version. It should look something like this:
Notice that Homebrew shows up in the information. The correct compiler is g++-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:
One last thing: If you don’t update your paths, make will may fail as it continues to combine Apple’s “gcc” toolchain with real gcc. (This seems to happen most often if you installed an older gcc like gcc5 with MacPorts earlier.) You may see errors like this:
To avoid this, run:
Note that you’ll need to open a new Terminal window for this fix to apply.
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.
Grab a sample parallelized program:
Download a Makefile and C++ source file, and save them to the GCC_test directory. Here are the links:
- Makefile: [click here]
- C++ source: [click here]
G++ Compiler For Windows 10
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:
Compile and run the test:
Go back to your (still open) command prompt. Compile and run the program:
The output should look something like this:
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.
G++ Compiler Mac Os X Download Windows 10
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.)
Download a copy of PhysiCell and try out the included examples! Visit BioFVM at MathCancer.org.
- PhysiCell links:
- PhysiCell Method Paper at bioRxiv: https://doi.org/10.1101/088773
- PhysiCell on MathCancer: http://PhysiCell.MathCancer.org
- PhysiCell on SourceForge: http://PhysiCell.sf.net
- PhysiCell on github: http://github.com/MathCancer/PhysiCell
- PhysiCell tutorials: [click here]
- BioFVM links:
- BioFVM announcement on this blog: [click here]
- BioFVM on MathCancer.org: http://BioFVM.MathCancer.org
- BioFVM on SourceForge: http://BioFVM.sf.net
- BioFVM Method Paper in BioInformatics: http://dx.doi.org/10.1093/bioinformatics/btv730
- BioFVM tutorials: [click here]