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How to compile Cytosim

The core of Cytosim is written in C++11 and it is necessary to recompile the programs after each modification of the source code. Some of the accessory tools use Python.

Compilation requires a C++ compiler: e.g. gcc, Clang or the Intel compiler, together with a few libraries. Compilation is started from a terminal, with a program called make.

Dimensionality

The dimensionality is backed into the executable during compilation. To change it, follow these instructions.

Mathematical libraries

Running cytosim with sim or play requires these mathematical libraries:

These libraries offer standard interface to linear algebra functions used in Cytosim. There is a public reference implementations. Compiling the reference code is possible with a FORTRAN compiler. Precompiled libraries are available for most platforms, within:

Apple's veclib is preinstalled on Mac OSX, and Intel's MKL is available free of charge. MKL has better performance on Intel processors.

Graphical libraries

Cytosim's play relies on OpenGL for display and uses POSIX threads for multithreading.

Interactivity is provided by GLUT, which can be replaced by freeGLUT.

GLUT and OpenGL are included in Mac OSX:

-framework GLUT -framework OpenGL

Cytosim program play will be able to export images only if it is linked with the PNG graphical libraries, but everything else works fine. See the compile options.

Getting Ready

Mac-OSX

On Mac OSX, install Xcode, which is available on the Mac App Store. After installing Xcode, install the Xcode 'Command-Line Tools', which is an optional package providing 'make'. All necessary libraries are already included in MacOSX.

We provide the Xcode project file for cytosim, which is a convenient way to access the code.

Optionally, Cytosim can use the mouse wheel to zoom in and out, if you use FreeGLUT, instead of Apple's GLUT, or Renaud Blanch's GLUT patch.

Linux

Check the dedicated pages.

On Linux, you need to install the GNU compiler collection, BLAS and LAPACK. This is sufficient to compile sim. Recent Linux distributions provide precompiled BLAS/LAPACK as optional installation (check your distribution).

To make play install the OpenGL developer libraries and FreeGLUT or OpenGLUT.

Windows

Native compilation on Windows is a Herculean task. We thus recommend installing Cygwin, which emulates a Linux-like environment. A fresh installation of Cygwin is recommended to ensure that all required reference libraries are installed.
You will need a compiler, the X window system, BLAS/LAPACK and GLUT.
Please, refer to the dedicated page.

Compilation

After installing a compiler and gnu's make you are ready to compile from a terminal, with the following commands in the root directory of cytosim:

make sim
make play

The command make without arguments will build sim and play.
If this does not work, you may need to manually edit makefile.in to adjust to your platform.

It is also possible to use cmake, which should require no adjustment:

mkdir build
cd build
cmake ..
make sim play report

You can then check the resulting executables, normally located in subdirectory bin:

bin/sim info
bin/sim
bin/play live

Optimizations

To speed up the calculation, follow these steps:

On line 10 or so of makefile.inc, set MODE to F:

MODE := F

Turn off assertions by defining NDEBUG in src/base/assert.h:

#define NDEBUG

Recompile Cytosim from scratch:

make clean
make

Troubleshooting sim

Compilation is specified in makefile and makefile.inc, and these files may need to be adjusted manually. Check makefile.inc first and verify the compile options.

Make attempts to automatically detect the platform:

#---------------- MACHINE = {mac, linux, cygwin, auto}
MACHINE := auto

But you may manually set MACHINE to mac, linux or cygwin depending on your platform, and check the parameters set lower in the makefile.inc, for this platform, for example:

ifeq ($(MACHINE),linux)
	...
endif

To pinpoint the problem, try to build objects that have fewer depencies first:

Check your compiler for C++11 support and compilation switches

make test_cxx

Check your BLAS/LAPACK directly:

make test_blas

If you get an error at this stage, check that the compiler is linking the correct libraries. To find the libraries on your system, this command may help:

find /usr/lib -name libblas.*

For example, if the result is:

/usr/lib/libblas.so

You should adjust makefile.inc to specify the corresponding path:

LIBDIR := /usr/lib

Ensure that no other line changes the value of LIBDIR. For example, this one is commented out with the #:

#LIBDIR := /usr/lib/x86_64-linux-gnu

Check if it can read a configuration file:

make test_glos

At this stage, you can attempt to compile sim:

make sim

Troubleshooting play

If you are having trouble compiling play, check its requirements independently:

Check for thread support:

make test_thread

Check for OpenGL support:

make test_opengl

Check for GLUT support:

make test_glut

Check for GLAP (our own extension of GLUT)):

make test_glapp

At this stage, you can compile play:

make play

Finally: contact us!

Please, write to feedbackATcytosimDOTorg.

Please, describe what fails and what you have tried. Attach your 'makefile.inc' and tell us the platform on which you compiled.