@@ -37,32 +37,24 @@ a) Clone the code from the GitHub repository using
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git clone https://github.com/sknepneklab/SAMoS.git
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- b) cd SAMoS (or the name of the directory you chose to download the code into)
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- c) mkdir build
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- d) cd build
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- e) ccmake ../
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- f) Use the CMake's GUI to chose appropriate settings
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- g) Press 'c' key several times to configure
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- h) If all libraries have been found, CMake will allow you to create a Makefile. If not, please exit CMake GUI and install missing libraries.
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- i) Press 'g' to create Make files. This will terminate CMake's GUI is return you to the shell
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- j) Type 'make -j 8' (-j option tells make how many parallel threads to use to compile; on a 4-core machine one can typically use 8 threads).
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+ b) cd SAMoS (or the name of the directory you chose to download the code into) <br />
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+ c) mkdir build <br />
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+ d) cd build <br />
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+ e) ccmake ../ <br />
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+ f) Use the CMake's GUI to chose appropriate settings <br />
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+ g) Press 'c' key several times to configure <br />
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+ h) If all libraries have been found, CMake will allow you to create a Makefile. If not, please exit CMake GUI and install missing libraries. <br />
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+ i) Press 'g' to create Make files. This will terminate CMake's GUI is return you to the shell. <br />
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+ j) Type 'make -j 8' (-j option tells make how many parallel threads to use to compile; on a 4-core machine one can typically use 8 threads). <br />
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+ k) If the compilation is successful, an executable 'samos' should appear in the build directory.
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** NOTE:** Some Linux distributions with newer C++ compilers may have problems with running 8 parallel threads and can cause the machine to crash.
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If this happens, use '-j 2', which is likely not to cause any problems on most modern computers.
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- k) If the compilation is successful, an executable 'samos' should appear in the build directory.
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-
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** NOTE:** SAMoS uses many templated libraries in Boost. Compiling it may take several minutes even on a very fast machine.
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** NOTE:** Depending on the compiler, you may get a number of warning messages. Those are harmless and you may safely ignore them.
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** NOTE:** SAMoS will fail to compile using the C++11 standard!
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** WARNING:** Some Mac users have reported problems with compiling SAMoS on Sierra and High Sierra using packages installed with 'brew'. Switching to
@@ -133,16 +125,14 @@ samos
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## 8. CREDITS
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- Lead developer:
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+ ### Lead developer:
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Rastko Sknepnek (University of Dundee, UK)
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- Major contributors to the code:
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- Silke Henkes (University of Aberdeen, UK) - many tools for building inital configurations and analysis tools
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- Daniel Barton (University of Dundee, UK) - tools for building and analysing tissue mechanics simulations
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+ ### Major contributors to the code:
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+ Silke Henkes (University of Aberdeen, UK) - many tools for building inital configurations and analysis tools <br />
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+ Daniel Barton (University of Dundee, UK) - tools for building and analysing tissue mechanics simulations <br />
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Amit Das (National Institute for Biological Sciences, India) - tools for building and analysing actomyosin simulations
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