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Introduction
OpenSim is software that lets users develop models of musculoskeletal structures and create dynamic simulations of movement
Usage
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module load misc/opensim/3.2.0
module load misc/opensim/3.2.0py
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
An example:
module purge
module load misc/opensim/3.2.0py
python
Python 3.6.1 (default, Apr 7 2017, 12:19:18)
[GCC 4.9.3] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import opensim
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Installation
opensim without python binding
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module load cmake/3.5.0 module load library/lapackBlas/3.6.0 module load gcc/4.9.3 module load misc/simbody/3.5.4 module load python/3.6.1 module load library/swig/2.0.12 download download and copy the models first to: /sw/misc/opensim/3.2.0/src/opensim-core-3.2.0 cd /sw/misc/opensim/3.2.0/src/opensim-core-3.2.0/ mv /sw/misc/opensim/3.2.0/src/opensim-core-3.2.0 /sw/misc/opensim/3.2.0/Models >>>>>>>>>>>BEGIN: These steps are not needed<<<<<<<<<<<<<<<<<<<<<<<<<<<< ##cd /sw/misc/opensim/3.2.0/src/opensim-core-3.2.0/opensim-models-master cmake##cmake . -DCMAKE_C_COMPILER=/sw/gcc/4.9.3/bin/gcc -DCMAKE_CXX_COMPILER=/sw/gcc/4.9.3/bin/g++ -DCMAKE_INSTALL_PREFIX=/sw/misc/opensim/3.2.0/Models 2>&1 | tee cmakeLog2.txt Next##make 2>&1 | tee makeLog.txt ##make install 2>&1 | tee makeInstallLog.txt >>>>>>>>>>>>>>>>>>>>>>>>END>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Next if CFSQ file source is not available in /sw/misc/opensim/3.2.0/src/opensim-core-3.2.0/Vendors, edit the CMakeLists.txt and edit out reference to CFSQ. (Not sure about the implication of this but would love to get feedback) ##SUBDIRS(CFSQP lepton) SUBDIRS(lepton) cd /sw/misc/opensim/3.2.0/src/opensim-core-3.2.0 cmake . -DCMAKE_C_COMPILER=/sw/gcc/4.9.3/bin/gcc -DCMAKE_CXX_COMPILER=/sw/gcc/4.9.3/bin/g++ -DCMAKE_INSTALL_PREFIX=/sw/misc/opensim/3.2.0 -DSimbody_INCLUDE_DIR=/sw/misc/simbody/3.5.4/include 2>&1 | tee cmakeLog1.txt make 2>&1 | tee makeLog.txt make install 2>&1 | tee makeInstallLog.txt |
opensim with python binding
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module load cmake/3.5.0
module load library/lapackBlas/3.6.0
module load gcc/4.9.3
module load misc/simbody/3.5.4
module load python/3.6.1
module load library/swig/2.0.12
mkdir -p /sw/misc/opensim/3.2.0py/src
cd /sw/misc/opensim/3.2.0py/src
tar -zxvf /sw/misc/opensim/3.2.0/src/v3.2.0.tar.gz
cd /sw/misc/opensim/3.2.0py/src/opensim-core-3.2.0
vi Vendors/CMakeLists.txt
unzip /tmp/opensim-models-master.zip
mv opensim-models-master Models
cmake . -DCMAKE_C_COMPILER=/sw/gcc/4.9.3/bin/gcc -DCMAKE_CXX_COMPILER=/sw/gcc/4.9.3/bin/g++ -DCMAKE_INSTALL_PREFIX=/sw/misc/opensim/3.2.0py 2>&1 | tee cmakeLog.txt
Then the easiest way to do it is to use ccmake as below:
>>>>>>>>>>>>>>>
cd /sw/misc/opensim/3.2.0py/src/opensim-core-3.2.0
ccmake .
Press [t] to toggle advanced mode
Change BUILD_PYTHON_WRAPPING ON
Press [c] to configure
There may be errors that needs to be fixed.
>>>>Errors>>>>>>>
PYTHON_EXECUTABLE */usr/bin/python2.6
PYTHON_INCLUDE_DIR */usr/include/python2.6
PYTHON_LIBRARY */usr/lib64/libpython2.6.so
PYTHON_LIBRARY_DEBUG *PYTHON_LIBRARY_DEBUG-NOTFOUND
SWIG_DIR */usr/share/swig/1.3.40
SWIG_EXECUTABLE */usr/bin/swig
SWIG_VERSION *1.3.40
>>>>>Change it to look like this>>>>>
PYTHON_EXECUTABLE */sw/python/2.7.10/bin/python
PYTHON_INCLUDE_DIR */sw/python/2.7.10/include/python2.7
PYTHON_LIBRARY */sw/python/2.7.10/lib/libpython2.7.so
PYTHON_LIBRARY_DEBUG *PYTHON_LIBRARY_DEBUG-NOTFOUND
SWIG_DIR */sw/library/swig/2.0.12
SWIG_EXECUTABLE */sw/library/swig/2.0.12/bin/swig
SWIG_VERSION *2.0.12
>>>>>>
Press [g] to generate and exit
make 2>&1 | tee makeLog.txt
make install 2>&1 | tee makeInstallLog.txt
>>>>>>>>
module load python/3.6.1
cd /sw/misc/opensim/3.2.0py/sdk/python
python setup.py install |
Citation
PLEASE CITE THESE PAPERS
Delp SL, Anderson FC, Arnold AS, Loan P, Habib A, John CT, Guendelman E, Thelen DG. OpenSim: Open-source Software to Create and Analyze Dynamic Simulations of Movement. IEEE Transactions on Biomedical Engineering. (2007)