Pre-requisites:
sudo apt-get install swig doxygen openjdk-7-jdk
Also, patience...the build can be temperamental. However, go through the steps enough times and it will work. Why, I don't know.
Also:
1. download (see error 4 below) py-dom-xpath-0.1 from here:
https://code.google.com/p/py-dom-xpath/downloads/list
sudo apt-get install python-setuptools
wget https://py-dom-xpath.googlecode.com/files/py-dom-xpath-0.1.tar.gz
2. Unzip it
3. Change to the directory py-dom-xpath-0.1/ and run
sudo python setup.py install
And
add this to your ~/.bashrc or /etc/profile
Start here:
As usual we'll do our work in ~/tmp
so
mkdir ~/tmp
if that directory doesn't exist
To download the OpenMM4.0-Source.zip file you need to register at simtk.org
Put the file in ~/tmp
Run:
cd ~/tmp
unzip OpenMM4.0-Source.zip
cd OpenMM4.0-Source/
cmake CMakeList.txt
make OpenMM
sudo make install
If all goes well (it took me three hours to iron out the details...) you'll see
Errors and solutions:
I hate cmake, possibly because I don't really understand it.
Anyway, every time you hit one of the errors below you need to do the following after fixing it:
make clean
cmake CMakeList.txt
make OpenMM
or you'll get error # 6
1. Doxygen missing:
Symptom:
sudo apt-get install swig doxygen openjdk-7-jdk
Also, patience...the build can be temperamental. However, go through the steps enough times and it will work. Why, I don't know.
Also:
1. download (see error 4 below) py-dom-xpath-0.1 from here:
https://code.google.com/p/py-dom-xpath/downloads/list
sudo apt-get install python-setuptools
wget https://py-dom-xpath.googlecode.com/files/py-dom-xpath-0.1.tar.gz
2. Unzip it
3. Change to the directory py-dom-xpath-0.1/ and run
sudo python setup.py install
And
add this to your ~/.bashrc or /etc/profile
export LD_LIBRARY_PATH=/lib/openmm:/usr/lib/nvidia-cuda-toolkit:/usr/lib/nvidia:$LD_LIBRARY_PATHFinally (and this is truly ridiculous):
export OPENMM_PLUGIN_DIR=/usr/local/openmm/lib/plugins
export OPENMM_ROOT_DIR=/usr/local/openmm
mkdir ~/tmp/OpenMM4.0-Source/docs/UsersGuide
cp OpenMM4.0-Source/docs/OpenMMUsersGuide.pdf OpenMM4.0-Source/docs/UsersGuide/
Start here:
As usual we'll do our work in ~/tmp
so
mkdir ~/tmp
if that directory doesn't exist
To download the OpenMM4.0-Source.zip file you need to register at simtk.org
Put the file in ~/tmp
Run:
cd ~/tmp
unzip OpenMM4.0-Source.zip
cd OpenMM4.0-Source/
cmake CMakeList.txt
make OpenMM
sudo make install
If all goes well (it took me three hours to iron out the details...) you'll see
[..]
-- Installing: /usr/local/openmm/include/openmm/internal/AmoebaUreyBradleyForceImpl.h
-- Installing: /usr/local/openmm/include/openmm/internal/AmoebaTorsionTorsionForceImpl.h
-- Installing: /usr/local/openmm/include/openmm/internal/AmoebaStretchBendForceImpl.h
-- Installing: /usr/local/openmm/lib/libOpenMMAmoeba.so
-- Removed runtime path from "/usr/local/openmm/lib/libOpenMMAmoeba.so"
-- Installing: /usr/local/openmm/lib/plugins/libOpenMMAmoebaCuda.so
-- Removed runtime path from "/usr/local/openmm/lib/plugins/libOpenMMAmoebaCuda.so"
-- Installing: /usr/local/openmm/lib/plugins/libOpenMMAmoebaSerialization.so
-- Removed runtime path from "/usr/local/openmm/lib/plugins/libOpenMMAmoebaSerialization.so"
-- Installing: /usr/local/openmm/include/openmm/RPMDIntegrator.h
-- Installing: /usr/local/openmm/include/openmm/RpmdKernels.h
-- Installing: /usr/local/openmm/lib/libOpenMMRPMD.so
-- Removed runtime path from "/usr/local/openmm/lib/libOpenMMRPMD.so"
-- Installing: /usr/local/openmm/lib/plugins/libOpenMMRPMDOpenCL.so
-- Removed runtime path from "/usr/local/openmm/lib/plugins/libOpenMMRPMDOpenCL.so"
-- Installing: /usr/local/openmm/include/openmm/serialization/SerializationNode.h
-- Installing: /usr/local/openmm/include/openmm/serialization/SerializationProxy.h
-- Installing: /usr/local/openmm/include/openmm/serialization/XmlSerializer.h
-- Installing: /usr/local/openmm/lib/libOpenMMSerialization.so
-- Removed runtime path from "/usr/local/openmm/lib/libOpenMMSerialization.so"
And you're are done! SUCCESS!
Errors and solutions:
I hate cmake, possibly because I don't really understand it.
Anyway, every time you hit one of the errors below you need to do the following after fixing it:
make clean
cmake CMakeList.txt
make OpenMM
or you'll get error # 6
1. Doxygen missing:
Symptom:
Swig version must be 1.3.39 or greater! (You have 0.0.0)
CMake Error at /usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:91 (MESSAGE):
Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
Call Stack (most recent call first):
/usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:252 (_FPHSA_FAILURE_MESSAGE)
/usr/share/cmake-2.8/Modules/FindDoxygen.cmake:80 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
wrappers/python/CMakeLists.txt:82 (find_package)
Solution:
sudo apt-get install doxygen
2. Swig missing:
Symptom:
Swig version must be 1.3.39 or greater! (You have 0.0.0)
-- Java version 1.6.0.24 configured successfully!
CMake Error at /usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:91 (MESSAGE):
Could NOT find Java (missing: Java_JAR_EXECUTABLE Java_JAVAC_EXECUTABLE)
(found version "1.6.0.24")
Call Stack (most recent call first):
/usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:252 (_FPHSA_FAILURE_MESSAGE)
/usr/share/cmake-2.8/Modules/FindJava.cmake:174 (find_package_handle_standard_args)
wrappers/python/CMakeLists.txt:85 (find_package)
Solution:
sudo apt-get install swig
3. Java found and missing at the same time
Symptom:
-- Java version 1.6.0.24 configured successfully!
CMake Error at /usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:91 (MESSAGE):
Could NOT find Java (missing: Java_JAR_EXECUTABLE Java_JAVAC_EXECUTABLE)
(found version "1.6.0.24")
Call Stack (most recent call first):
/usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:252 (_FPHSA_FAILURE_MESSAGE)
/usr/share/cmake-2.8/Modules/FindJava.cmake:174 (find_package_handle_standard_args)
wrappers/python/CMakeLists.txt:85 (find_package)
Solution:
sudo apt-get install openjdk-7-jdk
4. No module named xpath
Symptom:
Execution time: 1072 milliseconds
Memory used: 21270968
NamePool contents: 89 entries in 86 chains. 6 prefixes, 6 URIs
[ 87%] Creating OpenMM Python swig input files...
Traceback (most recent call last):
File "/home/me/tmp/OpenMM4.0-Source/python/src/swig_doxygen/swigInputBuilder.py", line 15, in <module>
import xpath
ImportError: No module named xpath
make[2]: *** [python/src/swig_doxygen/swig_lib/python/pythonprepend.i] Error 1
make[1]: *** [wrappers/python/CMakeFiles/BuildModule.dir/all] Error 2
make: *** [all] Error 2
Solution:
Download py-dom-xpath-0.1.tar.gz:
wget https://py-dom-xpath.googlecode.com/files/py-dom-xpath-0.1.tar.gz
Untar (tar -xvf) in ~/tmp
Untar (tar -xvf) in ~/tmp
cd py-dom-xpath-0.1/
sudo python setup.py install
What didn't work:
sudo apt-get install libxml-xpath-perl
sudo apt-get install libghc-hxt-xpath-dev
5. Missing OpenMMUsersGuide.pdf
Symptom:
-- Installing: /usr/local/openmm/docs/API Reference.html
CMake Error at cmake_install.cmake:119 (FILE):
file INSTALL cannot find
"/home/me/tmp/OpenMM4.0-Source/docs/UsersGuide/OpenMMUsersGuide.pdf".
make: *** [install] Error 1
Solution:
WTF??? The build can fail over something so trivial???
Anyway,
mkdir ~/tmp/OpenMM4.0-Source/docs/UsersGuide
cp ~/tmp/OpenMM4.0-Source/docs/OpenMMUsersGuide.pdf ~/tmp/OpenMM4.0-Source/docs/UsersGuide/
6. Linking CXX shared library libOpenMM.so failure
Symptom:
[ 6%] Building CXX object CMakeFiles/OpenMM.dir/src/cuda/kCalculateLocalForces.cu_OpenMMCuda_generated.cpp.o
Linking CXX shared library libOpenMM.so
CMakeFiles/OpenMM.dir/src/cuda/kCalculateCDLJForces.cu_OpenMMCuda_generated.cpp.o: In function `__device_stub__Z29kFindBlockBoundsCutoff_kernelv()':
kCalculateCDLJForces.cu_OpenMMCuda_generated.cpp:(.text+0x200): multiple definition of `__device_stub__Z29kFindBlockBoundsCutoff_kernelv()'
CMakeFiles/OpenMM.dir/src/cuda/kCalculateNonbondedSoftcore.cu_OpenMMFreeEnergyCuda_generated.cpp.o:kCalculateNonbondedSoftcore.cu_OpenMMFreeEnergyCuda_generated.cpp:(.text+0x1b0): first defined here
[..]
CMakeFiles/OpenMM.dir/src/cuda/kCalculateAmoebaCudaUtilities.cu_OpenMMAmoebaCuda_generated.cpp.o: In function `kFindInteractionsWithinBlocksPeriodic_kernel(unsigned int*)':
kCalculateAmoebaCudaUtilities.cu_OpenMMAmoebaCuda_generated.cpp:(.text+0x1d0): multiple definition of `kFindInteractionsWithinBlocksPeriodic_kernel(unsigned int*)'
CMakeFiles/OpenMM.dir/src/cuda/kCalculateNonbondedSoftcore.cu_OpenMMFreeEnergyCuda_generated.cpp.o:kCalculateNonbondedSoftcore.cu_OpenMMFreeEnergyCuda_generated.cpp:(.text+0x3a0): first defined here
collect2: ld returned 1 exit status
make[2]: *** [libOpenMM.so] Error 1
make[1]: *** [CMakeFiles/OpenMM.dir/all] Error 2
make: *** [all] Error 2
Solution:
You had one of errors 1-5, you solved it and tried to run make again. You need to do
make clean
cmake CMakeList.txt
first before proceeding with make or you end up with this error.
This is dummy text. It is not meant to be read. Accordingly, it is difficult to figure out when to end it. But then, this is dummy text. It is not meant to be read. Period.
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