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Build Notes:

These notes are intended to help build NamicExternalProjects (NEP). NEP is a fast developing project, and these notes are almost certainly out of date.

NEON

The following instructions work on 2016-06-01, Before building NEP, you will need to install several dependencies and ensure that you are using an up-to-date version of cmake and the gcc compiler.

Anaconda

1. Go to Anaconda's download page and find the Linux x86 64-bit distribution of the desired version (2.7 is recommended, but 3.4 should also work)
2. Right click on the download link and select "copy link location"
3. In terminal, type wget $downloadpath where $downloadpath is the pasted link location.
4. In terminal, type bash $filename
5. Follow the on-screen commands and allow the program to build. This will take a few minutes.

Configure Anaconda to use Python version 2.7

1. Create a python 2.7 environment using anaconda conda create --name py27 python=2.7

2. Activate the python 2.7 environment that you created. source activate py27

3. To check whether you have the correct version running, use the following command: python --version

Additional Python Libraries

1. Use pip to install docopt pip install docopt
2. Use pip to install future pip install future
3. Use pip to install prov pip install prov
4. Use pip to install nipype pip install nipype Alternatively: If nipype fails to find the correct shared libraries, you can instead install it with the following commands: git clone git://github.com/nipy/nipype.git cd nipype easy_install nipype

Intel Threading Building Blocks (TBB)

1. Go to https://www.threadingbuildingblocks.org/download and find the Linux distribution of the desired version (4.4 or greater)
2. Right click on the download link and select "copy link location"
3. In terminal, type wget $downloadpath where $downloadpath is the pasted link location.
4. Unzip the downloaded file using the tar -xzf $filename command

CMake

1. Go to https://cmake.org/download/ and find the Linux x86_64 distribution of the desired version (3.2 or later)
2. Right click on the download link for the '.sh' file and select "copy link location"
3. In terminal, type wget $downloadpath where $downloadpath is the pasted link location.
4. In terminal, type bash $filename
5. Open your .bashrc file and add the cmake installation to $PATH as follows:

PATH=$cmakebindirectory:$PATH

6. Update the version of your .bashrc file that is being used by your terminal session using the following command:

source ~/.bashrc

GCC

In order to build NEP, you will need to use a more recent version than the default gcc compiler on NEON. In order to use a newer version, edit your .bashrc file to include the following: module load gcc/4.8.2 export CC=$(which gcc) export CXX=$(which g++)

Then, update the version of your .bashrc file that is being used by your terminal session using the following command:

source ~/.bashrc

NamicExternalProjects

1. In terminal, type 'git clone https://github.com/BRAINSia/NAMICExternalProjects.git' to download the necessary files
2. Create a build folder and cd into it with the following commands: mkdir -p NEP-11 cd NEP-11
3. Run the following command:

CC=$(which gcc) CXX=$(which g++) cmake -DCMAKE_CXX_STANDARD:STRING=11 -DTBB_ROOT:PATH=${TBB_UNCOMPRESS_DIRCTORY}/tbb44_20151115oss/ ../NAMICExternalProjects/

OPTIONAL: You may be able to use one of the processing nodes, rather than the head node in order to compile the project in parallel using the following commands:

qlogin -pe smp 16 -q UI make -j 16

However, depending on permissions and load, this may not be possible.

4. Run make *This may take several hours