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exascale-brainsim/adding-new-code-to-nest.md

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Adding New Code to NEST

This document assumes that the reader already knows how to build NEST from source.

  • If you want to add a new library inside NEST, createa a new directory inside nest/nest-2.6.0. In my case, I created the directory nest/nest-2.6.0/nestgpu and wanted my new code to be inside the new library libnestgpu. Inside this directory, you add your new source/header files.
  • However, your code is still not part of the NEST build system. To have your code be built with NEST, you need to do few more things.
  • First, create a file named Makefile.am inside this new directory. Every source directory of NEST contains a Makefile.am file of its own. This file contains instructions for the automake tool so that it knows what to build, from which files, using which libraries, etc. For example, I had two source files: GpuDataAdapter.h`` and GpuDataAdapter.cpp`` which I wanted to be built into my new library libnestgpu. For this purpose, my ```nest/nest-2.6.0/nestgpu/Makefile.am``` file contained the following lines:
# Automake file for the GPU-port of the NEST simulation kernel library
#
# Saad Quader, January 2015
#

defs= @SLI_THREAD_DEFS@ $defs
MAKEFLAGS= @MAKE_FLAGS@

noinst_LTLIBRARIES=libnestgpu.la

libnestgpu_la_SOURCES=\
	gpu_data_adapter.h gpu_data_adapter.cpp

# do not change anything below this line ------------------------------

libnestgpu_la_CXXFLAGS= @AM_CXXFLAGS@

libnestgpu_la_LIBADD= @LIBLTDL@ @LIBADD_DL@

AM_CPPFLAGS=	-I$(top_srcdir)/libnestutil\
		-I$(top_srcdir)/librandom\
		-I$(top_srcdir)/sli\
		-I$(top_srcdir)/nestkernel\
		@INCLTDL@ @GSL_CFLAGS@ @MUSIC_INCLUDE@ @MPI_INCLUDE@

  • Suppose you want to use your code from any part of the original NEST code. In my case, I wanted to call GpuDataAdapter::init() from within the function neststartup() in the file nest/nest-2.6.0/nest/neststartup.cpp. For this, inside the cpp file, I added #include "gpudataadapter.h" and inside the definition of the function neststartup(), I added nest::gpu::GpuDataAdapter::init();.

  • Editing the existing source code was easy. However, how does the compiler/linker know where to find the declaration/definition of the code for the GpuDataAdapter::init() function? This is the hard part. For this, I had to modify the nest/nest-2.6.0/nest/Makefile.am file as follows:

    • I added nestgpu/libnestgpu.la to the existing definition of the variables nest_LDADD and nest_DEPENDENCIES so that the linker knows where to find the definition of my new functions.
    • I also added -I$(top_srcdir)/nestgpu to the existing value of the variable AM_CPPFLAGS so that the compiler knows where to look for the #include headers for my new code.
    • However, it turned out that the module nest/nest-2.6.0/pynest also uses the file nest/nest-2.6.0/nest/neststartup.cpp and its header. Therefore, I had to specify the nest/nest-2.6.0/nestgpu directory as an include directory in the file nest/nest-2.6.0/pynest/Makefile.am as well. However, I did not need to specify the library libnestgpu because the library pynestkernel.la was already linked to the library libnest.la which was also already linked to my library libnestgpu.la.

  • Next, you should tell the NEST build system to actually visit this subdirectory and build your code. For this, you have to edit the nest/nest-2.6.0/configure.ac.in. In particular, you need to edit two things:

    • You have to specify that you have a new source directory. You do this by editing the existing value of the variable SLI_CORE_LIBS and adding the word nestgpu in its existing list of directories.
    • You have to specify that you have a new Makefile to be created by the configure script. You do this by adding the following line: AC_CONFIG_FILES(nestgpu/Makefile) after the list of existing Makefiles. (Just search for the text AC_CONFIG_FILES) inside the file configure.ac.in.)

  • Now that we have specified that we have new code, we need to rebuild the system, by generating a new configure script using our recently modified configure.ac.in file. To do this, just run the script nest/nest-2.6.0/bootstrap.sh which would generate a new configure script.

  • Then, reconfigure NEST by typing cd /home/saad/nest/build && ../nest-2.6.0/configure ../nest-2.6.0/configure --prefix=/home/saad/venv/nest-dbg --with-mpi --with-openmp --with-debug --with-optimize=-O0.

  • Then, build NEST by running make and make install.

  • Now, when NEST runs, it does so with the modified code.