Initial commit

Makefile

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+
+PY_VER = 2.7.3
+SRC = $(shell readlink -f python)
+MIC_PY_HOME = $(SRC)/_install
+MIC_PY_PATH = $(MIC_PY_HOME)/lib/python2.7
+CTYPES = $(SRC)/Modules/_ctypes
+NP_UTILS = numpy/numpyxc.py numpy/setup.cfg numpy/site.cfg
+
+all: numpyxc
+
+install:
+	@echo "To install, copy $(MIC_PY_HOME) where it can be accessed from the MIC card."
+	$(error)
+
+python.tgz:
+	wget http://www.python.org/ftp/python/$(PY_VER)/Python-$(PY_VER).tgz -O $@
+
+$(SRC): python.tgz
+	mkdir -p $@
+	tar -xf $< -C $@ --strip-components=1
+
+$(SRC)/hostpython: | $(SRC)
+	# TODO: fail if patched
+	cd $< && ./configure && make
+	cd $< && mv python hostpython && mv Parser/pgen Parser/hostpgen && make distclean
+
+xcompile.patch:
+	wget http://randomsplat.com/wp-content/uploads/2012/10/Python-$(PY_VER)-xcompile.patch -O $@
+
+$(SRC)/patched: xcompile.patch $(SRC)/hostpython
+	cd $(SRC) && patch -p1 < ../$<
+	touch $@
+
+$(SRC)/Makefile: $(SRC)/patched $(CTYPES)/.git
+	# Must have unicode UCS4 to be compatible with Numpy on modern Linux systems
+	cd $(SRC) && ./configure CC="icc -mmic" CXX="icpc -mmic" --host=x86_64 --without-gcc --enable-unicode=ucs4
+
+$(CTYPES)/.git: | $(SRC)
+	mv $(CTYPES) $(CTYPES).orig
+	git clone https://github.com/bpartridge/xeon_phi_ctypes.git $(CTYPES)
+
+$(MIC_PY_HOME): $(SRC)/Makefile $(SRC)/patched $(CTYPES)/.git
+	sed -e "s/-OPT:Olimit=0//g" -i.backup $(SRC)/Makefile
+	cd $(SRC) && make HOSTPYTHON=./hostpython HOSTPGEN=./Parser/hostpgen \
+		CROSS_COMPILE=k1om- CROSS_COMPILE_TARGET=yes HOSTARCH=x86_64 BUILDARCH=x86_64-linux-gnu \
+		EXTRA_CFLAGS="-fp-model precise -shared -fPIC" LDFLAGS=""
+	mkdir -p $(MIC_PY_HOME)
+	cd $(SRC) && make install HOSTPYTHON=./hostpython CROSS_COMPILE_TARGET=yes prefix=$(MIC_PY_HOME)
+
+micclean: miccleanobjs
+	rm $(SRC)/Makefile
+
+miccleanobjs:
+	rm -rvf $(SRC)/**/*.o
+	rm -rf $(SRC)/build
+	rm -rf $(MIC_PY_HOME)
+
+numpy.tgz:
+	wget http://downloads.sourceforge.net/project/numpy/NumPy/1.8.0/numpy-1.8.0.tar.gz -O $@
+
+numpy: numpy.tgz
+	mkdir $@
+	tar -xf $< -C $@ --strip-components=1
+
+numpyclean: numpy
+	rm -rf numpy/build
+	rm -rvf numpy/**/*.o
+
+numpyxc: numpy | $(MIC_PY_HOME) $(NP_UTILS)
+	# build_clib forces config.h to be created; it needs to be modified before extensions are built
+	cd numpy && PYTHONXCPREFIX=$(MIC_PY_HOME) python numpyxc.py build_clib
+	sed '/INTRIN/ d' -i numpy/build/*/numpy/core/include/numpy/config.h
+	cd numpy && PYTHONXCPREFIX=$(MIC_PY_HOME) python numpyxc.py build
+	cd numpy && PYTHONXCPREFIX=$(MIC_PY_HOME) python numpyxc.py install --prefix=$(MIC_PY_HOME)
+
+nose:
+	pip install --install-option="--prefix=$(MIC_PY_HOME)" nose
+
+scipy.tgz:
+	wget http://downloads.sourceforge.net/project/scipy/scipy/0.13.2/scipy-0.13.2.tar.gz -O $@
+
+scipy: scipy.tgz
+	mkdir $@
+	tar -xf $< -C $@ --strip-components=1
+
+scipyclean: scipy
+	rm -rf scipy/build
+	rm -rvf scipy/**/*.o
+
+scipyxc: scipy | $(MIC_PY_HOME) $(NP_UTILS)
+	cp $(NP_UTILS) scipy/
+	cd scipy && PYTHONXCPREFIX=$(MIC_PY_HOME) python numpyxc.py install --prefix=$(MIC_PY_HOME)
+
+.PHONY: all micclean miccleanobjs numpyxc nose

README.md

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+# PyPhi
+## Python for Scientific Computing on Intel's Xeon Phi MIC Platform
+
+*Compiled by Brenton Partridge, Harvard University*
+*All utilities released under Creative Commons CC-BY.*
+
+This repository contains tools for cross-compiling a Python interpreter
+and the Numpy and Scipy libraries for an Intel Xeon Phi coprocessor,
+allowing you to run Python code using those libraries as a native
+executable on the coprocessor.
+
+Based on [Emilio Castillo Villar's work](http://software.intel.com/en-us/forums/topic/392736) to cross-compile Python.
+
+Numpy was never designed to be cross-compiled for anything, much less
+a system without a compiler of its own, so much effort was placed into
+re-engineering it to use the "MIC" architecture and the relevant Intel MKL
+libraries. Internal testing code for Numpy and Scipy also works.
+
+After downloading the Makefile into a folder and running `make`,
+that folder will then contain `python/_install` which will be the
+`$PYTHONHOME` whose `bin/python` can be executed on the Phi.
+See `mic_task.sh` for a usage example.
+
+## REQUIREMENTS
+
+- 64-bit Intel system for compiling.
+
+- Recent Python installed on that system;
+  tested with the Anaconda distribution.
+
+- Intel Composer XE 2013 SP1 installed with MKL and MPI support in
+  `/opt/intel/composer_xe_2013_sp1/`.
+
+- A Xeon Phi coprocessor for testing (not needed for compilation itself.)
+
+## TODO
+
+- Currently, SSE instructions are disabled for Numpy, since they are
+  very different on the Phi. This would require a native porting effort
+  for such files as `einsum.c.src`.
+
+- MPI such as mpi4py.
+
+- Pip/setuptools for non-native python packages.
+
+- A generic modified version of Pip for native python packages.
+
+## References
+
+- http://software.intel.com/en-us/forums/topic/392736
+
+- http://randomsplat.com/id5-cross-compiling-python-for-embedded-linux.html
+
+- http://www.nersc.gov/users/computational-systems/testbeds/babbage/#toc-anchor-12
+
+- http://www.scipy.org/scipylib/building/linux.html#any-distribution-with-intel-c-compiler-and-mkl
+
+- http://thread.gmane.org/gmane.comp.python.scientific.user/32036/focus=32037
+
+- http://whatschrisdoing.com/blog/2009/10/16/cross-compiling-python-extensions/
+

mic_launch_task.sh

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+
+get_micfile
+echo $MIC_LD_LIBRARY_PATH > $HOME/MIC_LD_LIBRARY_PATH
+ssh `head -n1 micfile.$PBS_JOBID` < $HOME/mic_task.sh

mic_task.py

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+import sys
+print 'sys.maxunicode:', sys.maxunicode
+
+import numpy as np
+
+np.seterr(all='ignore')
+print "errors:", np.geterr()
+
+# print 'NumPy version:', np.__version__
+print np.random.test(verbose=3)
+# print np.linalg.test()
+
+print np.log(np.arange(5))
+
+import scipy.stats
+
+print scipy.stats.test(verbose=3)

mic_task.sh

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+#!/bin/sh
+#Designed to run on a MIC card
+
+ulimit -s unlimited
+export LD_LIBRARY_PATH=`cat $HOME/MIC_LD_LIBRARY_PATH`
+export PYTHONHOME=$HOME/mic/python/_install
+export PYTHONPATH=$PYTHONHOME/lib/python2.7:$PYTHONHOME/lib/python2.7/site-packages
+export PATH=$PYTHONHOME/bin:$PATH
+echo "Number of cores:" `grep -c ^processor /proc/cpuinfo`
+# which python
+# python -V
+# python -m test.test_math
+# python -m test.test_ctypes
+# echo $PYTHONPATH
+# python -c "import sys; print 'sys.maxunicode', sys.maxunicode"
+# python -c "import numpy; print 'NumPy version:', numpy.__version__;"
+python mic_task.py
+# export NPHOME=$PYTHONHOME/lib/python2.7/site-packages/numpy
+# python $NPHOME/core/tests/test_arrayprint.py