[CIG-SHORT] Summary & tips: Pylith installation from source using installer
Ravi Kanda
kanda.vs.ravi at gmail.com
Thu Jul 7 15:07:53 PDT 2016
Hi Brad, Matt, and Charles,
I finally managed to install pylith-2.1.3-0 from source using the
installer on both my laptop and workstation (both running Ubuntu 14).
Along the way I had to make some tweaks to setup.sh & Makefile due to
two additional dependencies (Cython & PGen). All the unit-tests passed,
and I was able to get meaningful results from the 2d_gravity-vardensity
example problem we did in Tutorial 4 of the workshop.
I am not sure whether the above tweaks are specific to my systems or
might benefit a wider audience - so, I am briefly documenting what I did
below, and attaching my versions of the configure script, setup.sh and
Makefile+DIFF. I do not know if these tweaks are worth propagating
upstream to autotools input files (Makefile.am &/or configure.ac?) - you
would be a better judge of that.
A) CONFIGURE OPTIONS (attachment #1): In the end, I had to enable all
major dependencies except autotools, git, & cmake (but it turns out the
last one was installed anyway during petsc build). BTW, I also tried to
install pylith with --enable-autotools on one of the systems, which
worked only when I used GNU m4-1.4.17 instead of m4-1.4.16 that the
installer uses (turns out v.16 has a bug that was fixed in v.17 as per
link [1] below) - version updated in the Makefile (below).
B) SETUP.SH (attachment #2): For some reason, $PYTHON_VERSION (=2.7) is
not passed on to PYTHONPATH variable in the setup.sh generated by the
above config script (I see <PREFIX>/lib/python/site-packages, and
<PREFIX>/lib64/python/site-packages). So, I had to update the python
folder with 'python2.7' before sourcing, so the build environment used
the locally installed python & py-packages. Variable also updated in the
Makefile (below).
C) MAKEFILE (attachments #3,4): H5PY built successfully only when I
added a new rule for cython (which in turn required setuptools and
pcgen). Without cython, I got a "... failed to import Cython ..."
error. Cython, in turn needed setuptools installed first (see link [2]
below), as well as PGen (see [3] below). So, I added new Makefile rules
for pgen and cython, and the latter to the h5py rule dependencies. I
tried to keep all changes to a single section of the Makefile for
clarity. However, also see the attached DIFF of my Makefile version
w.r.t. the original installer version.
If you would like further details, or specific config files, feel free
to let me know. Again, thanks much for your help & tips during
CIG-2016, which eventually helped me figure out the build process.
Regards,
Ravi.
===============
Relevant links &/fixes:
===============
[1] m4 bug ("... 'gets' undeclared ..." similar to what I got), and the
fix to a similar problem (upgrade to v-17):
http://www.linuxquestions.org/questions/slackware-14/m4-need-some-love-4175471638/
[2] H5py install distutils error ("... AttributeError: install_layout
..."), and the fix to a similar problem (install/upgrade setuptools):
https://github.com/gotcha/ipdb/issues/60
[3] H5py install pcgen error ("... Unable to find pgen, not compiling
formal grammar ..."), and was able to fix it by installing PGen python
package.
===============
--
---------------------------------------------------------------------
Ravi Kanda
Adjunct Assistant Professor
Department of Geology
Utah State University
4505 Old Main Hill
Logan UT 84322-4505
--------------------------
Web Page: https://ravi-vs-kanda.github.io
----------------------------------------------------------------------
For a human being, the unexamined life is not worth living - SOCRATES
----------------------------------------------------------------------
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html-am:
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mostlyclean-am: mostlyclean-generic mostlyclean-libtool
pdf: pdf-recursive
pdf-am:
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uninstall-am:
.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) \
cscopelist-recursive ctags-recursive install-am install-strip \
tags-recursive
.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
all all-am am--refresh check check-am clean clean-cscope \
clean-generic clean-libtool clean-local cscope cscopelist \
cscopelist-recursive ctags ctags-recursive dist dist-all \
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dist-zip distcheck distclean distclean-generic \
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distuninstallcheck dvi dvi-am html html-am info info-am \
install install-am install-data install-data-am install-dvi \
install-dvi-am install-exec install-exec-am install-html \
install-html-am install-info install-info-am install-man \
install-pdf install-pdf-am install-ps install-ps-am \
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installdirs-am maintainer-clean maintainer-clean-generic \
mostlyclean mostlyclean-generic mostlyclean-libtool pdf pdf-am \
ps ps-am tags tags-recursive uninstall uninstall-am
# ----------------------------------------------------------------------
# Targets
# ----------------------------------------------------------------------
all: installed_pylith
deps: installed_cppunit installed_swig installed_netcdf installed_hdf5 installed_h5py installed_fiat installed_nemesis installed_pythia installed_netcdfpy installed_git installed_cmake installed_proj4
rebuild-all: finished_mkdest compilers python mpi cppunit swig numpy proj4 netcdf hdf5 h5py fiat nemesis spatialdata petsc pylith
# ----------------------------------------------------------------------
# Note on configure invocations
#
# Normally, we would like to do configure ARGS && make && make
# install. However a bug in autoconf results in d.SYM directories
# generating an error when configure tries to remove them with "rm"
# rather than "rm -r". As a result, we use configure ARGS ; make &&
# make install.
# ----------------------------------------------------------------------
# setup
# ----------------------------------------------------------------------
mkdest:
$(MKDIR_P) $(prefix)/include $(prefix)/lib $(prefix)/bin
finished_mkdest:
$(MAKE) $(AM_MAKEFLAGS) mkdest && touch $@
# ----------------------------------------------------------------------
# autotools
# ----------------------------------------------------------------------
autotools: finished_mkdest
# $(FETCH_SCRIPT) "$(downloader)" m4-$(M4_VER).tar.gz $(DEPS_URL)
# $(FETCH_SCRIPT) "$(downloader)" autoconf-$(AUTOCONF_VER).tar.gz $(DEPS_URL)
# $(FETCH_SCRIPT) "$(downloader)" automake-$(AUTOMAKE_VER).tar.gz $(DEPS_URL)
# $(FETCH_SCRIPT) "$(downloader)" libtool-$(LIBTOOL_VER).tar.gz $(DEPS_URL)
# $(TAR) -zxf m4-$(M4_VER).tar.gz
# mkdir -p m4-$(M4_VER)-build
# cd m4-$(M4_VER)-build && \
# ../m4-$(M4_VER)/configure --prefix=$(prefix) $(env_flags) && \
# make -j $(MAKE_THREADS) && \
# make install
# $(TAR) -zxf autoconf-$(AUTOCONF_VER).tar.gz
# mkdir -p autoconf-$(AUTOCONF_VER)-build
# cd autoconf-$(AUTOCONF_VER)-build && \
# ../autoconf-$(AUTOCONF_VER)/configure --prefix=$(prefix) $(env_flags) && \
# make -j $(MAKE_THREADS) && \
# make install
# $(TAR) -zxf automake-$(AUTOMAKE_VER).tar.gz
# mkdir -p automake-$(AUTOMAKE_VER)-build
# cd automake-$(AUTOMAKE_VER)-build && \
# ../automake-$(AUTOMAKE_VER)/configure --prefix=$(prefix) $(env_flags) && \
# make -j $(MAKE_THREADS) && \
# make install
# $(TAR) -zxf libtool-$(LIBTOOL_VER).tar.gz
# mkdir -p libtool-$(LIBTOOL_VER)-build
# cd libtool-$(LIBTOOL_VER)-build && \
# ../libtool-$(LIBTOOL_VER)/configure --prefix=$(prefix) $(env_flags) && \
# make -j $(MAKE_THREADS) && \
# make install && \
# touch ../installed_autotools
@echo "$@ already installed. Skipping installation."
touch installed_autotools
installed_autotools:
$(MAKE) $(AM_MAKEFLAGS) autotools
# ----------------------------------------------------------------------
# compilers
# ----------------------------------------------------------------------
compilers: finished_mkdest
$(FETCH_SCRIPT) "$(downloader)" gcc-$(GCC_VER).tar.bz2 $(DEPS_URL)
$(FETCH_SCRIPT) "$(downloader)" mpc-$(MPC_VER).tar.gz $(DEPS_URL)
$(FETCH_SCRIPT) "$(downloader)" gmp-$(GMP_VER).tar.gz $(DEPS_URL)
$(FETCH_SCRIPT) "$(downloader)" mpfr-$(MPFR_VER).tar.bz2 $(DEPS_URL)
$(TAR) -jxf gcc-$(GCC_VER).tar.bz2
cd gcc-$(GCC_VER) ; \
tar -zxf ../gmp-$(GMP_VER).tar.gz; \
ln -sf gmp-$(GMP_VER)/ gmp; \
tar -zxf ../mpc-$(MPC_VER).tar.gz; \
ln -sf mpc-$(MPC_VER)/ mpc; \
tar -jxf ../mpfr-$(MPFR_VER).tar.bz2; \
ln -sf mpfr-$(MPFR_VER)/ mpfr
$(MKDIR_P) gcc-build
cd gcc-build && \
../gcc-$(GCC_VER)/configure --prefix=$(prefix) \
--disable-multilib \
--enable-languages=$(gcc_languages) \
$(env_flags) && \
make -j $(make_threads) $(env_flags) && \
make install && \
touch ../installed_compilers
# @echo "$@ already installed. Skipping installation."
# touch installed_compilers
installed_compilers:
$(MAKE) $(AM_MAKEFLAGS) compilers
# ----------------------------------------------------------------------
# python
# ----------------------------------------------------------------------
python: installed_compilers
$(FETCH_SCRIPT) "$(downloader)" Python-$(PYTHON_VER).tgz $(DEPS_URL)
$(TAR) -zxf Python-$(PYTHON_VER).tgz
$(MKDIR_P) python-build
cd python-build && \
../Python-$(PYTHON_VER)/configure --prefix=$(prefix) \
--enable-shared $(env_flags) $(env_compilers) && \
make -j $(make_threads) && \
make install && \
touch ../installed_python
# @echo "$@ already installed. Skipping installation."
# touch installed_python
installed_python:
$(MAKE) $(AM_MAKEFLAGS) python
# ----------------------------------------------------------------------
# mpi
# ----------------------------------------------------------------------
#mpi: openmpi
mpi: mpich
#mpi:
# @echo "$@ already installed. Skipping installation."
# touch installed_mpi
installed_mpi:
$(MAKE) $(AM_MAKEFLAGS) mpi
# ----------------------------------------------------------------------
# openmpi
# ----------------------------------------------------------------------
openmpi: installed_compilers
$(FETCH_SCRIPT) "$(downloader)" openmpi-$(OPENMPI_VER).tar.gz $(DEPS_URL)
$(TAR) -zxf openmpi-$(OPENMPI_VER).tar.gz
$(MKDIR_P) openmpi-build
cd openmpi-build && \
../openmpi-$(OPENMPI_VER)/configure \
--prefix=$(prefix) $(env_flags) $(env_compilers); \
make -j $(make_threads) && \
make install && \
touch ../installed_mpi
if [ ! -x $(prefix)/bin/mpirun ]; then cd $(prefix)/bin && $(LN_S) mpiexec mpirun; fi
mpich: installed_compilers
$(FETCH_SCRIPT) "$(downloader)" mpich-$(MPICH_VER).tar.gz $(DEPS_URL)
$(TAR) -zxf mpich-$(MPICH_VER).tar.gz
$(MKDIR_P) mpich-build
cd mpich-build && \
../mpich-$(MPICH_VER)/configure \
--with-pm=gforker \
--enable-shared \
--enable-sharedlibs=$(mpich_sharedarch) \
--disable-static --disable-mpe \
--prefix=$(prefix) \
$(env_flags) $(env_compilers) $(mpich_options) ; \
make -j $(make_threads) && \
make install && \
touch ../installed_mpi
if [ ! -x $(prefix)/bin/mpirun ]; then cd $(prefix)/bin && $(LN_S) mpiexec mpirun; fi
# ----------------------------------------------------------------------
# cppunit
# ----------------------------------------------------------------------
cppunit: installed_compilers
$(FETCH_SCRIPT) "$(downloader)" cppunit-$(CPPUNIT_VER).tar.gz $(DEPS_URL)
$(TAR) -zxf cppunit-$(CPPUNIT_VER).tar.gz
$(MKDIR_P) cppunit-build
cd cppunit-build && \
../cppunit-$(CPPUNIT_VER)/configure \
--prefix=$(prefix) $(env_flags) $(env_compilers); \
make -j $(make_threads) && \
make install && \
touch ../installed_cppunit
# @echo "$@ already installed. Skipping installation."
# touch installed_cppunit
installed_cppunit:
$(MAKE) $(AM_MAKEFLAGS) cppunit
# ----------------------------------------------------------------------
# pcre
# ----------------------------------------------------------------------
pcre: installed_compilers
$(FETCH_SCRIPT) "$(downloader)" pcre-$(PCRE_VER).tar.gz $(DEPS_URL)
$(TAR) -zxf pcre-$(PCRE_VER).tar.gz
$(MKDIR_P) pcre-build
cd pcre-build && \
../pcre-$(PCRE_VER)/configure \
--prefix=$(prefix) $(env_flags) $(env_compilers) ; \
make -j $(make_threads) && \
make install && \
touch ../installed_pcre
# @echo "$@ already installed. Skipping installation."
# touch installed_pcre
installed_pcre:
$(MAKE) $(AM_MAKEFLAGS) pcre
# ----------------------------------------------------------------------
# swig
# ----------------------------------------------------------------------
swig: installed_pcre installed_compilers installed_python
$(FETCH_SCRIPT) "$(downloader)" swig-$(SWIG_VER).tar.gz $(DEPS_URL)
$(TAR) -zxf swig-$(SWIG_VER).tar.gz
$(MKDIR_P) swig-build
cd swig-build && \
../swig-$(SWIG_VER)/configure \
--prefix=$(prefix) $(env_flags) $(env_compilers) ; \
make -j $(make_threads) && \
make install && \
touch ../installed_swig
## @echo "$@ already installed. Skipping installation."
# @echo "$@ not required. Skipping installation."
# touch installed_swig
installed_swig:
$(MAKE) $(AM_MAKEFLAGS) swig
# ----------------------------------------------------------------------
# numpy
# ----------------------------------------------------------------------
numpy: installed_python
$(FETCH_SCRIPT) "$(downloader)" numpy-$(NUMPY_VER).tar.gz $(DEPS_URL)
$(TAR) -zxf numpy-$(NUMPY_VER).tar.gz
# $(CP) $(top_srcdir)/numpy_blaslapack.cfg numpy-$(NUMPY_VER)/site.cfg
cd numpy-$(NUMPY_VER) && \
$(PYTHON) setup.py install --prefix=$(prefix) && \
touch ../installed_numpy
# @echo "$@ already installed. Skipping installation."
# touch installed_numpy
installed_numpy:
$(MAKE) $(AM_MAKEFLAGS) numpy
# ----------------------------------------------------------------------
# proj4
# ----------------------------------------------------------------------
proj4: installed_compilers
$(FETCH_SCRIPT) "$(downloader)" proj-$(PROJ4_VER).tar.gz $(DEPS_URL)
$(FETCH_SCRIPT) "$(downloader)" proj-datumgrid-1.3.zip $(DEPS_URL)
$(TAR) -zxf proj-$(PROJ4_VER).tar.gz
$(MKDIR_P) proj4-build/nad
cd proj4-build/nad && \
unzip ../../proj-datumgrid-1.3.zip
cd proj4-build && \
../proj-$(PROJ4_VER)/configure \
--prefix=$(prefix) $(env_flags) $(env_compilers) ; \
make -j $(make_threads) && \
make install && \
touch ../installed_proj4
# @echo "$@ already installed. Skipping installation."
# touch installed_proj4
installed_proj4:
$(MAKE) $(AM_MAKEFLAGS) proj4
# ----------------------------------------------------------------------
# hdf5
# ----------------------------------------------------------------------
hdf5: installed_mpi
$(FETCH_SCRIPT) "$(downloader)" hdf5-$(HDF5_VER).tar.gz $(DEPS_URL)
$(TAR) -zxf hdf5-$(HDF5_VER).tar.gz
$(MKDIR_P) hdf5-build
cd hdf5-build && \
../hdf5-$(HDF5_VER)/configure \
--enable-parallel --enable-shared --enable-unsupported \
--disable-static --prefix=$(prefix) $(hdf5_options) \
$(env_flags) $(env_mpicompilers) ; \
make -j $(make_threads) && \
make install && \
touch ../installed_hdf5
# @echo "$@ already installed. Skipping installation."
## @echo "hdf5 option not requested. To enable HDF5 option, "
## @echo "reconfigure with --enable-hdf5 (to install HDF5) or "
## @echo "--with-hdf5 (to use an existing installation)."
# touch installed_hdf5
installed_hdf5:
$(MAKE) $(AM_MAKEFLAGS) hdf5
# ----------------------------------------------------------------------
# pcgen
# ----------------------------------------------------------------------
pcgen: installed_python
$(eval UNZIP = /usr/bin/unzip)
$(eval PKG_URL_BASE = https://pypi.python.org/packages)
$(eval PCGEN_VERSION = 0.2.1)
$(eval PCGEN_URL := ${PKG_URL_BASE}/3c/68/3cd7faa8bc9b060eea452c5d6f27919dfb664cc4d1259998718a2360e05c)
#
$(FETCH_SCRIPT) "$(downloader)" PGen-${PCGEN_VERSION}.zip ${PCGEN_URL}
$(UNZIP) PGen-${PCGEN_VERSION}.zip
cd PGen-${PCGEN_VERSION} && \
CC=mpicc $(env_flags) python setup.py build && \
python setup.py install --prefix=$(prefix) && \
touch ../installed_pcgen
installed_pcgen:
$(MAKE) $(AM_MAKEFLAGS) pcgen
# ----------------------------------------------------------------------
# cython
# ----------------------------------------------------------------------
cython: installed_python installed_setuptools installed_pcgen
$(eval PKG_URL_BASE = https://pypi.python.org/packages)
$(eval CYTHON_VERSION := 0.24)
$(eval CYTHON_URL := ${PKG_URL_BASE}/b1/51/bd5ef7dff3ae02a2c6047aa18d3d06df2fb8a40b00e938e7ea2f75544cac)
#
$(FETCH_SCRIPT) "$(downloader)" Cython-${CYTHON_VERSION}.tar.gz ${CYTHON_URL}
$(TAR) -xzf Cython-${CYTHON_VERSION}.tar.gz
cd Cython-${CYTHON_VERSION} && \
CC=mpicc $(env_flags) python setup.py build && \
python setup.py install --prefix=$(prefix) && \
touch ../installed_cython
installed_cython:
$(MAKE) $(AM_MAKEFLAGS) cython
# ----------------------------------------------------------------------
# h5py
# ----------------------------------------------------------------------
h5py: installed_hdf5 installed_numpy installed_cython
$(FETCH_SCRIPT) "$(downloader)" h5py-$(H5PY_VER).tar.gz $(DEPS_URL)
$(TAR) -zxf h5py-$(H5PY_VER).tar.gz
cd h5py-$(H5PY_VER) && \
CC=mpicc $(env_flags) python setup.py build --hdf5=$(prefix) && \
python setup.py install --prefix=$(prefix) && \
touch ../installed_h5py
# @echo "$@ already installed. Skipping installation."
## @echo "h5py option not requested. To enable h5py option, "
## @echo "reconfigure with --enable-h5py (to install H5PY)."
# touch installed_h5py
installed_h5py:
$(MAKE) $(AM_MAKEFLAGS) h5py
# ----------------------------------------------------------------------
# netcdf
# ----------------------------------------------------------------------
netcdf: installed_compilers installed_hdf5
$(FETCH_SCRIPT) "$(downloader)" netcdf-$(NETCDF_VER).tar.gz $(DEPS_URL)
$(TAR) -zxf netcdf-$(NETCDF_VER).tar.gz
$(MKDIR_P) netcdf-build
cd netcdf-build && \
../netcdf-$(NETCDF_VER)/configure \
--prefix=$(prefix) $(env_flags) $(env_mpicompilers) \
--enable-shared --disable-static $(netcdf_4_options) --disable-dap ; \
sed -e "s/-l //g" libtool > libtool.tmp && mv -f libtool.tmp libtool; \
make -j $(make_threads) && \
make install && \
touch ../installed_netcdf
# @echo "$@ already installed. Skipping installation."
## @echo "netcdf option not requested. To enable NetCDF option, "
## @echo "reconfigure with --enable-netcdf (to install NetCDF) or "
## @echo "--with-netcdf (to use an existing installation)."
# touch installed_netcdf
installed_netcdf:
$(MAKE) $(AM_MAKEFLAGS) netcdf
# ----------------------------------------------------------------------
# netcdfpy
# ----------------------------------------------------------------------
netcdfpy: installed_netcdf installed_numpy
$(FETCH_SCRIPT) "$(downloader)" netCDF4-$(NETCDFPY_VER).tar.gz $(DEPS_URL)
$(TAR) -zxf netCDF4-$(NETCDFPY_VER).tar.gz
cd netCDF4-$(NETCDFPY_VER) && \
CC=mpicc $(env_flags) python setup.py build && \
python setup.py install --prefix=$(prefix) && \
touch ../installed_netcdfpy
# @echo "$@ already installed. Skipping installation."
## @echo "netCDF4 option not requested. To enable netCDF4 option, "
## @echo "reconfigure with --enable-netcdfpy (to install netCDF4)."
# touch installed_netcdfpy
installed_netcdfpy:
$(MAKE) $(AM_MAKEFLAGS) netcdfpy
# ----------------------------------------------------------------------
# fiat
# ----------------------------------------------------------------------
fiat: installed_numpy
$(FETCH_SCRIPT) "$(downloader)" ScientificPython-$(SCIENTIFICPYTHON_VER).tar.gz $(DEPS_URL)
$(TAR) -zxf ScientificPython-$(SCIENTIFICPYTHON_VER).tar.gz
cd ScientificPython-$(SCIENTIFICPYTHON_VER) && $(PYTHON) setup.py install --prefix=$(prefix)
$(FETCH_SCRIPT) "$(downloader)" fiat-$(FIAT_VER).tar.gz $(DEPS_URL)
$(TAR) -zxf fiat-$(FIAT_VER).tar.gz
cd fiat-$(FIAT_VER) && $(PYTHON) setup.py install --prefix=$(prefix) && touch ../installed_fiat
# @echo "$@ already installed. Skipping installation."
# touch installed_fiat
installed_fiat:
$(MAKE) $(AM_MAKEFLAGS) fiat
# ----------------------------------------------------------------------
# setuptools
# ----------------------------------------------------------------------
setuptools:
$(FETCH_SCRIPT) "$(downloader)" setuptools-$(SETUPTOOLS_VER).tar.gz $(DEPS_URL)
$(eval SETUPTOOLS_PFX = setuptools-$(SETUPTOOLS_VER))
#
# NEWER setuptools: USE ONLY IF ABOVE OLDER SETUPTOOLS DOES NOT WORK WITH H5PY BUILD
# COMMENT-OUT ABOVE TWO LINES, & UNCOMMENT NEXT FOUR LINES ...
# RECOMPILE WITH 'make h5py', OR CLEAN INSTALL FULL PYLITH SUITE.
# $(eval SETUPTOOLS_VERSION = 24.0.2)
# $(eval SETUPTOOLS_URL := ${PKG_URL_BASE}/21/d7/3e7e4b42d40469d2b770e10aee5b49538ecf2853eb5635d2d2536b286e2d)
# $(FETCH_SCRIPT) "$(downloader)" setuptools-${SETUPTOOLS_VERSION} ${SETUPTOOLS_URL}
# $(eval SETUPTOOLS_PFX = setuptools-$(SETUPTOOLS_VERSION))
#
$(TAR) -xzvf ${SETUPTOOLS_PFX}.tar.gz
cd ${SETUPTOOLS_PFX} && \
CC=mpicc $(env_flags) python setup.py build && \
python setup.py install --prefix=$(prefix) && \
touch ../installed_setuptools
# @echo "$@ already installed. Skipping installation."
# touch installed_setuptools
installed_setuptools:
$(MAKE) $(AM_MAKEFLAGS) setuptools
# ----------------------------------------------------------------------
# pythia
# ----------------------------------------------------------------------
pythia: installed_python installed_setuptools
$(FETCH_SCRIPT) "$(downloader)" setuptools-0.6c11.tar.gz $(DEPS_URL)
$(FETCH_SCRIPT) "$(downloader)" pythia-$(PYTHIA_VER).tar.gz https://github.com/geodynamics/pythia/releases/download/v$(PYTHIA_VER)
$(TAR) -zxvf pythia-$(PYTHIA_VER).tar.gz
$(CP) -p setuptools-0.6c11.tar.gz pythia-$(PYTHIA_VER)
cd pythia-$(PYTHIA_VER) && $(PYTHON) setup.py install --prefix=$(prefix) && touch ../installed_pythia
# @echo "$@ already installed. Skipping installation."
# touch installed_pythia
installed_pythia:
$(MAKE) $(AM_MAKEFLAGS) pythia
# ----------------------------------------------------------------------
# nemesis
# ----------------------------------------------------------------------
nemesis: installed_mpi installed_python installed_pythia
$(FETCH_SCRIPT) "$(downloader)" nemesis-$(NEMESIS_VER).tar.gz https://github.com/geodynamics/nemesis/releases/download/v$(NEMESIS_VER)
$(TAR) -zxvf nemesis-$(NEMESIS_VER).tar.gz
$(MKDIR_P) nemesis-build
cd nemesis-build && \
../nemesis-$(NEMESIS_VER)/configure \
--prefix=$(prefix) $(env_flags) $(env_mpicompilers); \
make && \
make install && \
touch ../installed_nemesis
# @echo "$@ already installed. Skipping installation."
# touch installed_nemesis
installed_nemesis:
$(MAKE) $(AM_MAKEFLAGS) nemesis
# ----------------------------------------------------------------------
# spatialdata
# ----------------------------------------------------------------------
spatialdata: installed_numpy installed_pythia installed_proj4 installed_swig installed_cppunit installed_autotools
# $(GIT) clone --recursive https://github.com/geodynamics/spatialdata.git spatialdata-$(SPATIALDATA_VER)
# cd spatialdata-$(SPATIALDATA_VER) && $(AUTORECONF) -if
$(FETCH_SCRIPT) "$(downloader)" spatialdata-$(SPATIALDATA_VER).tgz https://github.com/geodynamics/spatialdata/releases/download/v$(SPATIALDATA_VER)
$(TAR) -zxvf spatialdata-$(SPATIALDATA_VER).tgz
$(MKDIR_P) spatialdata-build
cd spatialdata-build && \
../spatialdata-$(SPATIALDATA_VER)/configure \
--prefix=$(prefix) $(env_flags) $(env_compilers) \
$(spatialdata_options) ; \
make -j $(make_threads) && \
make install && \
touch ../installed_spatialdata
cd spatialdata-build && make -j $(make_threads) check
# @echo "$@ already installed. Skipping installation."
# touch installed_spatialdata
installed_spatialdata:
$(MAKE) $(AM_MAKEFLAGS) spatialdata
# ----------------------------------------------------------------------
# git
# ----------------------------------------------------------------------
git: installed_python
# $(FETCH_SCRIPT) "$(downloader)" git-$(GIT_VER).tar.gz $(DEPS_URL)
# $(TAR) -zxf git-$(GIT_VER).tar.gz
# cd git-$(GIT_VER) && \
# make prefix=$(prefix) NO_EXPAT=1 NO_TCLTK=1 NO_GETTEXT=1 all install && \
# touch ../installed_git
@echo "$@ already installed. Skipping installation."
touch installed_git
installed_git:
$(MAKE) $(AM_MAKEFLAGS) git
# ----------------------------------------------------------------------
# cmake
# ----------------------------------------------------------------------
cmake:
$(FETCH_SCRIPT) "$(downloader)" cmake-$(CMAKE_VER).tar.gz $(DEPS_URL)
$(TAR) -zxf cmake-$(CMAKE_VER).tar.gz
cd cmake-$(CMAKE_VER) && \
./bootstrap --prefix=$(prefix) && make && make install && \
touch ../installed_cmake
# @echo "Skipping $@ installation."
# touch installed_cmake
installed_cmake:
$(MAKE) $(AM_MAKEFLAGS) cmake
# ----------------------------------------------------------------------
# petsc
# ----------------------------------------------------------------------
petsc: installed_mpi installed_hdf5 installed_git installed_cmake
$(FETCH_SCRIPT) "$(downloader)" petsc-pylith-$(PETSC_VER).tgz https://github.com/geodynamics/pylith/releases/download/v$(PETSC_VER)
$(TAR) -zxf petsc-pylith-$(PETSC_VER).tgz
# git clone -b knepley/pylith https://bitbucket.org/petsc/petsc.git petsc-pylith
cd petsc-pylith && \
./configure --prefix=$(prefix) \
--with-c2html=0 --with-x=0 \
--with-clanguage=C \
--with-mpicompilers=1 \
--with-debugging=0 \
--with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 \
$(petsc_options) $(env_flags) \
PETSC_DIR=$(abs_builddir) PETSC_ARCH=$(PETSC_ARCH) ; \
make $(petsc_build_options) PETSC_DIR=$(abs_builddir) PETSC_ARCH=$(PETSC_ARCH) && \
make PETSC_DIR=$(abs_builddir) install && \
make PETSC_DIR=$(abs_builddir) test && \
touch ../installed_petsc
# @echo "$@ already installed. Skipping installation."
# touch installed_petsc
installed_petsc:
$(MAKE) $(AM_MAKEFLAGS) petsc
# ----------------------------------------------------------------------
# pylith
# ----------------------------------------------------------------------
pylith: installed_cppunit installed_swig installed_netcdf installed_hdf5 installed_h5py installed_fiat installed_nemesis installed_pythia installed_spatialdata installed_petsc installed_netcdfpy installed_autotools
# $(GIT) clone --recursive -b $(pylith_git) https://github.com/geodynamics/pylith.git pylith-$(PYLITH_VER)
# cd pylith-$(PYLITH_VER) && $(AUTORECONF) -if
$(FETCH_SCRIPT) "$(downloader)" pylith-$(PYLITH_VER).tgz https://github.com/geodynamics/pylith/releases/download/v$(PYLITH_VER)
$(TAR) -zxvf pylith-$(PYLITH_VER).tgz
$(MKDIR_P) pylith-build
cd pylith-build && \
../pylith-$(PYLITH_VER)/configure \
--prefix=$(prefix) $(pylith_options) \
$(env_flags) $(env_mpicompilers) \
PETSC_DIR=$(PETSC_DIR) PETSC_ARCH=$(PETSC_ARCH) ; \
make -j $(make_threads) && \
make install && \
touch ../installed_pylith
cd pylith-build && make -j $(make_threads) check
installed_pylith:
$(MAKE) $(AM_MAKEFLAGS) pylith
clean-builddirs:
$(RM) $(RMFLAGS) -r $(noinst_builddirs)
clean-srcdirs:
$(RM) $(RMFLAGS) -r $(noinst_srcdirs)
clean-local: clean-builddirs clean-srcdirs
# End of file
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:
-------------- next part --------------
281c281
< PYTHON_VERSION =
---
> PYTHON_VERSION = 2.7
382c382
< M4_VER = 1.4.16
---
> M4_VER = 1.4.17
1286a1287,1323
> # pcgen
> # ----------------------------------------------------------------------
> pcgen: installed_python
> $(eval UNZIP = /usr/bin/unzip)
> $(eval PKG_URL_BASE = https://pypi.python.org/packages)
> $(eval PCGEN_VERSION = 0.2.1)
> $(eval PCGEN_URL := ${PKG_URL_BASE}/3c/68/3cd7faa8bc9b060eea452c5d6f27919dfb664cc4d1259998718a2360e05c)
> #
> $(FETCH_SCRIPT) "$(downloader)" PGen-${PCGEN_VERSION}.zip ${PCGEN_URL}
> $(UNZIP) PGen-${PCGEN_VERSION}.zip
> cd PGen-${PCGEN_VERSION} && \
> CC=mpicc $(env_flags) python setup.py build && \
> python setup.py install --prefix=$(prefix) && \
> touch ../installed_pcgen
>
> installed_pcgen:
> $(MAKE) $(AM_MAKEFLAGS) pcgen
>
> # ----------------------------------------------------------------------
> # cython
> # ----------------------------------------------------------------------
> cython: installed_python installed_setuptools installed_pcgen
> $(eval PKG_URL_BASE = https://pypi.python.org/packages)
> $(eval CYTHON_VERSION := 0.24)
> $(eval CYTHON_URL := ${PKG_URL_BASE}/b1/51/bd5ef7dff3ae02a2c6047aa18d3d06df2fb8a40b00e938e7ea2f75544cac)
> #
> $(FETCH_SCRIPT) "$(downloader)" Cython-${CYTHON_VERSION}.tar.gz ${CYTHON_URL}
> $(TAR) -xzf Cython-${CYTHON_VERSION}.tar.gz
> cd Cython-${CYTHON_VERSION} && \
> CC=mpicc $(env_flags) python setup.py build && \
> python setup.py install --prefix=$(prefix) && \
> touch ../installed_cython
>
> installed_cython:
> $(MAKE) $(AM_MAKEFLAGS) cython
>
> # ----------------------------------------------------------------------
1289c1326
< h5py: installed_hdf5 installed_numpy
---
> h5py: installed_hdf5 installed_numpy installed_cython
1369,1370c1406,1420
< $(TAR) -zxvf setuptools-$(SETUPTOOLS_VER).tar.gz
< cd setuptools-$(SETUPTOOLS_VER) && $(PYTHON) setup.py install --prefix=$(prefix) && touch ../installed_setuptools
---
> $(eval SETUPTOOLS_PFX = setuptools-$(SETUPTOOLS_VER))
> #
> # NEWER setuptools: USE ONLY IF ABOVE OLDER SETUPTOOLS DOES NOT WORK WITH H5PY BUILD
> # COMMENT-OUT ABOVE TWO LINES, & UNCOMMENT NEXT FOUR LINES ...
> # RECOMPILE WITH 'make h5py', OR CLEAN INSTALL FULL PYLITH SUITE.
> # $(eval SETUPTOOLS_VERSION = 24.0.2)
> # $(eval SETUPTOOLS_URL := ${PKG_URL_BASE}/21/d7/3e7e4b42d40469d2b770e10aee5b49538ecf2853eb5635d2d2536b286e2d)
> # $(FETCH_SCRIPT) "$(downloader)" setuptools-${SETUPTOOLS_VERSION} ${SETUPTOOLS_URL}
> # $(eval SETUPTOOLS_PFX = setuptools-$(SETUPTOOLS_VERSION))
> #
> $(TAR) -xzvf ${SETUPTOOLS_PFX}.tar.gz
> cd ${SETUPTOOLS_PFX} && \
> CC=mpicc $(env_flags) python setup.py build && \
> python setup.py install --prefix=$(prefix) && \
> touch ../installed_setuptools
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