diff --git a/docker/Dockerfile b/docker/Dockerfile new file mode 100644 index 0000000..bd2f661 --- /dev/null +++ b/docker/Dockerfile @@ -0,0 +1,59 @@ +FROM ubuntu:jammy + +RUN apt-get update && \ + DEBIAN_FRONTEND='noninteractive' \ + DEBCONF_NONINTERACTIVE_SEEN='true' \ + apt-get install --yes \ + gfortran \ + build-essential \ + git \ + curl \ + libblas-dev \ + liblapack-dev \ + autoconf \ + automake \ + autoconf-archive \ + libpython2.7-dev \ + libpython2.7 \ + python2.7 \ + libtool \ + libc6-dev \ + mpich \ + sudo \ + nano + +RUN useradd \ + --create-home \ + lithomop_user && echo "lithomop_user:password" | chpasswd + + +RUN sudo adduser lithomop_user sudo + +# Need to create this link so that pythia will compile +RUN ln -s /usr/bin/python2.7 /usr/bin/python; + +WORKDIR /home/lithomop_user + +USER lithomop_user + +#apt will install pip3, so need to do this to install pip 2.7 +RUN curl -L -O "https://bootstrap.pypa.io/pip/2.7/get-pip.py"; echo "password" | sudo -S python2.7 get-pip.py; pip install setuptools; pip install ez_setup; + + +ENV PETSC_DIR="/home/lithomop_user/petsc-2.3.3-p16" +ENV PETSC_ARCH="/home/lithomop_user/petsc-2.3.3-p16/lib/linux-gnu-c-debug" +ENV PATH="/home/lithomop_user/petsc-2.3.3-p16/externalpackages/mpich2-1.0.5p4/bin:${PATH}" + +RUN curl -L -O "https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-2.3.3.tar.gz"; tar -xvf petsc-2.3.3.tar.gz; cd petsc-2.3.3-p16; mkdir externalpackages; cd externalpackages; curl -L -O "https://www.mpich.org/static/downloads/1.0.5p4/mpich2-1.0.5p4.tar.gz"; tar -xvf mpich2-1.0.5p4.tar.gz; cd mpich2-1.0.5p4; ./configure; echo "password" | sudo -S make all; echo "password" | sudo -S make install; +RUN cd petsc-2.3.3-p16; ./config/configure.py PETSC_ARCH=linux-gnu-c-debug --with_mpi=1; make all PETSC_ARCH=linux-gnu-c-debug; make install PETSC_ARCH=linux-gnu-c-debug; + +RUN curl -L -O "https://github.com/geodynamics/pythia/releases/download/v0.8.1.16/pythia-0.8.1.16.tar.gz"; tar -xvf pythia-0.8.1.16.tar.gz; cd pythia-0.8.1.16; curl -L -O "https://pypi.python.org/packages/2.7/s/setuptools/setuptools-0.6c11-py2.7.egg"; echo "password" | sudo -S python setup.py build; echo "password" | sudo -S python setup.py build install; + +#ENV PYTHONPATH=/usr/bin/python + +RUN git clone --recurse-submodules 'https://github.com/jarettbakerdunn/lithomop.git'; cd lithomop; git checkout devel; git fetch; git pull; curl -L -O "https://pypi.python.org/packages/2.7/s/setuptools/setuptools-0.6c11-py2.7.egg"; mkdir aux-config; autoreconf -i; + +RUN cd lithomop; git checkout devel; git fetch; git pull; mv docker/ez_setup.py /home/lithomop_user/.local/lib/python2.7/site-packages/; rm /home/lithomop_user/lithomop/m4/cit_python.m4; mv docker/cit_python.m4 /home/lithomop_user/lithomop/m4/; + +RUN cd lithomop; autoupdate; automake --add-missing; autoreconf; +WORKDIR /home/lithomop_user/lithomop \ No newline at end of file diff --git a/docker/cit_python.m4 b/docker/cit_python.m4 new file mode 100644 index 0000000..cb0ea97 --- /dev/null +++ b/docker/cit_python.m4 @@ -0,0 +1,463 @@ +# -*- Autoconf -*- + + +## --------------------------- ## +## Autoconf macros for Python. ## +## --------------------------- ## + + +# CIT_PYTHON_INCDIR +# ----------------- +# Determine the directory containing using distutils. +AC_DEFUN([CIT_PYTHON_INCDIR], [ +# $Id$ +AC_REQUIRE([AM_PATH_PYTHON]) +AC_CACHE_CHECK([for $am_display_PYTHON include directory], + [_cv_PYTHON_INCDIR], + [_cv_PYTHON_INCDIR=`$PYTHON -c "from distutils import sysconfig; print(sysconfig.get_python_inc())" 2>/dev/null || + echo "$PYTHON_PREFIX/include/python$PYTHON_VERSION"`]) +AC_SUBST([PYTHON_INCDIR], [$_cv_PYTHON_INCDIR]) +])dnl CIT_PYTHON_INCDIR + + +# CIT_CHECK_PYTHON_HEADER +# ----------------------- +# Checking the existence of Python.h +AC_DEFUN([CIT_CHECK_PYTHON_HEADER], [ +# $Id$ +AC_REQUIRE([CIT_PYTHON_INCDIR]) +cit_save_CPPFLAGS=$CPPFLAGS +CPPFLAGS="-I$PYTHON_INCDIR $cit_save_CPPFLAGS" +AC_CHECK_HEADER([Python.h], [], [ + AC_MSG_ERROR([Header file 'Python.h' not found; maybe you don't have the python development package, e.g. 'python-dev', installed?]) + ]) +CPPFLAGS=$cit_save_CPPFLAGS +])dnl CIT_CHECK_PYTHON_HEADER + + +# CIT_CHECK_PYTHON_SHARED +# ----------------------- +# Check whether -lpythonX.X is a shared library. +AC_DEFUN([CIT_CHECK_PYTHON_SHARED], [ +# $Id$ +AC_REQUIRE([CIT_PYTHON_CONFIG]) +AC_MSG_CHECKING([whether -lpython$PYTHON_VERSION is a shared library]) +cit_save_CPPFLAGS=$CPPFLAGS +cit_save_LDFLAGS=$LDFLAGS +cit_save_LIBS=$LIBS +CPPFLAGS="$PYTHON_CPPFLAGS $cit_save_CPPFLAGS" +LDFLAGS="$PYTHON_LDFLAGS $cit_save_LDFLAGS" +LIBS="$PYTHON_LIBS $cit_save_LIBS" +AC_RUN_IFELSE([AC_LANG_PROGRAM([[ +#include "Python.h" +]], [[ + int status; + Py_Initialize(); + status = PyRun_SimpleString("import binascii") != 0; + Py_Finalize(); + return status; +]])], [ + AC_MSG_RESULT(yes) +], [ + AC_MSG_RESULT(no) + AC_MSG_ERROR([-lpython$PYTHON_VERSION is not a shared library]) +]) +CPPFLAGS=$cit_save_CPPFLAGS +LDFLAGS=$cit_save_LDFLAGS +LIBS=$cit_save_LIBS +])dnl CIT_CHECK_PYTHON_SHARED + + +# CIT_PYTHON_CONFIG +# ----------------- +AC_DEFUN([CIT_PYTHON_CONFIG], [ +# $Id$ +AC_REQUIRE([AM_PATH_PYTHON]) +AC_MSG_CHECKING([$am_display_PYTHON config]) +cat >python-config.py </dev/null` +if test -n "$PYTHON_CPPFLAGS"; then + AC_MSG_RESULT(ok) +else + AC_MSG_ERROR(["failed + +Run '$PYTHON python-config.py' to see what went wrong. +"]) +fi +rm -f python-config.py +AC_SUBST([PYTHON_CPPFLAGS], [$PYTHON_CPPFLAGS]) +AC_SUBST([PYTHON_LDFLAGS], [$PYTHON_LDFLAGS]) +AC_SUBST([PYTHON_LIBS], [$PYTHON_LIBS]) +])dnl CIT_PYTHON_CONFIG + + +# CIT_PYTHON_SYSCONFIG +# -------------------- +AC_DEFUN([CIT_PYTHON_SYSCONFIG], [ +# $Id$ +AC_REQUIRE([AM_PATH_PYTHON]) +AC_MSG_CHECKING([$am_display_PYTHON sysconfig]) +cat >local_sysconfig.py </dev/null` +if test -n "$PYTHON_INCDIR"; then + AC_MSG_RESULT(ok) +else + AC_MSG_ERROR(["failed + +Run '$PYTHON local_sysconfig.py' to see what went wrong. +"]) +fi +rm -f local_sysconfig.py +AC_SUBST([PYTHON_INCDIR], [$PYTHON_INCDIR]) +AC_SUBST([PYTHON_BLDLIBRARY], [$PYTHON_BLDLIBRARY]) +AC_SUBST([PYTHON_LDFLAGS], [$PYTHON_LDFLAGS]) +AC_SUBST([PYTHON_LDLAST], [$PYTHON_LDLAST]) +AC_SUBST([PYTHON_LDLIBRARY], [$PYTHON_LDLIBRARY]) +AC_SUBST([PYTHON_LIBDIR], [$PYTHON_LIBDIR]) +AC_SUBST([PYTHON_LIBP], [$PYTHON_LIBP]) +AC_SUBST([PYTHON_LIBPL], [$PYTHON_LIBPL]) +AC_SUBST([PYTHON_LIBS], [$PYTHON_LIBS]) +AC_SUBST([PYTHON_LINKFORSHARED], [$PYTHON_LINKFORSHARED]) +AC_SUBST([PYTHON_MODLIBS], [$PYTHON_MODLIBS]) +AC_SUBST([PYTHON_SYSLIBS], [$PYTHON_SYSLIBS]) +AC_SUBST([PYTHON_LA_LDFLAGS], [$PYTHON_LA_LDFLAGS]) +])dnl CIT_PYTHON_SYSCONFIG + + +# CIT_PYTHON_SITE +# --------------- +AC_DEFUN([CIT_PYTHON_SITE], [ +# $Id$ +AC_REQUIRE([AM_PATH_PYTHON]) +AC_MSG_CHECKING([whether we are installing to Python's prefix]) +cit_python_prefix=`$PYTHON -c "import sys; print(sys.prefix)"` +if test "$cit_python_prefix" = "$prefix"; then + AC_MSG_RESULT(yes) + cit_cond_python_site=true +else + AC_MSG_RESULT(no) + cit_cond_python_site=false +fi +AC_MSG_CHECKING([whether we are installing to Python's exec prefix]) +cit_python_exec_prefix=`$PYTHON -c "import sys; print(sys.exec_prefix)"` +cit_exec_prefix=$exec_prefix +test "x$cit_exec_prefix" = xNONE && cit_exec_prefix=$prefix +if test "$cit_python_exec_prefix" = "$cit_exec_prefix"; then + AC_MSG_RESULT(yes) + cit_cond_pyexec_site=true +else + AC_MSG_RESULT(no) + cit_cond_pyexec_site=false +fi +AM_CONDITIONAL([COND_PYTHON_SITE], [$cit_cond_python_site]) +AM_CONDITIONAL([COND_PYEXEC_SITE], [$cit_cond_pyexec_site]) +])dnl CIT_PYTHON_SITE + + +# CIT_CHECK_PYTHON_EGG(REQUIREMENT, +# [ACTION-IF-FOUND, [ACTION-IF-NOT-FOUND]]) +# -------------------------------------------------------------- + +# Check for REQUIREMENT using pkg_resources.require(). If the +# corresponding distribution is found, execute ACTION-IF-FOUND. +# Otherwise, execute ACTION-IF-NOT-FOUND. + +AC_DEFUN([CIT_CHECK_PYTHON_EGG], [ +# $Id$ + +AC_MSG_CHECKING([for "$1"]) + +cat >check_python_egg.py <conftest.sh 2>&AS_MESSAGE_LOG_FD])], + [], + [AC_MSG_RESULT(failed) + AC_MSG_FAILURE([cannot check for Python eggs])]) +eval `cat conftest.sh` +rm -f conftest.sh check_python_egg.py + +if test "$cit_egg_status" == 0; then + AC_MSG_RESULT(yes) + $2 +else + AC_MSG_RESULT(no) + m4_default([$3], [AC_MSG_ERROR([required Python package not found: $1])]) +fi + +])dnl CIT_CHECK_PYTHON_EGG + + +# CIT_PYTHON_EGG_SETUP +# -------------------- + +AC_DEFUN([CIT_PYTHON_EGG_SETUP], [ +# $Id$ +AC_REQUIRE([AM_PATH_PYTHON]) + +cit_builddir=`pwd` +cit_save_PYTHONPATH="$PYTHONPATH" +PYTHONPATH="$cit_builddir/python:$PYTHONPATH"; export PYTHONPATH +cd $srcdir + +#AC_MSG_NOTICE([downloading missing Python dependencies]) +#AS_IF([AC_TRY_COMMAND([$PYTHON setup.py install_deps -f $cit_builddir/deps -zmxd $cit_builddir/deps >&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD])], +# [], +# [AC_MSG_FAILURE([cannot download missing Python dependencies])]) +# +#AC_MSG_NOTICE([building Python dependencies]) +#AS_IF([AC_TRY_COMMAND([$PYTHON setup.py develop -H None -f $cit_builddir/deps -x -d $cit_builddir/python >&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD])], +# [], +# [AC_MSG_FAILURE([building Python dependencies])]) + +AC_MSG_NOTICE([Generating Python egg info]) +AS_IF([AC_TRY_COMMAND([$PYTHON setup.py egg_info >&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD])], + [], + [AC_MSG_FAILURE([generating Python egg info])]) +#commented out egg-related flags because it seems to break the build. +#AC_MSG_CHECKING([for egg-related flags]) +#AS_IF([AC_TRY_COMMAND([$PYTHON setup.py egg_flags >&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD])], +# [AC_MSG_RESULT(ok) +# . ./egg-flags.sh +# rm -f egg-flags.sh +# ], +# [AC_MSG_RESULT(failed) +# AC_MSG_FAILURE([cannot scan Python eggs for flags])]) + +cd $cit_builddir +PYTHONPATH="$cit_save_PYTHONPATH" +PYTHONPATH="${pythondir}:${pyexecdir}${cit_save_PYTHONPATH:+:${cit_save_PYTHONPATH}}" + +AC_SUBST(PYTHONPATH) +AC_SUBST(PYTHON_EGG_CFLAGS) +AC_SUBST(PYTHON_EGG_CPPFLAGS) +AC_SUBST(PYTHON_EGG_LDFLAGS) +AC_SUBST(PYTHON_EGG_LIBS) +AC_SUBST(PYTHON_EGG_PYXFLAGS) + +])dnl CIT_PYTHON_EGG_SETUP + + +# CIT_PROG_PYCONFIG +# ----------------- +# Provide a simple Python script which generates a Python module to +# expose our package configuration, similar to Python's +# distutils.sysconfig. +AC_DEFUN([CIT_PROG_PYCONFIG], [ +# $Id$ +PYCONFIG='$(top_builddir)/pyconfig' +AC_SUBST(PYCONFIG) +ofile=pyconfig +cfgfile="${ofile}T" +trap "rm \"$cfgfile\"; exit 1" 1 2 15 +rm -f "$cfgfile" +AC_MSG_NOTICE([creating $ofile]) +cat >"$cfgfile" </dev/null +if test $? == 0; then + eval s=`$PYTHON -c "import $1; print($1.__""file__)"` + AC_MSG_RESULT([found $s]) +else + AC_MSG_FAILURE(not found) +fi +if test -n "$2" ; then + AC_MSG_CHECKING([for $1 version]) + [eval `$PYTHON -c "import $1; print($1.__version__)" | sed 's/\([0-9]\{1,\}\)\.\([0-9]\{1,\}\)\.\([0-9]\{1,\}\)/avail_major=\1; avail_minor=\2; avail_patch=\3/'`] + [eval `echo $2 | sed 's/\([0-9]\{1,\}\)\.\([0-9]\{1,\}\)\.\([0-9]\{1,\}\)/req_major=\1; req_minor=\2; req_patch=\3/' 2>/dev/null`] + if test -n "$avail_major" -a -n "$avail_minor" -a -n "$avail_patch"; then + if test $avail_major -lt $req_major ; then + AC_MSG_FAILURE([$1 version >= $2 is required. You have $avail_major.$avail_minor.$avail_patch.]) + elif test $avail_major -eq $req_major -a $avail_minor -lt $req_minor; then + AC_MSG_FAILURE([$1 version >= $2 is required. You have $avail_major.$avail_minor.$avail_patch.]) + elif test $avail_major -eq $req_major -a $avail_minor -eq $req_minor -a $avail_patch -lt $req_patch; then + AC_MSG_FAILURE([$1 version >= $2 is required. You have $avail_major.$avail_minor.$avail_patch.]) + else + AC_MSG_RESULT([$avail_major.$avail_minor.$avail_patch]) + fi + else + AC_MSG_FAILURE([Could not determine version of module $1. Version >= $2 is required.]) + fi +fi + +]) \ No newline at end of file diff --git a/docker/ez_setup.py b/docker/ez_setup.py new file mode 100644 index 0000000..6a65d21 --- /dev/null +++ b/docker/ez_setup.py @@ -0,0 +1,485 @@ +#!python +"""Bootstrap distribute installation + +If you want to use setuptools in your package's setup.py, just include this +file in the same directory with it, and add this to the top of your setup.py:: + + from distribute_setup import use_setuptools + use_setuptools() + +If you want to require a specific version of setuptools, set a download +mirror, or use an alternate download directory, you can do so by supplying +the appropriate options to ``use_setuptools()``. + +This file can also be run as a script to install or upgrade setuptools. +""" +import os +import sys +import time +import fnmatch +import tempfile +import tarfile +from distutils import log + +try: + from site import USER_SITE +except ImportError: + USER_SITE = None + +try: + import subprocess + + def _python_cmd(*args): + args = (sys.executable,) + args + return subprocess.call(args) == 0 + +except ImportError: + # will be used for python 2.3 + def _python_cmd(*args): + args = (sys.executable,) + args + # quoting arguments if windows + if sys.platform == 'win32': + def quote(arg): + if ' ' in arg: + return '"%s"' % arg + return arg + args = [quote(arg) for arg in args] + return os.spawnl(os.P_WAIT, sys.executable, *args) == 0 + +DEFAULT_VERSION = "0.6.14" +DEFAULT_URL = "https://pypi.python.org/packages/source/d/distribute/" +SETUPTOOLS_FAKED_VERSION = "0.6c11" + +SETUPTOOLS_PKG_INFO = """\ +Metadata-Version: 1.0 +Name: setuptools +Version: %s +Summary: xxxx +Home-page: xxx +Author: xxx +Author-email: xxx +License: xxx +Description: xxx +""" % SETUPTOOLS_FAKED_VERSION + + +def _install(tarball): + # extracting the tarball + tmpdir = tempfile.mkdtemp() + log.warn('Extracting in %s', tmpdir) + old_wd = os.getcwd() + try: + os.chdir(tmpdir) + tar = tarfile.open(tarball) + _extractall(tar) + tar.close() + + # going in the directory + subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0]) + os.chdir(subdir) + log.warn('Now working in %s', subdir) + + # installing + log.warn('Installing Distribute') + if not _python_cmd('setup.py', 'install'): + log.warn('Something went wrong during the installation.') + log.warn('See the error message above.') + finally: + os.chdir(old_wd) + + +def _build_egg(egg, tarball, to_dir): + # extracting the tarball + tmpdir = tempfile.mkdtemp() + log.warn('Extracting in %s', tmpdir) + old_wd = os.getcwd() + try: + os.chdir(tmpdir) + tar = tarfile.open(tarball) + _extractall(tar) + tar.close() + + # going in the directory + subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0]) + os.chdir(subdir) + log.warn('Now working in %s', subdir) + + # building an egg + log.warn('Building a Distribute egg in %s', to_dir) + _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir) + + finally: + os.chdir(old_wd) + # returning the result + log.warn(egg) + if not os.path.exists(egg): + raise IOError('Could not build the egg.') + + +def _do_download(version, download_base, to_dir, download_delay): + egg = os.path.join(to_dir, 'distribute-%s-py%d.%d.egg' + % (version, sys.version_info[0], sys.version_info[1])) + if not os.path.exists(egg): + tarball = download_setuptools(version, download_base, + to_dir, download_delay) + _build_egg(egg, tarball, to_dir) + sys.path.insert(0, egg) + import setuptools + setuptools.bootstrap_install_from = egg + + +def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL, + to_dir=os.curdir, download_delay=15, no_fake=True): + # making sure we use the absolute path + to_dir = os.path.abspath(to_dir) + was_imported = 'pkg_resources' in sys.modules or \ + 'setuptools' in sys.modules + try: + try: + import pkg_resources + if not hasattr(pkg_resources, '_distribute'): + if not no_fake: + _fake_setuptools() + raise ImportError + except ImportError: + return _do_download(version, download_base, to_dir, download_delay) + try: + pkg_resources.require("distribute>="+version) + return + except pkg_resources.VersionConflict: + e = sys.exc_info()[1] + if was_imported: + sys.stderr.write( + "The required version of distribute (>=%s) is not available,\n" + "and can't be installed while this script is running. Please\n" + "install a more recent version first, using\n" + "'easy_install -U distribute'." + "\n\n(Currently using %r)\n" % (version, e.args[0])) + sys.exit(2) + else: + del pkg_resources, sys.modules['pkg_resources'] # reload ok + return _do_download(version, download_base, to_dir, + download_delay) + except pkg_resources.DistributionNotFound: + return _do_download(version, download_base, to_dir, + download_delay) + finally: + if not no_fake: + _create_fake_setuptools_pkg_info(to_dir) + +def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL, + to_dir=os.curdir, delay=15): + """Download distribute from a specified location and return its filename + + `version` should be a valid distribute version number that is available + as an egg for download under the `download_base` URL (which should end + with a '/'). `to_dir` is the directory where the egg will be downloaded. + `delay` is the number of seconds to pause before an actual download + attempt. + """ + # making sure we use the absolute path + to_dir = os.path.abspath(to_dir) + try: + from urllib.request import urlopen + except ImportError: + from urllib2 import urlopen + tgz_name = "distribute-%s.tar.gz" % version + url = download_base + tgz_name + saveto = os.path.join(to_dir, tgz_name) + src = dst = None + if not os.path.exists(saveto): # Avoid repeated downloads + try: + log.warn("Downloading %s", url) + src = urlopen(url) + # Read/write all in one block, so we don't create a corrupt file + # if the download is interrupted. + data = src.read() + dst = open(saveto, "wb") + dst.write(data) + finally: + if src: + src.close() + if dst: + dst.close() + return os.path.realpath(saveto) + +def _no_sandbox(function): + def __no_sandbox(*args, **kw): + try: + from setuptools.sandbox import DirectorySandbox + if not hasattr(DirectorySandbox, '_old'): + def violation(*args): + pass + DirectorySandbox._old = DirectorySandbox._violation + DirectorySandbox._violation = violation + patched = True + else: + patched = False + except ImportError: + patched = False + + try: + return function(*args, **kw) + finally: + if patched: + DirectorySandbox._violation = DirectorySandbox._old + del DirectorySandbox._old + + return __no_sandbox + +def _patch_file(path, content): + """Will backup the file then patch it""" + existing_content = open(path).read() + if existing_content == content: + # already patched + log.warn('Already patched.') + return False + log.warn('Patching...') + _rename_path(path) + f = open(path, 'w') + try: + f.write(content) + finally: + f.close() + return True + +_patch_file = _no_sandbox(_patch_file) + +def _same_content(path, content): + return open(path).read() == content + +def _rename_path(path): + new_name = path + '.OLD.%s' % time.time() + log.warn('Renaming %s into %s', path, new_name) + os.rename(path, new_name) + return new_name + +def _remove_flat_installation(placeholder): + if not os.path.isdir(placeholder): + log.warn('Unkown installation at %s', placeholder) + return False + found = False + for file in os.listdir(placeholder): + if fnmatch.fnmatch(file, 'setuptools*.egg-info'): + found = True + break + if not found: + log.warn('Could not locate setuptools*.egg-info') + return + + log.warn('Removing elements out of the way...') + pkg_info = os.path.join(placeholder, file) + if os.path.isdir(pkg_info): + patched = _patch_egg_dir(pkg_info) + else: + patched = _patch_file(pkg_info, SETUPTOOLS_PKG_INFO) + + if not patched: + log.warn('%s already patched.', pkg_info) + return False + # now let's move the files out of the way + for element in ('setuptools', 'pkg_resources.py', 'site.py'): + element = os.path.join(placeholder, element) + if os.path.exists(element): + _rename_path(element) + else: + log.warn('Could not find the %s element of the ' + 'Setuptools distribution', element) + return True + +_remove_flat_installation = _no_sandbox(_remove_flat_installation) + +def _after_install(dist): + log.warn('After install bootstrap.') + placeholder = dist.get_command_obj('install').install_purelib + _create_fake_setuptools_pkg_info(placeholder) + +def _create_fake_setuptools_pkg_info(placeholder): + if not placeholder or not os.path.exists(placeholder): + log.warn('Could not find the install location') + return + pyver = '%s.%s' % (sys.version_info[0], sys.version_info[1]) + setuptools_file = 'setuptools-%s-py%s.egg-info' % \ + (SETUPTOOLS_FAKED_VERSION, pyver) + pkg_info = os.path.join(placeholder, setuptools_file) + if os.path.exists(pkg_info): + log.warn('%s already exists', pkg_info) + return + + log.warn('Creating %s', pkg_info) + f = open(pkg_info, 'w') + try: + f.write(SETUPTOOLS_PKG_INFO) + finally: + f.close() + + pth_file = os.path.join(placeholder, 'setuptools.pth') + log.warn('Creating %s', pth_file) + f = open(pth_file, 'w') + try: + f.write(os.path.join(os.curdir, setuptools_file)) + finally: + f.close() + +_create_fake_setuptools_pkg_info = _no_sandbox(_create_fake_setuptools_pkg_info) + +def _patch_egg_dir(path): + # let's check if it's already patched + pkg_info = os.path.join(path, 'EGG-INFO', 'PKG-INFO') + if os.path.exists(pkg_info): + if _same_content(pkg_info, SETUPTOOLS_PKG_INFO): + log.warn('%s already patched.', pkg_info) + return False + _rename_path(path) + os.mkdir(path) + os.mkdir(os.path.join(path, 'EGG-INFO')) + pkg_info = os.path.join(path, 'EGG-INFO', 'PKG-INFO') + f = open(pkg_info, 'w') + try: + f.write(SETUPTOOLS_PKG_INFO) + finally: + f.close() + return True + +_patch_egg_dir = _no_sandbox(_patch_egg_dir) + +def _before_install(): + log.warn('Before install bootstrap.') + _fake_setuptools() + + +def _under_prefix(location): + if 'install' not in sys.argv: + return True + args = sys.argv[sys.argv.index('install')+1:] + for index, arg in enumerate(args): + for option in ('--root', '--prefix'): + if arg.startswith('%s=' % option): + top_dir = arg.split('root=')[-1] + return location.startswith(top_dir) + elif arg == option: + if len(args) > index: + top_dir = args[index+1] + return location.startswith(top_dir) + if arg == '--user' and USER_SITE is not None: + return location.startswith(USER_SITE) + return True + + +def _fake_setuptools(): + log.warn('Scanning installed packages') + try: + import pkg_resources + except ImportError: + # we're cool + log.warn('Setuptools or Distribute does not seem to be installed.') + return + ws = pkg_resources.working_set + try: + setuptools_dist = ws.find(pkg_resources.Requirement.parse('setuptools', + replacement=False)) + except TypeError: + # old distribute API + setuptools_dist = ws.find(pkg_resources.Requirement.parse('setuptools')) + + if setuptools_dist is None: + log.warn('No setuptools distribution found') + return + # detecting if it was already faked + setuptools_location = setuptools_dist.location + log.warn('Setuptools installation detected at %s', setuptools_location) + + # if --root or --preix was provided, and if + # setuptools is not located in them, we don't patch it + if not _under_prefix(setuptools_location): + log.warn('Not patching, --root or --prefix is installing Distribute' + ' in another location') + return + + # let's see if its an egg + if not setuptools_location.endswith('.egg'): + log.warn('Non-egg installation') + res = _remove_flat_installation(setuptools_location) + if not res: + return + else: + log.warn('Egg installation') + pkg_info = os.path.join(setuptools_location, 'EGG-INFO', 'PKG-INFO') + if (os.path.exists(pkg_info) and + _same_content(pkg_info, SETUPTOOLS_PKG_INFO)): + log.warn('Already patched.') + return + log.warn('Patching...') + # let's create a fake egg replacing setuptools one + res = _patch_egg_dir(setuptools_location) + if not res: + return + log.warn('Patched done.') + _relaunch() + + +def _relaunch(): + log.warn('Relaunching...') + # we have to relaunch the process + # pip marker to avoid a relaunch bug + if sys.argv[:3] == ['-c', 'install', '--single-version-externally-managed']: + sys.argv[0] = 'setup.py' + args = [sys.executable] + sys.argv + sys.exit(subprocess.call(args)) + + +def _extractall(self, path=".", members=None): + """Extract all members from the archive to the current working + directory and set owner, modification time and permissions on + directories afterwards. `path' specifies a different directory + to extract to. `members' is optional and must be a subset of the + list returned by getmembers(). + """ + import copy + import operator + from tarfile import ExtractError + directories = [] + + if members is None: + members = self + + for tarinfo in members: + if tarinfo.isdir(): + # Extract directories with a safe mode. + directories.append(tarinfo) + tarinfo = copy.copy(tarinfo) + tarinfo.mode = 448 # decimal for oct 0700 + self.extract(tarinfo, path) + + # Reverse sort directories. + if sys.version_info < (2, 4): + def sorter(dir1, dir2): + return cmp(dir1.name, dir2.name) + directories.sort(sorter) + directories.reverse() + else: + directories.sort(key=operator.attrgetter('name'), reverse=True) + + # Set correct owner, mtime and filemode on directories. + for tarinfo in directories: + dirpath = os.path.join(path, tarinfo.name) + try: + self.chown(tarinfo, dirpath) + self.utime(tarinfo, dirpath) + self.chmod(tarinfo, dirpath) + except ExtractError: + e = sys.exc_info()[1] + if self.errorlevel > 1: + raise + else: + self._dbg(1, "tarfile: %s" % e) + + +def main(argv, version=DEFAULT_VERSION): + """Install or upgrade setuptools and EasyInstall""" + tarball = download_setuptools() + _install(tarball) + + +if __name__ == '__main__': + main(sys.argv[1:]) \ No newline at end of file diff --git a/docker/readme.md b/docker/readme.md new file mode 100644 index 0000000..9cac66b --- /dev/null +++ b/docker/readme.md @@ -0,0 +1,27 @@ +This is a work-in-progress Dockerfile for Lithomop. + +This readme should serve as a guide to the work I've done so far, which should make it easier to build on this work in the future. + +I've made some progress towards getting Lithomop to compile, but so far I have not been able to successfully compile Lithomop. If you find any errors here, or if you know how to get Lithomop to compile, please contact me at github.com/JarettBakerDunn. +--------------------- +Here is a summary and explanation of the work done on the Dockerfile: + +1. Use aptitude to install some required libraries. -NOTE- as far as I know, not all of the libraries required by Lithomop are available in package managers, or at least the versions available are too recent to work with Lithomop. + +2. Create a user with the password set to "password", so that sudo can be used in the Dockerfile and in the container – this is needed for some other steps + +3. manually install pip2.7. pip2.7 is needed to install python2.7's ez_setup utility, which is used by Lithomop + +4. Set a number of environment variables needed by Lithomop + +5. Manually download and install mpich2-1.0.5, which is required by PETSC, which is in turn required by Lithomop. + +6. Manually download and install PETSC 2.3.3, which is required by lithomop. + +7. Download, install pythia + +8. Clone lithomop, along with steuptools 2.7. + +9. move cit_python.m4 and ez_setup.py from /docker into the places Lithomop expects them + +The files ez_setup.py and cit_python.m4 are included in the /docker directory, because they are needed to compile Lithomop but are not readily available or included in the Lithomop directory at the moment. \ No newline at end of file