def _install_spec(self):
"""
Install the Sage IPython kernel
It is safe to call this method multiple times, only one Sage
kernel spec is ever installed for any given Sage
version. However, it resets the IPython kernel spec directory
so additional resources symlinked there are lost. See
:meth:`symlink_resources`.
EXAMPLES::
sage: from sage.repl.ipython_kernel.install import SageKernelSpec
sage: spec = SageKernelSpec()
sage: spec._install_spec() # not tested
"""
import json
temp = tmp_dir()
kernel_spec = os.path.join(temp, "kernel.json")
with open(kernel_spec, "w") as f:
json.dump(self.kernel_spec(), f)
identifier = self.identifier()
install_kernel_spec(temp, identifier, user=True, replace=True)
self._spec = get_kernel_spec(identifier)
def launch_script_filename(self):
"""
Return a launch script suitable to display the scene.
This method saves the scene to disk and creates a launch
script. The latter contains an absolute path to the scene
file. The launch script is often necessary to make jmol
render the 3d scene.
OUTPUT:
String. The file name of a suitable launch script.
EXAMPLES::
sage: from sage.repl.rich_output.output_catalog import OutputSceneJmol
sage: rich_output = OutputSceneJmol.example(); rich_output
OutputSceneJmol container
sage: filename = rich_output.launch_script_filename(); filename
'/.../scene.spt'
sage: with open(filename) as fobj:
....: print(fobj.read())
set defaultdirectory "/.../scene.spt.zip"
script SCRIPT
"""
from sage.misc.temporary_file import tmp_dir
basedir = tmp_dir()
scene_filename = os.path.join(basedir, 'scene.spt.zip')
script_filename = os.path.join(basedir, 'scene.spt')
self.scene_zip.save_as(scene_filename)
with open(script_filename, 'w') as f:
f.write('set defaultdirectory "{0}"\n'.format(scene_filename))
f.write('script SCRIPT\n')
return script_filename
def launch_script_filename(self):
"""
Return a launch script suitable to display the scene.
This method saves the scene to disk and creates a launch
script. The latter contains an absolute path to the scene
file. The launch script is often necessary to make jmol
render the 3d scene.
OUTPUT:
String. The file name of a suitable launch script.
EXAMPLES::
sage: from sage.repl.rich_output.output_catalog import OutputSceneJmol
sage: rich_output = OutputSceneJmol.example(); rich_output
OutputSceneJmol container
sage: filename = rich_output.launch_script_filename(); filename
'/.../scene.spt'
sage: print(open(filename).read())
set defaultdirectory "/.../scene.spt.zip"
script SCRIPT
"""
from sage.misc.temporary_file import tmp_dir
basedir = tmp_dir()
scene_filename = os.path.join(basedir, 'scene.spt.zip')
script_filename = os.path.join(basedir, 'scene.spt')
self.scene_zip.save_as(scene_filename)
with open(script_filename, 'w') as f:
f.write('set defaultdirectory "{0}"\n'.format(scene_filename))
f.write('script SCRIPT\n')
return script_filename
def __init__(self, n, time):
self._n = n
if time:
cmd = 'time QuadraticSieve'
else:
cmd = 'QuadraticSieve'
env = os.environ.copy()
env['TMPDIR'] = tmp_dir('qsieve')
self._p = SageSpawn(cmd, env=env)
cleaner.cleaner(self._p.pid, 'QuadraticSieve')
self._p.sendline(str(self._n) + '\n\n\n')
self._done = False
self._out = ''
self._time = ''
self._do_time = time
def obj_filename(self):
"""
Return the file name of the ``.obj`` file
This method saves the object and texture to separate files in
a temporary directory and returns the object file name. This
is often used to launch a 3d viewer.
OUTPUT:
String. The file name (absolute path) of the saved obj file.
EXAMPLES::
sage: from sage.repl.rich_output.output_catalog import OutputSceneWavefront
sage: rich_output = OutputSceneWavefront.example(); rich_output
OutputSceneWavefront container
sage: obj = rich_output.obj_filename(); obj
'/.../scene.obj'
sage: with open(obj) as fobj:
....: print(fobj.read())
mtllib scene.mtl
g obj_1
...
f 3 2 6 8
sage: path = os.path.dirname(obj)
sage: mtl = os.path.join(path, 'scene.mtl'); mtl
'/.../scene.mtl'
sage: os.path.exists(mtl)
True
sage: os.path.dirname(obj) == os.path.dirname(mtl)
True
sage: with open(mtl) as fobj:
....: print(fobj.read())
newmtl texture177
Ka 0.2 0.2 0.5
...
d 1
"""
from sage.misc.temporary_file import tmp_dir
basedir = tmp_dir()
obj_filename = os.path.join(basedir, 'scene.obj')
mtl_filename = os.path.join(basedir, self.mtllib())
self.obj.save_as(obj_filename)
self.mtl.save_as(mtl_filename)
return os.path.abspath(obj_filename)
def obj_filename(self):
"""
Return the file name of the ``.obj`` file
This method saves the object and texture to separate files in
a temporary directory and returns the object file name. This
is often used to launch a 3d viewer.
OUTPUT:
String. The file name (absolute path) of the saved obj file.
EXAMPLES::
sage: from sage.repl.rich_output.output_catalog import OutputSceneWavefront
sage: rich_output = OutputSceneWavefront.example(); rich_output
OutputSceneWavefront container
sage: obj = rich_output.obj_filename(); obj
'/.../scene.obj'
sage: with open(obj) as fobj:
....: print(fobj.read())
mtllib scene.mtl
g obj_1
...
f 3 2 6 8
sage: path = os.path.dirname(obj)
sage: mtl = os.path.join(path, 'scene.mtl'); mtl
'/.../scene.mtl'
sage: os.path.exists(mtl)
True
sage: os.path.dirname(obj) == os.path.dirname(mtl)
True
sage: with open(mtl) as fobj:
....: print(fobj.read())
newmtl texture177
Ka 0.2 0.2 0.5
...
d 1
"""
from sage.misc.temporary_file import tmp_dir
basedir = tmp_dir()
obj_filename = os.path.join(basedir, 'scene.obj')
mtl_filename = os.path.join(basedir, self.mtllib())
self.obj.save_as(obj_filename)
self.mtl.save_as(mtl_filename)
return os.path.abspath(obj_filename)
def directory(self):
r"""
Return the directory where the input files for 4ti2 are
written by Sage and where 4ti2 is run.
EXAMPLES::
sage: from sage.interfaces.four_ti_2 import FourTi2
sage: f = FourTi2("/tmp/")
sage: f.directory()
'/tmp/'
"""
from sage.misc.temporary_file import tmp_dir
if self._directory is None:
# we have to put this here rather than in the __init__
# method since apparently importing sage.misc.misc does not
# work until Sage is done starting up.
self._directory = tmp_dir()
return self._directory
def directory(self):
r"""
Return the directory where the input files for 4ti2 are
written by Sage and where 4ti2 is run.
EXAMPLES::
sage: from sage.interfaces.four_ti_2 import FourTi2
sage: f = FourTi2("/tmp/")
sage: f.directory()
'/tmp/'
"""
from sage.misc.temporary_file import tmp_dir
if self._directory is None:
# we have to put this here rather than in the __init__
# method since apparently importing sage.misc.misc does not
# work until Sage is done starting up.
self._directory = tmp_dir()
return self._directory
def png(self, dir=None):
r"""
Render PNG images of the frames in this animation, saving them
in ``dir``. Return the absolute path to that directory. If
the frames have been previously rendered and ``dir`` is
``None``, just return the directory in which they are stored.
When ``dir`` is other than ``None``, force re-rendering of
frames.
INPUT:
- ``dir`` -- Directory in which to store frames. Default
``None``; in this case, a temporary directory will be
created for storing the frames.
EXAMPLES::
sage: a = animate([plot(x^2 + n) for n in range(4)])
sage: d = a.png()
sage: v = os.listdir(d); v.sort(); v
['00000000.png', '00000001.png', '00000002.png', '00000003.png']
"""
if dir is None:
try:
return self._png_dir
except AttributeError:
pass
d = tmp_dir()
else:
d = dir
G = self._frames
for i, frame in enumerate(self._frames):
filename = '%s/%s'%(d,sage.misc.misc.pad_zeros(i,8))
try:
frame.save_image(filename + '.png', **self._kwds)
except AttributeError:
self.make_image(frame, filename + '.png', **self._kwds)
self._png_dir = d
return d
def png(self, dir=None):
r"""
Render PNG images of the frames in this animation, saving them
in ``dir``. Return the absolute path to that directory. If
the frames have been previously rendered and ``dir`` is
``None``, just return the directory in which they are stored.
When ``dir`` is other than ``None``, force re-rendering of
frames.
INPUT:
- ``dir`` -- Directory in which to store frames. Default
``None``; in this case, a temporary directory will be
created for storing the frames.
EXAMPLES::
sage: a = animate([plot(x^2 + n) for n in range(4)])
sage: d = a.png()
sage: v = os.listdir(d); v.sort(); v
['00000000.png', '00000001.png', '00000002.png', '00000003.png']
"""
if dir is None:
try:
return self._png_dir
except AttributeError:
pass
d = tmp_dir()
else:
d = dir
G = self._frames
for i, frame in enumerate(self._frames):
filename = '%s/%s'%(d,sage.misc.misc.pad_zeros(i,8))
try:
frame.save_image(filename + '.png', **self._kwds)
except AttributeError:
self.make_image(frame, filename + '.png', **self._kwds)
self._png_dir = d
return d
def png(self, dir=None):
"""
Return the absolute path to a temp directory that contains the
rendered PNG's of all the images in this animation.
EXAMPLES::
sage: a = animate([plot(x^2 + n) for n in range(4)])
sage: d = a.png()
sage: v = os.listdir(d); v.sort(); v
['00000000.png', '00000001.png', '00000002.png', '00000003.png']
"""
try:
return self._png_dir
except AttributeError:
pass
d = tmp_dir()
G = self._frames
for i, frame in enumerate(self._frames):
filename = '%s/%s'%(d,sage.misc.misc.pad_zeros(i,8))
frame.save(filename + '.png', **self._kwds)
self._png_dir = d
return d
def png(self, dir=None):
"""
Return the absolute path to a temp directory that contains the
rendered PNG's of all the images in this animation.
EXAMPLES::
sage: a = animate([plot(x^2 + n) for n in range(4)])
sage: d = a.png()
sage: v = os.listdir(d); v.sort(); v
['00000000.png', '00000001.png', '00000002.png', '00000003.png']
"""
try:
return self._png_dir
except AttributeError:
pass
d = tmp_dir()
G = self._frames
for i, frame in enumerate(self._frames):
filename = '%s/%s' % (d, sage.misc.misc.pad_zeros(i, 8))
frame.save(filename + '.png', **self._kwds)
self._png_dir = d
return d
def qsieve_block(n, time, verbose=False):
"""
Compute the factorization of n using Hart's quadratic Sieve
blocking until complete.
"""
cmd = ['QuadraticSieve']
if time:
cmd = ['time'] + cmd
env = os.environ.copy()
env['TMPDIR'] = tmp_dir('qsieve')
p = sp.Popen(cmd,
env=env,
stdout=sp.PIPE,
stderr=sp.STDOUT,
stdin=sp.PIPE,
encoding='latin1')
out, err = p.communicate(str(n))
z = data_to_list(out, n, time=time)
if verbose:
print(z[-1])
return z[:2]
def _install_spec(self):
"""
Install the Sage IPython kernel
It is safe to call this method multiple times, only one Sage
kernel spec is ever installed for any given Sage
version. However, it resets the IPython kernel spec directory
so additional resources symlinked there are lost. See
:meth:`symlink_resources`.
EXAMPLES::
sage: from sage.repl.ipython_kernel.install import SageKernelSpec
sage: spec = SageKernelSpec()
sage: spec._install_spec() # not tested
"""
import json
temp = tmp_dir()
kernel_spec = os.path.join(temp, 'kernel.json')
with open(kernel_spec, 'w') as f:
json.dump(self.kernel_spec(), f)
identifier = self.identifier()
install_kernel_spec(temp, identifier, user=True, replace=True)
self._spec = get_kernel_spec(identifier)
def eval(self, x, globals=None, locals=None):
"""
EXAMPLES::
sage: from sage.misc.inline_fortran import InlineFortran, _example
sage: fortran = InlineFortran(globals())
sage: fortran(_example)
sage: import numpy
sage: n = numpy.array(range(10),dtype=float)
sage: fib(n,int(10))
sage: n
array([ 0., 1., 1., 2., 3., 5., 8., 13., 21., 34.])
TESTS::
sage: os.chdir(SAGE_ROOT)
sage: fortran.eval("SYNTAX ERROR !@#$")
Traceback (most recent call last):
...
RuntimeError: failed to compile Fortran code:...
sage: os.getcwd() == SAGE_ROOT
True
"""
if len(x.splitlines()) == 1 and os.path.exists(x):
filename = x
x = open(x).read()
if filename.lower().endswith('.f90'):
x = '!f90\n' + x
from numpy import f2py
# Create everything in a temporary directory
mytmpdir = tmp_dir()
try:
old_cwd = os.getcwd()
os.chdir(mytmpdir)
old_import_path = os.sys.path
os.sys.path.append(mytmpdir)
name = "fortran_module" # Python module name
# if the first line has !f90 as a comment, gfortran will
# treat it as Fortran 90 code
if x.startswith('!f90'):
fortran_file = name + '.f90'
else:
fortran_file = name + '.f'
s_lib_path = ""
s_lib = ""
for s in self.library_paths:
s_lib_path = s_lib_path + "-L%s "
for s in self.libraries:
s_lib = s_lib + "-l%s "%s
log = name + ".log"
extra_args = '--quiet --f77exec=sage-inline-fortran --f90exec=sage-inline-fortran %s %s >"%s" 2>&1'%(
s_lib_path, s_lib, log)
f2py.compile(x, name, extra_args = extra_args, source_fn=fortran_file)
log_string = open(log).read()
# f2py.compile() doesn't raise any exception if it fails.
# So we manually check whether the compiled file exists.
# NOTE: the .so extension is used, even on OS X where .dylib
# might be expected.
soname = name + '.so'
if not os.path.isfile(soname):
raise RuntimeError("failed to compile Fortran code:\n" + log_string)
if self.verbose:
print log_string
m = __builtin__.__import__(name)
finally:
os.sys.path = old_import_path
os.chdir(old_cwd)
try:
import shutil
shutil.rmtree(mytmpdir)
except OSError:
# This can fail for example over NFS
pass
for k, x in m.__dict__.iteritems():
if k[0] != '_':
self.globals[k] = x
def eval(self, x, globals=None, locals=None):
"""
Compile fortran code ``x`` and adds the functions in it to
``globals``.
INPUT:
- ``x`` -- Fortran code
- ``globals`` -- a dict to which to add the functions from the
fortran module
- ``locals`` -- ignored
EXAMPLES::
sage: code = '''
....: C FILE: FIB1.F
....: SUBROUTINE FIB(A,N)
....: C
....: C CALCULATE FIRST N FIBONACCI NUMBERS
....: C
....: INTEGER N
....: REAL*8 A(N)
....: DO I=1,N
....: IF (I.EQ.1) THEN
....: A(I) = 0.0D0
....: ELSEIF (I.EQ.2) THEN
....: A(I) = 1.0D0
....: ELSE
....: A(I) = A(I-1) + A(I-2)
....: ENDIF
....: ENDDO
....: END
....: C END FILE FIB1.F
....: '''
sage: fortran(code, globals())
sage: import numpy
sage: a = numpy.array(range(10), dtype=float)
sage: fib(a, 10)
sage: a
array([ 0., 1., 1., 2., 3., 5., 8., 13., 21., 34.])
TESTS::
sage: os.chdir(SAGE_ROOT)
sage: fortran.eval("SYNTAX ERROR !@#$")
Traceback (most recent call last):
...
RuntimeError: failed to compile Fortran code:...
sage: os.getcwd() == SAGE_ROOT
True
"""
if len(x.splitlines()) == 1 and os.path.exists(x):
from sage.misc.superseded import deprecation
deprecation(
2891,
"Calling fortran() with a filename is deprecated, use fortran(open(f).read) instead"
)
filename = x
x = open(x).read()
if filename.lower().endswith('.f90'):
x = '!f90\n' + x
if globals is None:
globals = self.globs
from numpy import f2py
# Create everything in a temporary directory
mytmpdir = tmp_dir()
try:
old_cwd = os.getcwd()
os.chdir(mytmpdir)
name = "fortran_module" # Python module name
# if the first line has !f90 as a comment, gfortran will
# treat it as Fortran 90 code
if x.startswith('!f90'):
fortran_file = name + '.f90'
else:
fortran_file = name + '.f'
s_lib_path = ""
s_lib = ""
for s in self.library_paths:
s_lib_path = s_lib_path + "-L%s "
for s in self.libraries:
s_lib = s_lib + "-l%s " % s
log = name + ".log"
extra_args = '--quiet --f77exec=sage-inline-fortran --f90exec=sage-inline-fortran %s %s >"%s" 2>&1' % (
s_lib_path, s_lib, log)
f2py.compile(x,
name,
extra_args=extra_args,
source_fn=fortran_file)
log_string = open(log).read()
# Note that f2py() doesn't raise an exception if it fails.
# In that case, the import below will fail.
try:
file, pathname, description = imp.find_module(name, [mytmpdir])
except ImportError:
raise RuntimeError("failed to compile Fortran code:\n" +
log_string)
try:
m = imp.load_module(name, file, pathname, description)
finally:
file.close()
if self.verbose:
print(log_string)
finally:
os.chdir(old_cwd)
try:
shutil.rmtree(mytmpdir)
except OSError:
# This can fail for example over NFS
pass
for k, x in m.__dict__.iteritems():
if k[0] != '_':
globals[k] = x
def eval(self, x, globals=None, locals=None):
"""
Compile fortran code ``x`` and adds the functions in it to
``globals``.
INPUT:
- ``x`` -- Fortran code
- ``globals`` -- a dict to which to add the functions from the
fortran module
- ``locals`` -- ignored
EXAMPLES::
sage: code = '''
....: C FILE: FIB1.F
....: SUBROUTINE FIB(A,N)
....: C
....: C CALCULATE FIRST N FIBONACCI NUMBERS
....: C
....: INTEGER N
....: REAL*8 A(N)
....: DO I=1,N
....: IF (I.EQ.1) THEN
....: A(I) = 0.0D0
....: ELSEIF (I.EQ.2) THEN
....: A(I) = 1.0D0
....: ELSE
....: A(I) = A(I-1) + A(I-2)
....: ENDIF
....: ENDDO
....: END
....: C END FILE FIB1.F
....: '''
sage: fortran(code, globals())
sage: import numpy
sage: a = numpy.array(range(10), dtype=float)
sage: fib(a, 10)
sage: a
array([ 0., 1., 1., 2., 3., 5., 8., 13., 21., 34.])
TESTS::
sage: os.chdir(SAGE_ROOT)
sage: fortran.eval("SYNTAX ERROR !@#$")
Traceback (most recent call last):
...
RuntimeError: failed to compile Fortran code:...
sage: os.getcwd() == SAGE_ROOT
True
"""
if len(x.splitlines()) == 1 and os.path.exists(x):
from sage.misc.superseded import deprecation
deprecation(2891, "Calling fortran() with a filename is deprecated, use fortran(open(f).read) instead")
filename = x
x = open(x).read()
if filename.lower().endswith('.f90'):
x = '!f90\n' + x
if globals is None:
globals = self.globs
from numpy import f2py
# Create everything in a temporary directory
mytmpdir = tmp_dir()
try:
old_cwd = os.getcwd()
os.chdir(mytmpdir)
name = "fortran_module" # Python module name
# if the first line has !f90 as a comment, gfortran will
# treat it as Fortran 90 code
if x.startswith('!f90'):
fortran_file = name + '.f90'
else:
fortran_file = name + '.f'
s_lib_path = ""
s_lib = ""
for s in self.library_paths:
s_lib_path = s_lib_path + "-L%s "
for s in self.libraries:
s_lib = s_lib + "-l%s "%s
log = name + ".log"
extra_args = '--quiet --f77exec=sage-inline-fortran --f90exec=sage-inline-fortran %s %s >"%s" 2>&1'%(
s_lib_path, s_lib, log)
f2py.compile(x, name, extra_args = extra_args, source_fn=fortran_file)
log_string = open(log).read()
# Note that f2py() doesn't raise an exception if it fails.
# In that case, the import below will fail.
try:
file, pathname, description = imp.find_module(name, [mytmpdir])
except ImportError:
raise RuntimeError("failed to compile Fortran code:\n" + log_string)
try:
m = imp.load_module(name, file, pathname, description)
finally:
file.close()
if self.verbose:
print(log_string)
finally:
os.chdir(old_cwd)
try:
shutil.rmtree(mytmpdir)
except OSError:
# This can fail for example over NFS
pass
for k, x in m.__dict__.iteritems():
if k[0] != '_':
globals[k] = x
def run_val_gdb(self, testing=False):
"""
Spawns a subprocess to run tests under the control of gdb or valgrind.
INPUT:
- ``testing`` -- boolean; if True then the command to be run
will be printed rather than a subprocess started.
EXAMPLES:
Note that the command lines include unexpanded environment
variables. It is safer to let the shell expand them than to
expand them here and risk insufficient quoting. ::
sage: from sage.doctest.control import DocTestDefaults, DocTestController
sage: DD = DocTestDefaults(gdb=True)
sage: DC = DocTestController(DD, ["hello_world.py"])
sage: DC.run_val_gdb(testing=True)
exec gdb -x "...sage-gdb-commands" --args sage-runtests --serial --timeout=0 hello_world.py
::
sage: DD = DocTestDefaults(valgrind=True, optional="all", timeout=172800)
sage: DC = DocTestController(DD, ["hello_world.py"])
sage: DC.run_val_gdb(testing=True)
exec valgrind --tool=memcheck --leak-resolution=high --leak-check=full --num-callers=25 --suppressions="...valgrind/pyalloc.supp" --suppressions="...valgrind/sage.supp" --suppressions="...valgrind/sage-additional.supp" --log-file=".../valgrind/sage-memcheck.%p" sage-runtests --serial --timeout=172800 --optional=all hello_world.py
"""
try:
sage_cmd = self._assemble_cmd()
except ValueError:
self.log(sys.exc_info()[1])
return 2
opt = self.options
if opt.gdb:
cmd = '''exec gdb -x "%s" --args ''' % (os.path.join(
SAGE_VENV, "bin", "sage-gdb-commands"))
flags = ""
if opt.logfile:
sage_cmd += " --logfile %s" % (opt.logfile)
else:
if opt.logfile is None:
default_log = os.path.join(DOT_SAGE, "valgrind")
if os.path.exists(default_log):
if not os.path.isdir(default_log):
self.log("%s must be a directory" % default_log)
return 2
else:
os.makedirs(default_log)
logfile = os.path.join(default_log, "sage-%s")
else:
logfile = opt.logfile
if opt.valgrind:
toolname = "memcheck"
flags = os.getenv("SAGE_MEMCHECK_FLAGS")
if flags is None:
flags = "--leak-resolution=high --leak-check=full --num-callers=25 "
flags += '''--suppressions="%s" ''' % (os.path.join(
SAGE_EXTCODE, "valgrind", "pyalloc.supp"))
flags += '''--suppressions="%s" ''' % (os.path.join(
SAGE_EXTCODE, "valgrind", "sage.supp"))
flags += '''--suppressions="%s" ''' % (os.path.join(
SAGE_EXTCODE, "valgrind", "sage-additional.supp"))
elif opt.massif:
toolname = "massif"
flags = os.getenv("SAGE_MASSIF_FLAGS", "--depth=6 ")
elif opt.cachegrind:
toolname = "cachegrind"
flags = os.getenv("SAGE_CACHEGRIND_FLAGS", "")
elif opt.omega:
toolname = "exp-omega"
flags = os.getenv("SAGE_OMEGA_FLAGS", "")
cmd = "exec valgrind --tool=%s " % (toolname)
flags += ''' --log-file="%s" ''' % logfile
if opt.omega:
toolname = "omega"
if "%s" in flags:
flags %= toolname + ".%p" # replace %s with toolname
cmd += flags + sage_cmd
sys.stdout.flush()
sys.stderr.flush()
self.log(cmd)
if testing:
return
# Setup signal handlers.
# Save crash logs in temporary directory.
os.putenv('CYSIGNALS_CRASH_LOGS', tmp_dir("crash_logs_"))
init_cysignals()
import signal
import subprocess
p = subprocess.Popen(cmd, shell=True)
if opt.timeout > 0:
signal.alarm(opt.timeout)
try:
return p.wait()
except AlarmInterrupt:
self.log(" Timed out")
return 4
except KeyboardInterrupt:
self.log(" Interrupted")
return 128
finally:
signal.alarm(0)
if p.returncode is None:
p.terminate()
def eval(self, x, globals=None, locals=None):
"""
Compile fortran code ``x`` and adds the functions in it to
``globals``.
INPUT:
- ``x`` -- Fortran code
- ``globals`` -- a dict to which to add the functions from the
fortran module
- ``locals`` -- ignored
EXAMPLES::
sage: code = '''
....: C FILE: FIB1.F
....: SUBROUTINE FIB(A,N)
....: C
....: C CALCULATE FIRST N FIBONACCI NUMBERS
....: C
....: INTEGER N
....: REAL*8 A(N)
....: DO I=1,N
....: IF (I.EQ.1) THEN
....: A(I) = 0.0D0
....: ELSEIF (I.EQ.2) THEN
....: A(I) = 1.0D0
....: ELSE
....: A(I) = A(I-1) + A(I-2)
....: ENDIF
....: ENDDO
....: END
....: C END FILE FIB1.F
....: '''
sage: fortran(code, globals())
sage: import numpy
sage: a = numpy.array(range(10), dtype=float)
sage: fib(a, 10)
sage: a
array([ 0., 1., 1., 2., 3., 5., 8., 13., 21., 34.])
TESTS::
sage: os.chdir(SAGE_ROOT)
sage: fortran.eval("SYNTAX ERROR !@#$")
Traceback (most recent call last):
...
RuntimeError: failed to compile Fortran code:...
sage: os.getcwd() == SAGE_ROOT
True
"""
if globals is None:
globals = self.globs
if globals is None:
from sage.repl.user_globals import get_globals
globals = get_globals()
from numpy import f2py
# Create everything in a temporary directory
mytmpdir = tmp_dir()
try:
old_cwd = os.getcwd()
os.chdir(mytmpdir)
name = "fortran_module" # Python module name
# if the first line has !f90 as a comment, gfortran will
# treat it as Fortran 90 code
if x.startswith('!f90'):
fortran_file = name + '.f90'
else:
fortran_file = name + '.f'
s_lib_path = ""
s_lib = ""
for s in self.library_paths:
s_lib_path = s_lib_path + "-L%s "
for s in self.libraries:
s_lib = s_lib + "-l%s "%s
log = name + ".log"
extra_args = ('--quiet --f77exec=sage-inline-fortran '
'--f90exec=sage-inline-fortran {lib_path} {lib} '
'> {log} 2>&1'.format(lib_path=s_lib_path,
lib=s_lib, log=log))
f2py.compile(x, name, extra_args=extra_args,
source_fn=fortran_file)
with open(log) as fobj:
log_string = fobj.read()
# Note that f2py() doesn't raise an exception if it fails.
# In that case, the import below will fail.
try:
mod = _import_module_from_path(name, [mytmpdir])
except ImportError:
raise RuntimeError("failed to compile Fortran code:\n" +
log_string)
if self.verbose:
print(log_string)
finally:
os.chdir(old_cwd)
if sys.platform != 'cygwin':
# Do not delete temporary DLLs on Cygwin; this will cause
# future forks of this process to fail. Instead temporary DLLs
# will be cleaned up upon process exit
try:
shutil.rmtree(mytmpdir)
except OSError:
# This can fail for example over NFS
pass
for k, x in iteritems(mod.__dict__):
if k[0] != '_':
globals[k] = x
import csv
import os
from IPython.display import display, Image
from sage.matrix.constructor import Matrix
from sage.misc.temporary_file import tmp_dir, tmp_filename
dirname = tmp_dir()
def nb_show(graphics_object, ext='.png'):
name = os.path.join(dirname, tmp_filename(ext=ext))
graphics_object.save(name)
display(Image(name))
def matrix_of_csv(fname):
with open(fname, 'rb') as csvfile:
mreader = csv.reader(csvfile, delimiter=',', quotechar="'")
return Matrix([[int(x) for x in row] for row in mreader])
def __call__(self, f, inputs):
"""
Parallel iterator using ``fork()``.
INPUT:
- ``f`` -- a function (or more general, any callable)
- ``inputs`` -- a list of pairs ``(args, kwds)`` to be used as
arguments to ``f``, where ``args`` is a tuple and ``kwds`` is
a dictionary.
OUTPUT:
EXAMPLES::
sage: F = sage.parallel.use_fork.p_iter_fork(2,3)
sage: sorted(list( F( (lambda x: x^2), [([10],{}), ([20],{})])))
[(([10], {}), 100), (([20], {}), 400)]
sage: sorted(list( F( (lambda x, y: x^2+y), [([10],{'y':1}), ([20],{'y':2})])))
[(([10], {'y': 1}), 101), (([20], {'y': 2}), 402)]
TESTS:
The output of functions decorated with :func:`parallel` is read
as a pickle by the parent process. We intentionally break the
unpickling and demonstrate that this failure is handled
gracefully (the exception is put in the list instead of the
answer)::
sage: Polygen = parallel(polygen)
sage: list(Polygen([QQ]))
[(((Rational Field,), {}), x)]
sage: from sage.misc.persist import unpickle_override, register_unpickle_override
sage: register_unpickle_override('sage.rings.polynomial.polynomial_rational_flint', 'Polynomial_rational_flint', Integer)
sage: L = list(Polygen([QQ]))
sage: L
[(((Rational Field,), {}),
'INVALID DATA __init__() takes at most 2 positional arguments (4 given)')]
Fix the unpickling::
sage: del unpickle_override[('sage.rings.polynomial.polynomial_rational_flint', 'Polynomial_rational_flint')]
sage: list(Polygen([QQ,QQ]))
[(((Rational Field,), {}), x), (((Rational Field,), {}), x)]
"""
n = self.ncpus
v = list(inputs)
import os
import sys
import signal
from sage.misc.persist import loads
from sage.misc.temporary_file import tmp_dir
dir = tmp_dir()
timeout = self.timeout
workers = {}
try:
while v or workers:
# Spawn up to n subprocesses
while v and len(workers) < n:
v0 = v.pop(0) # Input value for the next subprocess
with ContainChildren():
pid = os.fork()
# The way fork works is that pid returns the
# nonzero pid of the subprocess for the master
# process and returns 0 for the subprocess.
if not pid:
# This is the subprocess.
self._subprocess(f, dir, *v0)
workers[pid] = WorkerData(v0)
if len(workers) > 0:
# Now wait for one subprocess to finish and report the result.
# However, wait at most the time since the oldest process started.
T = walltime()
if timeout:
oldest = min(W.starttime for W in workers.values())
alarm(max(timeout - (T - oldest), 0.1))
try:
pid = os.wait()[0]
cancel_alarm()
W = workers.pop(pid)
except AlarmInterrupt:
# Kill workers that are too old
for pid, W in workers.items():
if T - W.starttime > timeout:
if self.verbose:
print(
"Killing subprocess %s with input %s which took too long"
% (pid, W.input))
os.kill(pid, signal.SIGKILL)
W.failure = " (timed out)"
except KeyError:
# Some other process exited, not our problem...
pass
else:
# collect data from process that successfully terminated
sobj = os.path.join(dir, '%s.sobj' % pid)
try:
with open(sobj, "rb") as file:
data = file.read()
except IOError:
answer = "NO DATA" + W.failure
else:
os.unlink(sobj)
try:
answer = loads(data, compress=False)
except Exception as E:
answer = "INVALID DATA {}".format(E)
out = os.path.join(dir, '%s.out' % pid)
try:
with open(out) as file:
sys.stdout.write(file.read())
os.unlink(out)
except IOError:
pass
yield (W.input, answer)
finally:
# Send SIGKILL signal to workers that are left.
if workers:
if self.verbose:
print("Killing any remaining workers...")
sys.stdout.flush()
for pid in workers:
try:
os.kill(pid, signal.SIGKILL)
except OSError:
# If kill() failed, it is most likely because
# the process already exited.
pass
else:
try:
os.waitpid(pid, 0)
except OSError as msg:
if self.verbose:
print(msg)
# Clean up all temporary files.
rmtree(dir)
def eval(self, x, globals=None, locals=None):
"""
EXAMPLES::
sage: from sage.misc.inline_fortran import InlineFortran, _example
sage: fortran = InlineFortran(globals())
sage: fortran(_example)
sage: import numpy
sage: n = numpy.array(range(10),dtype=float)
sage: fib(n,int(10))
sage: n
array([ 0., 1., 1., 2., 3., 5., 8., 13., 21., 34.])
TESTS::
sage: os.chdir(SAGE_ROOT)
sage: fortran.eval("SYNTAX ERROR !@#$")
Traceback (most recent call last):
...
RuntimeError: failed to compile Fortran code:...
sage: os.getcwd() == SAGE_ROOT
True
"""
if len(x.splitlines()) == 1 and os.path.exists(x):
filename = x
x = open(x).read()
if filename.lower().endswith('.f90'):
x = '!f90\n' + x
from numpy import f2py
# Create everything in a temporary directory
mytmpdir = tmp_dir()
try:
old_cwd = os.getcwd()
os.chdir(mytmpdir)
old_import_path = os.sys.path
os.sys.path.append(mytmpdir)
name = "fortran_module" # Python module name
# if the first line has !f90 as a comment, gfortran will
# treat it as Fortran 90 code
if x.startswith('!f90'):
fortran_file = name + '.f90'
else:
fortran_file = name + '.f'
s_lib_path = ""
s_lib = ""
for s in self.library_paths:
s_lib_path = s_lib_path + "-L%s "
for s in self.libraries:
s_lib = s_lib + "-l%s " % s
log = name + ".log"
extra_args = '--quiet --f77exec=sage-inline-fortran --f90exec=sage-inline-fortran %s %s >"%s" 2>&1' % (
s_lib_path, s_lib, log)
f2py.compile(x,
name,
extra_args=extra_args,
source_fn=fortran_file)
log_string = open(log).read()
# f2py.compile() doesn't raise any exception if it fails.
# So we manually check whether the compiled file exists.
# NOTE: the .so extension is used expect on Cygwin,
# that is even on OS X where .dylib might be expected.
soname = name
uname = os.uname()[0].lower()
if uname[:6] == "cygwin":
soname += '.dll'
else:
soname += '.so'
if not os.path.isfile(soname):
raise RuntimeError("failed to compile Fortran code:\n" +
log_string)
if self.verbose:
print(log_string)
m = __builtin__.__import__(name)
finally:
os.sys.path = old_import_path
os.chdir(old_cwd)
try:
import shutil
shutil.rmtree(mytmpdir)
except OSError:
# This can fail for example over NFS
pass
for k, x in m.__dict__.iteritems():
if k[0] != '_':
self.globals[k] = x
def eval(self, x, globals=None, locals=None):
"""
Compile fortran code ``x`` and adds the functions in it to
``globals``.
INPUT:
- ``x`` -- Fortran code
- ``globals`` -- a dict to which to add the functions from the
fortran module
- ``locals`` -- ignored
EXAMPLES::
sage: code = '''
....: C FILE: FIB1.F
....: SUBROUTINE FIB(A,N)
....: C
....: C CALCULATE FIRST N FIBONACCI NUMBERS
....: C
....: INTEGER N
....: REAL*8 A(N)
....: DO I=1,N
....: IF (I.EQ.1) THEN
....: A(I) = 0.0D0
....: ELSEIF (I.EQ.2) THEN
....: A(I) = 1.0D0
....: ELSE
....: A(I) = A(I-1) + A(I-2)
....: ENDIF
....: ENDDO
....: END
....: C END FILE FIB1.F
....: '''
sage: fortran(code, globals())
sage: import numpy
sage: a = numpy.array(range(10), dtype=float)
sage: fib(a, 10)
sage: a
array([ 0., 1., 1., 2., 3., 5., 8., 13., 21., 34.])
TESTS::
sage: os.chdir(DOT_SAGE)
sage: fortran.eval("SYNTAX ERROR !@#$")
Traceback (most recent call last):
...
RuntimeError: failed to compile Fortran code:...
sage: os.getcwd() == os.path.realpath(DOT_SAGE)
True
"""
if globals is None:
globals = self.globs
if globals is None:
from sage.repl.user_globals import get_globals
globals = get_globals()
# Create everything in a temporary directory
mytmpdir = tmp_dir()
try:
old_cwd = os.getcwd()
os.chdir(mytmpdir)
name = "fortran_module" # Python module name
# if the first line has !f90 as a comment, gfortran will
# treat it as Fortran 90 code
if x.startswith('!f90'):
fortran_file = name + '.f90'
else:
fortran_file = name + '.f'
s_lib_path = ['-L' + p for p in self.library_paths]
s_lib = ['-l' + l for l in self.libraries]
with open(fortran_file, 'w') as fobj:
fobj.write(x)
# This is basically the same as what f2py.compile() does, but we
# do it manually here in order to customize running the subprocess
# a bit more (in particular to capture stderr)
cmd = [
sys.executable, '-c', 'import numpy.f2py; numpy.f2py.main()'
]
# What follows are the arguments to f2py itself (appended later
# just for logical separation)
cmd += [
'-c', '-m', name, fortran_file, '--quiet',
'--f77exec=sage-inline-fortran',
'--f90exec=sage-inline-fortran'
] + s_lib_path + s_lib
try:
out = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
except subprocess.CalledProcessError as exc:
raise RuntimeError(
"failed to compile Fortran code:\n{}".format(exc.output))
# Note that f2py() doesn't raise an exception if it fails.
# In that case, the import below will fail.
try:
mod = _import_module_from_path(name, [mytmpdir])
except ImportError as exc:
# Failed to import the module; include any output from building
# the module (even though it was ostensibly successful) in case
# it might help
msg = "failed to load compiled Fortran code: {}".format(exc)
if out:
msg += '\n' + out
raise RuntimeError(msg)
if self.verbose:
print(out)
finally:
os.chdir(old_cwd)
if sys.platform != 'cygwin':
# Do not delete temporary DLLs on Cygwin; this will cause
# future forks of this process to fail. Instead temporary DLLs
# will be cleaned up upon process exit
try:
shutil.rmtree(mytmpdir)
except OSError:
# This can fail for example over NFS
pass
for k, x in mod.__dict__.items():
if k[0] != '_':
globals[k] = x
def run_val_gdb(self, testing=False):
"""
Spawns a subprocess to run tests under the control of gdb or valgrind.
INPUT:
- ``testing`` -- boolean; if True then the command to be run
will be printed rather than a subprocess started.
EXAMPLES:
Note that the command lines include unexpanded environment
variables. It is safer to let the shell expand them than to
expand them here and risk insufficient quoting. ::
sage: from sage.doctest.control import DocTestDefaults, DocTestController
sage: DD = DocTestDefaults(gdb=True)
sage: DC = DocTestController(DD, ["hello_world.py"])
sage: DC.run_val_gdb(testing=True)
exec gdb -x "$SAGE_LOCAL/bin/sage-gdb-commands" --args python "$SAGE_LOCAL/bin/sage-runtests" --serial --timeout=0 hello_world.py
::
sage: DD = DocTestDefaults(valgrind=True, optional="all", timeout=172800)
sage: DC = DocTestController(DD, ["hello_world.py"])
sage: DC.run_val_gdb(testing=True)
exec valgrind --tool=memcheck --leak-resolution=high --leak-check=full --num-callers=25 --suppressions="$SAGE_EXTCODE/valgrind/pyalloc.supp" --suppressions="$SAGE_EXTCODE/valgrind/sage.supp" --suppressions="$SAGE_EXTCODE/valgrind/sage-additional.supp" --log-file=".../valgrind/sage-memcheck.%p" python "$SAGE_LOCAL/bin/sage-runtests" --serial --timeout=172800 --optional=all hello_world.py
"""
try:
sage_cmd = self._assemble_cmd()
except ValueError:
self.log(sys.exc_info()[1])
return 2
opt = self.options
if opt.gdb:
cmd = '''exec gdb -x "$SAGE_LOCAL/bin/sage-gdb-commands" --args '''
flags = ""
if opt.logfile:
sage_cmd += " --logfile %s"%(opt.logfile)
else:
if opt.logfile is None:
default_log = os.path.join(DOT_SAGE, "valgrind")
if os.path.exists(default_log):
if not os.path.isdir(default_log):
self.log("%s must be a directory"%default_log)
return 2
else:
os.makedirs(default_log)
logfile = os.path.join(default_log, "sage-%s")
else:
logfile = opt.logfile
if opt.valgrind:
toolname = "memcheck"
flags = os.getenv("SAGE_MEMCHECK_FLAGS")
if flags is None:
flags = "--leak-resolution=high --leak-check=full --num-callers=25 "
flags += '''--suppressions="%s" '''%(os.path.join("$SAGE_EXTCODE","valgrind","pyalloc.supp"))
flags += '''--suppressions="%s" '''%(os.path.join("$SAGE_EXTCODE","valgrind","sage.supp"))
flags += '''--suppressions="%s" '''%(os.path.join("$SAGE_EXTCODE","valgrind","sage-additional.supp"))
elif opt.massif:
toolname = "massif"
flags = os.getenv("SAGE_MASSIF_FLAGS", "--depth=6 ")
elif opt.cachegrind:
toolname = "cachegrind"
flags = os.getenv("SAGE_CACHEGRIND_FLAGS", "")
elif opt.omega:
toolname = "exp-omega"
flags = os.getenv("SAGE_OMEGA_FLAGS", "")
cmd = "exec valgrind --tool=%s "%(toolname)
flags += ''' --log-file="%s" ''' % logfile
if opt.omega:
toolname = "omega"
if "%s" in flags:
flags %= toolname + ".%p" # replace %s with toolname
cmd += flags + sage_cmd
sys.stdout.flush()
sys.stderr.flush()
self.log(cmd)
if testing:
return
# Setup signal handlers.
# Save crash logs in temporary directory.
os.putenv('CYSIGNALS_CRASH_LOGS', tmp_dir("crash_logs_"))
init_cysignals()
import signal, subprocess
p = subprocess.Popen(cmd, shell=True)
if opt.timeout > 0:
signal.alarm(opt.timeout)
try:
return p.wait()
except AlarmInterrupt:
self.log(" Timed out")
return 4
except KeyboardInterrupt:
self.log(" Interrupted")
return 128
finally:
signal.alarm(0)
if p.returncode is None:
p.terminate()
def __call__(self, f, inputs):
"""
Parallel iterator using ``fork()``.
INPUT:
- ``f`` -- a function (or more general, any callable)
- ``inputs`` -- a list of pairs ``(args, kwds)`` to be used as
arguments to ``f``, where ``args`` is a tuple and ``kwds`` is
a dictionary.
OUTPUT:
EXAMPLES::
sage: F = sage.parallel.use_fork.p_iter_fork(2,3)
sage: sorted(list( F( (lambda x: x^2), [([10],{}), ([20],{})])))
[(([10], {}), 100), (([20], {}), 400)]
sage: sorted(list( F( (lambda x, y: x^2+y), [([10],{'y':1}), ([20],{'y':2})])))
[(([10], {'y': 1}), 101), (([20], {'y': 2}), 402)]
TESTS:
The output of functions decorated with :func:`parallel` is read
as a pickle by the parent process. We intentionally break the
unpickling and demonstrate that this failure is handled
gracefully (the exception is put in the list instead of the
answer)::
sage: Polygen = parallel(polygen)
sage: list(Polygen([QQ]))
[(((Rational Field,), {}), x)]
sage: from sage.structure.sage_object import unpickle_override, register_unpickle_override
sage: register_unpickle_override('sage.rings.polynomial.polynomial_rational_flint', 'Polynomial_rational_flint', Integer)
sage: L = list(Polygen([QQ]))
sage: L
[(((Rational Field,), {}),
'INVALID DATA __init__() takes at most 2 positional arguments (4 given)')]
Fix the unpickling::
sage: del unpickle_override[('sage.rings.polynomial.polynomial_rational_flint', 'Polynomial_rational_flint')]
sage: list(Polygen([QQ,QQ]))
[(((Rational Field,), {}), x), (((Rational Field,), {}), x)]
"""
n = self.ncpus
v = list(inputs)
import os, sys, signal
from sage.structure.sage_object import loads
from sage.misc.temporary_file import tmp_dir
dir = tmp_dir()
timeout = self.timeout
workers = {}
try:
while len(v) > 0 or len(workers) > 0:
# Spawn up to n subprocesses
while len(v) > 0 and len(workers) < n:
v0 = v.pop(0) # Input value for the next subprocess
with ContainChildren():
pid = os.fork()
# The way fork works is that pid returns the
# nonzero pid of the subprocess for the master
# process and returns 0 for the subprocess.
if not pid:
# This is the subprocess.
self._subprocess(f, dir, *v0)
workers[pid] = WorkerData(v0)
if len(workers) > 0:
# Now wait for one subprocess to finish and report the result.
# However, wait at most the time since the oldest process started.
T = walltime()
if timeout:
oldest = min(W.starttime for W in workers.values())
alarm(max(timeout - (T - oldest), 0.1))
try:
pid = os.wait()[0]
cancel_alarm()
W = workers.pop(pid)
except AlarmInterrupt:
# Kill workers that are too old
for pid, W in workers.items():
if T - W.starttime > timeout:
if self.verbose:
print(
"Killing subprocess %s with input %s which took too long"
% (pid, W.input) )
os.kill(pid, signal.SIGKILL)
W.failure = " (timed out)"
except KeyError:
# Some other process exited, not our problem...
pass
else:
# collect data from process that successfully terminated
sobj = os.path.join(dir, '%s.sobj'%pid)
try:
with open(sobj) as file:
data = file.read()
except IOError:
answer = "NO DATA" + W.failure
else:
os.unlink(sobj)
try:
answer = loads(data, compress=False)
except Exception as E:
answer = "INVALID DATA {}".format(E)
out = os.path.join(dir, '%s.out'%pid)
try:
with open(out) as file:
sys.stdout.write(file.read())
os.unlink(out)
except IOError:
pass
yield (W.input, answer)
finally:
# Send SIGKILL signal to workers that are left.
if workers:
if self.verbose:
print("Killing any remaining workers...")
sys.stdout.flush()
for pid in workers:
try:
os.kill(pid, signal.SIGKILL)
except OSError:
# If kill() failed, it is most likely because
# the process already exited.
pass
else:
try:
os.waitpid(pid, 0)
except OSError as msg:
if self.verbose:
print(msg)
# Clean up all temporary files.
rmtree(dir)
