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Commit fa1c55ed authored by Theresa Pollinger's avatar Theresa Pollinger
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exastencils working for any unknown name

parent 7af43381
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interview_kernel/example_interview.ipynb
View file @ fa1c55ed
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interview_kernel/exaoutput.py
View file @ fa1c55ed
......@@ -27,6 +27,9 @@ class ExaOutput:
if probname is None:
self.probname = self.username
else:
self.probname = probname
#output parameters which should also be made adaptable at some point
self.platform = OrderedDict([
("targetOS", "Linux"),
......@@ -73,8 +76,10 @@ class ExaOutput:
l1path = str(self.filespath.with_suffix('.exa1'))
domain_name = utf8tolatex(simdata["domain"]["name"], non_ascii_only=True, brackets=False)
op = utf8tolatex(simdata["pdes"]["pdes"][-1]["op"], non_ascii_only=True, brackets=False)
bcrhs = self.replace_boundary_x(simdata["bcs"]["bcs"][-1]["rhsstring_expanded"]) #TODO expand
pderhs = simdata["pdes"]["pdes"][-1]["rhsstring_expanded"]
bc_rhs = self.replace_boundary_x(simdata["bcs"]["bcs"][-1]["rhsstring_expanded"]) #TODO expand
pde_rhs = simdata["pdes"]["pdes"][-1]["rhsstring_expanded"]
unknowns = [*simdata["unknowns"]]
first_unknown = unknowns[0]
with open(l1path, 'w') as l1:
l1.write(
"/// inline knowledge \n"
......@@ -89,33 +94,33 @@ class ExaOutput:
" \n"
"Domain \Omega = ( " + str(simdata["domain"]["from"]) + ", " + str(simdata["domain"]["to"]) + " ) \n"
" \n"
"Field f@finest \in \Omega = " + pderhs + " \n"
"Field u \in \Omega = 0.0 \n"
"Field f@finest \in \Omega = " + pde_rhs + " \n"
"Field " + first_unknown + " \in \Omega = 0.0 \n"
" \n"
"Field u@finest \in \partial \Omega = " + bcrhs + " \n" #"sin ( 0.5 * PI * vf_boundaryCoord_x ) \n" #TODO expand
"Field u@(all but finest) \in \partial \Omega = 0.0 \n"
"Field " + first_unknown + "@finest \in \partial \Omega = " + bc_rhs + " \n" #"sin ( 0.5 * PI * vf_boundaryCoord_x ) \n" #TODO expand
"Field " + first_unknown + "@(all but finest) \in \partial \Omega = 0.0 \n"
" \n"
"Operator op = " + op + " // alt: - \partial_{xx} \n"
" \n"
"Equation uEq@finest op * u == f \n" #insert pde
"Equation uEq@(all but finest) op * u == 0.0 \n"
"Equation " + first_unknown + "Eq@finest op * " + first_unknown + " == f \n" #insert pde
"Equation " + first_unknown + "Eq@(all but finest) op * " + first_unknown + " == 0.0 \n"
" \n"
"/// configuration of inter-layer transformations \n"
" \n"
"DiscretizationHints { // alt: Discretize, L2Hint(s) \n"
" f on Node \n"
" u on Node \n"
" " + first_unknown + " on Node \n"
" \n"
" op on \Omega \n"
" \n"
" uEq \n"
" " + first_unknown + "Eq \n"
" \n"
" // paramters \n"
" discr_type = \"" + simdata["sim"]["type"] + "\" \n"
"} \n"
" \n"
"SolverHints { // alt: Solve, L3Hint(s) \n"
" generate solver for u in uEq \n"
" generate solver for " + first_unknown + " in " + first_unknown + "Eq \n"
" \n"
" // parameters \n"
" solver_targetResReduction = 1e-6 \n"
......@@ -124,7 +129,7 @@ class ExaOutput:
"ApplicationHints { // alt L4Hint(s) \n"
" // parameters \n"
" l4_genDefaultApplication = true \n"
" l4_defAppl_FieldToPrint = \"u\" \n" #TODO
" l4_defAppl_FieldToPrint = \"" + unknowns[0] + "\" \n" #TODO
"} \n"
)
......@@ -258,12 +263,12 @@ class ExaRunner:
print(out)
@lru_cache()
def load_data(self, data_name="u"): #TODO name of unknowns
def load_data(self, data_name="u"): # TODO more dimensions
import pandas as pd
data_path = self.exaout.exastencils_path.joinpath("generated").joinpath(self.exaout.probname).joinpath(data_name).with_suffix(".dat")
df = pd.read_csv(data_path, sep=' ', index_col=0)
try:
df.columns = ['u']
df.columns = [data_name]
except ValueError: # length mismatch because additional column of nans was read
df.columns = ['u', 'nan']
df.columns = [data_name, 'nan']
return df
interview_kernel/interview_kernel.py
View file @ fa1c55ed
......@@ -210,50 +210,52 @@ class Interview(MetaKernel):
def display_html(self, code=None):
# highlight some of the code entered and show line numbers (just to play around)
self.Display(HTML("""
<style type="text/css">
.styled-background { background-color: #ff7; }
</style>
<script>
if (typeof markedText !== 'undefined') {
markedText.clear();
}
IPython.notebook.select_prev()
var cell = IPython.notebook.get_selected_cell();
markedText = cell.code_mirror.markText({line: %s, col: %s},
{line: %s, col: %s},
{className: "styled-background"});
cell.show_line_numbers(1)
IPython.notebook.select_next()
</script>
""" % (1, 0, 3, 0)))
#self.Display(HTML("""
#<style type="text/css">
# .styled-background { background-color: #ff7; }
#</style>
#<script>
#if (typeof markedText !== 'undefined') {
# markedText.clear();
#}
#IPython.notebook.select_prev()
#var cell = IPython.notebook.get_selected_cell();
#markedText = cell.code_mirror.markText({line: %s, col: %s},
# {line: %s, col: %s},
# {className: "styled-background"});
#cell.show_line_numbers(1)
#IPython.notebook.select_next()
#</script>
# """ % (1, 0, 3, 0)))
output_notebook()
if code:
self.Display(HTML(code))
def display_tgview(self, args=''):
"""displays the theory graph viewer as html, cf. https://github.com/UniFormal/TGView/wiki/"""
args = args.replace("tgview ", '', 1).strip()
server_url = str(self.state_machine.mmtinterface.serverInstance)
args_dict = {
url_args_dict = {
"type": "thgraph",
}
args = args.replace("tgview ", '', 1).strip()
if args == '':
args_dict["graphdata"] = self.state_machine.mmtinterface.URIprefix + \
self.state_machine.mmtinterface.namespace + "?u"
url_args_dict["graphdata"] = self.state_machine.mmtinterface.URIprefix + \
self.state_machine.mmtinterface.namespace
else:
args_dict["graphdata"] = self.state_machine.mmtinterface.URIprefix + \
url_args_dict["graphdata"] = self.state_machine.mmtinterface.URIprefix + \
self.state_machine.mmtinterface.namespace + "?" + args
# if applicable, highlight the ephemeral parts https://github.com/UniFormal/TGView/issues/25
thynames = get_recursively(self.state_machine.simdata, "theoryname")
if thynames:
args_dict["highlight"] = ",".join(thynames)
url_args_dict["highlight"] = ",".join(thynames)
tgview_url = build_url(server_url, "graphs/tgview.html", args_dict=args_dict)
tgview_url = build_url(server_url, "graphs/tgview.html", args_dict=url_args_dict)
code = """
<iframe
......
interview_kernel/mmtinterface.py
View file @ fa1c55ed
......@@ -23,11 +23,10 @@ from lxml import etree
def start_mmt_server(port_number, mmtjar):
p = subprocess.run(["/usr/bin/java", "-jar", mmtjar, # "--file=server-interview.msl",
"server", "on", str(port_number),
"--keepalive"],
"server", "on", str(port_number), "--keepalive"],
stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
out = p.stdout
if p.returncode != 0 and p.returncode != 130:
if p.returncode != 0 and p.returncode != 130: # if not closed gracefully or through ctrl-c
raise MMTServerError("Server aborted, return code " + str(p.returncode) + ", " + str(out))
......@@ -38,8 +37,8 @@ def exit_mmt_server(port_number, mmtjar, timeout=3.0):
if completed.stdout != None and "(Connection refused)" in str(completed.stdout):
if timeout > 0.0:
exit_mmt_server(port_number, mmtjar, timeout - 0.1)
else:
raise MMTServerError("unable to exit mmt server")
# else:
# raise MMTServerError("unable to exit mmt server")
def start_mmt_extension(port_number, mmtjar, timeout=3.0):
......@@ -194,6 +193,9 @@ class MMTInterface:
def __exit__(self, exc_type, exc_val, exc_tb):
self.exit_mmt()
def __del__(self):
self.exit_mmt()
def exit_mmt(self):
exit_mmt_server(self.port_number, self.mmt_jar)
......
interview_kernel/pde_state_machine.py
View file @ fa1c55ed
......@@ -131,16 +131,16 @@ class PDE_States:
])
# to include all the necessary theories every time
self.bgthys = OrderedDict([
('domain', ["mInterval", "http://mathhub.info/MitM/smglom/arithmetics?realarith"]),
('domain', ["mInterval", "http://mathhub.info/MitM/smglom/arithmetics?RealArithmetics"]),
# new: RealArithmetics
('unknowns', ["http://mathhub.info/MitM/Foundation?Strings", "ephdomain",
"http://mathhub.info/MitM/smglom/calculus?higherderivative"]),
('parameters', ["http://mathhub.info/MitM/smglom/arithmetics?realarith", "ephdomain",
('unknowns', ["http://mathhub.info/MitM/Foundation?Strings", "ephdomain"]),
#"http://mathhub.info/MitM/smglom/calculus?higherderivative"]),
('parameters', ["http://mathhub.info/MitM/smglom/arithmetics?RealArithmetics", "ephdomain",
"http://mathhub.info/MitM/Foundation?Math"]),
('pdes', ["mDifferentialOperators"]), # +params, unknowns,
('bcs',
["ephdomain", "mLinearity",
"http://mathhub.info/MitM/smglom/arithmetics?realarith"]), # +params, unknowns, pdes, bctypes
"http://mathhub.info/MitM/smglom/arithmetics?RealArithmetics"]), # +params, unknowns, pdes, bctypes
('props',
["mLinearity",
"http://mathhub.info/MitM/Foundation?Strings"]), # +bcs, pde
......@@ -277,6 +277,8 @@ class PDE_States:
'sim': {},
}
self.exaout = None
self.mmtinterface = MMTInterface()
#with MMTInterface() as self.mmtinterface:
"""Variables to signal callbacks depending on yes/no prompts"""
......@@ -304,7 +306,7 @@ class PDE_States:
self.poutput("")
self.poutput("To get explanations, enter \"explain <optional keyword>\". ")
self.poutput("To see a recap of what we know so far, enter \"recap <optional keyword>\". ")
self.poutput("To interact with the current theory graph, enter \"tgwiev <optional theory name>\". ")
self.poutput("To interactively visualize ther current theory graph, enter \"tgwiev <optional theory name>\". ")
self.poutput("Otherwise, you can always try and use LaTeX-type input.")
self.poutput("")
self.poutput("You can inspect the currently loaded MMT theories under " + self.mmtinterface.serverInstance)
......@@ -800,21 +802,23 @@ class PDE_States:
##### for state sim
def sim_begin(self):
self.please_prompt("Would you like to try and solve the PDE using the Finite Difference Method in ExaStencils?"
self.please_prompt("Would you like to try and solve the PDE using the Finite Difference Method in ExaStencils? "
"If yes, you can provide a configuration name, or we'll just use your name.",
self.sim_ok_fd)
if_yes=self.sim_ok_fd, if_no=None, pass_other=True)
def sim_handle_input(self, userstring):
self.please_prompt("Would you like to try and solve the PDE using the Finite Difference Method in ExaStencils?"
"If yes, you can provide a configuration name, or we'll just use your name.",
self.sim_ok_fd)
self.sim_exit(userstring)
def sim_exit(self):
def sim_ok_fd(self):
self.sim_exit()
def sim_exit(self, problem_name=None):
self.simdata["sim"]["type"] = "FiniteDifferences"
# generate output
exaout = ExaOutput(self.simdata)
self.exaout = ExaOutput(self.simdata, getpass.getuser(), problem_name)
print("Generated ExaStencils input; running ExaStencils")
# generate and run simulation
runner = ExaRunner(exaout)
runner = ExaRunner(self.exaout)
runner.run_exastencils()
print("Ran ExaStencils; preparing visualization")
# output
......@@ -824,18 +828,19 @@ class PDE_States:
# cf. nbviewer.jupyter.org/github/bokeh/bokeh-notebooks/blob/master/tutorial/01 - Basic Plotting.ipynb
def display_result_as_bokeh(self):
unknowns = [*self.simdata["unknowns"]]
# create a new plot with default tools, using figure
p = figure(plot_width=1000, plot_height=400)
runner = ExaRunner(ExaOutput())
data = runner.load_data("u")
#source = ColumnDataSource(data=data)
source = ColumnDataSource(data=dict(x=[], u=[]))
runner = ExaRunner(self.exaout)
data = runner.load_data(unknowns[0]) # TODO more dimensions
source = ColumnDataSource(data=data)
source.data = source.from_df(data)
source.add(data.index, 'index')
# add a circle renderer with a size, color, and alpha
p.circle(x='index', y='u', size=2, line_color="navy", fill_color="orange", fill_alpha=0.5, source=source)
p.circle(x='index', y=unknowns[0], size=2, line_color="navy", fill_color="orange", fill_alpha=0.5, source=source)
#show(p)
output_notebook()
......@@ -843,17 +848,11 @@ class PDE_States:
self.display_html(file_html(p, CDN, "my plot")) # show the results
# using JS requires jupyter widgets extension
#script, div = components(p)
#div = notebook_div(p)
#self.Display(Javascript(script + div)) # show the results
def sim_ok_fd(self):
self.simdata["sim"]["type"] = "FiniteDifferences"
self.sim_exit()
# script, div = components(p)
# div = notebook_div(p)
# self.Display(Javascript(script + div)) # show the results
#### functions for user interaction
# functions for user interaction
def obviously_stupid_input(self):
self.poutput("Trying to be funny, huh?")
......
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