Migrate and remove test/apps submodule

We decided to merge the sample app integrations submodule back because
working with git submodules turned out to be really painful. The only
blocker for this was the fact, that previously it contained a lot of
binary blobs and copy-pasted sources, but this was cleaned up recently.

Credits: (authors of particular integration examples, extracted from
commits and PR history in https://github.com/oscarlab/graphene-tests)

apache:     Chia-Che Tsai <chiache@tamu.edu>, Dmitrii Kuvaiskii <dmitrii.kuvaiskii@intel.com>
bash:       Chia-Che Tsai <chiache@tamu.edu>, Dmitrii Kuvaiskii <dmitrii.kuvaiskii@intel.com>
blender:    borysp <borysp@invisiblethingslab.com>
busybox:    borysp <borysp@invisiblethingslab.com>
capnproto:  Dmitrii Kuvaiskii <dmitrii.kuvaiskii@intel.com>
curl:       Dmitrii Kuvaiskii <dmitrii.kuvaiskii@intel.com>
gcc:        Thomas Knauth <thomas.knauth@intel.com>
lighttpd:   Chia-Che Tsai <chiache@tamu.edu>, Thomas Knauth <thomas.knauth@intel.com>
lmbench:    Chia-Che Tsai <chiache@tamu.edu>
memcached:  Dmitrii Kuvaiskii <dmitrii.kuvaiskii@intel.com>
nginx:      Dmitrii Kuvaiskii <dmitrii.kuvaiskii@intel.com>
nodejs:     jack.wxz <jack.wxz@alibaba-inc.com>
nodejs-express-server: Eduardo Rodriguez <erodrig@us.ibm.com>
openvino:   Dmitrii Kuvaiskii <dmitrii.kuvaiskii@intel.com>
python-scipy-insecure: Chia-Che Tsai <chiache@tamu.edu>, Dmitrii Kuvaiskii <dmitrii.kuvaiskii@intel.com>
python-simple:         Chia-Che Tsai <chiache@tamu.edu>, Dmitrii Kuvaiskii <dmitrii.kuvaiskii@intel.com>
pytorch:    Thomas Knauth <thomas.knauth@intel.com>
r:          Chia-Che Tsai <chiache@tamu.edu>
redis:      Dmitrii Kuvaiskii <dmitrii.kuvaiskii@intel.com>
tensorflow: Thomas Knauth <thomas.knauth@intel.com>

LTP was moved to LibOS/shim/test/ltp. It was recently rewritten by
Wojtek Porczyk <woju@invisiblethingslab.com>.

Examples/python-simple/scripts/benchrun.py

@@ -0,0 +1,116 @@
+"""
+Downloaded from https://code.google.com/p/benchrun/
+
+A benchmark is defined by creating a subclass of Benchmark.
+The subclass should define a method run() that executes the code
+to be timed and returns the elapsed time in seconds (as a float),
+or None if the benchmark should be skipped.
+
+See fibonacci.py for example.
+"""
+
+import sys
+if sys.platform == 'win32':
+    from time import clock
+else:
+    from time import time as clock
+
+# http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/302478
+def combinations(*seqin):
+    def rloop(seqin,comb):
+        if seqin:
+            for item in seqin[0]:
+                newcomb = comb + [item]
+                for item in rloop(seqin[1:],newcomb):   
+                    yield item
+        else:
+            yield comb
+    return rloop(seqin,[])
+
+
+class Benchmark:
+    sort_by = []
+    reference = None
+
+    def __init__(self):
+        self.pnames = []
+        self.pvalues = []
+        self.results = []
+        self.results_dict = {}
+        for pname in self.parameters:
+            value = getattr(self, pname)
+            self.pnames.append(pname)
+            self.pvalues.append(value)
+        self.pcombos = list(combinations(*self.pvalues))
+        if self.reference:
+            self.reference_param = self.reference[0]
+            self.reference_value = self.reference[1]
+
+    def time_all(self):
+        """Run benchmark for all versions and parameters."""
+        for params in self.pcombos:
+            args = dict(zip(self.pnames, params))
+            t = self.run(**args)
+            self.results.append(tuple(params) + (t,))
+            self.results_dict[tuple(params)] = t
+
+    def sort_results(self):
+        sort_keys = []
+        for name in self.sort_by:
+            sort_keys += [self.pnames.index(name)]
+        for i, name in enumerate(self.pnames):
+            if i not in sort_keys:
+                sort_keys += [i]
+        def key(v):
+            return list(v[i] for i in sort_keys)
+        self.results.sort(key=key)
+
+    def get_factor(self, pvalues, time):
+        if not self.reference or not time:
+            return None
+        pvalues = list(pvalues)
+        i = self.pnames.index(self.reference_param)
+        if pvalues[i] == self.reference_value:
+            return None
+        else:
+            pvalues[i] = self.reference_value
+        ref = self.results_dict[tuple(pvalues)]
+        if ref == None:
+            return None
+        return ref / time
+
+    def print_result(self):
+        """Run benchmark for all versions and parameters and print results
+        in tabular form to the standard output."""
+        self.time_all()
+        self.sort_results()
+
+        print("=" * 78)
+        print()
+        print(self.__class__.__name__)
+        print(self.__doc__ + "\n")
+
+        colwidth = 15
+        reftimes = {}
+
+        ts = "seconds"
+        if self.reference:
+            ts += " (x faster than " + (str(self.reference_value)) + ")"
+        print("  " + "   ".join([str(r).ljust(colwidth) for r in self.pnames + [ts]]))
+        print("-" * 79)
+
+        rows = []
+        for vals in self.results:
+            pvalues =  vals[:-1]
+            time = vals[-1]
+            if time == None:
+                stime = "(n/a)"
+            else:
+                stime = "%.8f" % time
+                factor = self.get_factor(pvalues, time)
+                if factor != None:
+                    stime += ("  (%.2f)" % factor)
+            vals = pvalues + (stime,)
+            row = [str(val).ljust(colwidth) for val in vals]
+            print("  " + "   ".join(row))
+        print()

Examples/python-simple/scripts/dummy-web-server.py

@@ -0,0 +1,54 @@
+#!/usr/bin/env python3
+
+"""
+Very simple HTTP server in python.
+Downloaded from: https://gist.github.com/bradmontgomery/2219997
+
+Usage::
+    ./dummy-web-server.py [<port>]
+
+Send a GET request::
+    curl http://localhost
+
+Send a HEAD request::
+    curl -I http://localhost
+
+Send a POST request::
+    curl -d "foo=bar&bin=baz" http://localhost
+
+"""
+
+from http.server import BaseHTTPRequestHandler, HTTPServer
+import socketserver
+
+class S(BaseHTTPRequestHandler):
+    def _set_headers(self):
+        self.send_response(200)
+        self.send_header('Content-type', 'text/html')
+        self.end_headers()
+
+    def do_GET(self):
+        self._set_headers()
+        self.wfile.write("<html><body><h1>hi!</h1></body></html>".encode())
+
+    def do_HEAD(self):
+        self._set_headers()
+
+    def do_POST(self):
+        # Doesn't do anything with posted data
+        self._set_headers()
+        self.wfile.write("<html><body><h1>POST!</h1></body></html>".encode())
+
+def run(server_class=HTTPServer, handler_class=S, port=80):
+    server_address = ('', port)
+    httpd = server_class(server_address, handler_class)
+    print('Starting httpd...')
+    httpd.serve_forever()
+
+if __name__ == "__main__":
+    from sys import argv
+
+    if len(argv) == 2:
+        run(port=int(argv[1]))
+    else:
+        run()

Examples/python-simple/scripts/fibonacci.py

@@ -0,0 +1,54 @@
+"""
+Downloaded from https://code.google.com/p/benchrun/
+
+Fibonacci numbers test benchmark
+"""
+
+from benchrun import Benchmark, clock
+
+def fib1(n):
+    if n < 2:
+        return n
+    return fib1(n-1) + fib1(n-2)
+
+def fib2(n):
+    if n < 2:
+        return n
+    a, b = 1, 0
+    for i in range(n-1):
+        a, b = a+b, a
+    return a
+
+class FibonacciBenchmark(Benchmark):
+    """Compare time to compute the nth Fibonacci number recursively
+    (fib1) and iteratively (fib2)."""
+
+    # Execute for all combinations of these parameters
+    parameters = ['version', 'n']
+    version = ['fib1', 'fib2']
+    n = range(0, 60, 5)
+
+    # Compare timings against this parameter value
+    reference = ('version', 'fib1')
+
+    def run(self, n, version):
+        f = globals()[version]
+        # Don't repeat when slow
+        if version == 'fib1' and n > 10:
+            # Skip altogether
+            if n > 30:
+                return None
+            t1 = clock()
+            f(n)
+            t2 = clock()
+            return t2-t1
+        # Need to repeat many times to get accurate timings for small n
+        else:
+            t1 = clock()
+            f(n); f(n); f(n); f(n); f(n); f(n); f(n)
+            f(n); f(n); f(n); f(n); f(n); f(n); f(n)
+            t2 = clock()
+            return (t2 - t1) / 14
+
+if __name__ == '__main__':
+    FibonacciBenchmark().print_result()

Examples/python-simple/scripts/helloworld.py

@@ -0,0 +1,3 @@
+#!/usr/bin/env python3
+
+print("Hello World")

Examples/python-simple/scripts/test-http.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+
+import sys
+import urllib.request
+
+request = urllib.request.Request("http://" + sys.argv[1] + ":" + sys.argv[2] + "/index.html")
+opener = urllib.request.build_opener()
+response = opener.open(request, timeout=10)
+while True:
+    data = response.read(1024)
+    if data:
+        print(data.decode())
+    else:
+        break