Mossaiby 2009a - Revision history

Cinmemj: Cinmemj moved page Draft Samper 671502359 to Mossaiby 2009a

2018-04-09T14:47:35Z

Cinmemj moved page Draft Samper 671502359 to Mossaiby 2009a

Cinmemj at 14:47, 9 April 2018

2018-04-09T14:47:06Z

Cinmemj at 14:46, 9 April 2018

2018-04-09T14:46:06Z

Cinmemj at 14:38, 9 April 2018

2018-04-09T14:38:50Z

Cinmemj at 14:25, 9 April 2018

2018-04-09T14:25:48Z

Cinmemj at 14:22, 9 April 2018

2018-04-09T14:22:19Z

Cinmemj at 13:50, 9 April 2018

2018-04-09T13:50:08Z

Cinmemj at 13:42, 9 April 2018

2018-04-09T13:42:57Z

Cinmemj at 13:41, 9 April 2018

2018-04-09T13:41:50Z

Cinmemj at 13:38, 9 April 2018

2018-04-09T13:38:21Z

← Older revision		Revision as of 14:47, 9 April 2018
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−
−	~~==Implementation of an Automated Benchmarking module for Kratos==~~
−
−	~~'''F. Mossaiby'''~~
−
−
−	~~===Contents===~~
−
−	~~1. Introduction<br />~~
−	~~2. Features<br />~~
−	~~3. Implementation Details<br />~~
−	~~4. Adding automatic benchmarking capability to existing test examples<br />~~
−	~~5. References~~
−

	==Introduction==		==Introduction==

@@ Line 129: / Line 129: @@
 Integrating automatic benchmarking capability in existing test examples is very simple. One needs to add lines marked in '''bold''' to his / her code first:
-<span style="text-align: center; font-size: 75%;">##################################################################</span>
+<pre>
-<span style="text-align: center; font-size: 75%;">##################################################################</span>
+#including kratos path
-<span style="text-align: center; font-size: 75%;">## ATTENTION: here the order is important</span>
+import sys
-<span style="text-align: center; font-size: 75%;">#including kratos path</span>
+#importing Kratos main library
-<span style="text-align: center; font-size: 75%;">kratos_libs_path = '../../../../libs' ##kratos_root/libs</span>
+#importing applications
-<span style="text-align: center; font-size: 75%;">kratos_applications_path = '../../../../applications' ##kratos_root/applications</span>
+import benchmarking
 ## from now on the order is not anymore crucial
-<span style="text-align: center; font-size: 75%;">'''kratos_benchmarking_path = '../../../../benchmarking' '''##kratos_root/benchmarking</span>
+##################################################################
+##################################################################</pre>
-<span style="text-align: center; font-size: 75%;">import sys</span>
-−
-<span style="text-align: center; font-size: 75%;">sys.path.append(kratos_libs_path)</span>
-−
-<span style="text-align: center; font-size: 75%;">sys.path.append(kratos_applications_path)</span>
-−
-<span style="text-align: center; font-size: 75%;">'''sys.path.append(kratos_benchmarking_path)'''</span>
-−
-<span style="text-align: center; font-size: 75%;">#importing Kratos main library</span>
-−
-<span style="text-align: center; font-size: 75%;">from Kratos import *</span>
-−
-<span style="text-align: center; font-size: 75%;">kernel = Kernel()   #defining kernel</span>
-−
-<span style="text-align: center; font-size: 75%;">#importing applications</span>
-−
-<span style="text-align: center; font-size: 75%;">import applications_interface</span>
-−
-<span style="text-align: center; font-size: 75%;">applications_interface.Import_IncompressibleFluidApplication = True</span>
-−
-<span style="text-align: center; font-size: 75%;">applications_interface.Import_PFEMApplication = True</span>
-−
-<span style="text-align: center; font-size: 75%;">applications_interface.ImportApplications(kernel, kratos_applications_path)</span>
-−
-<span style="text-align: center; font-size: 75%;">'''import benchmarking'''</span>
-−
-<span style="text-align: center; font-size: 75%;">## from now on the order is not anymore crucial</span>
-−
-<span style="text-align: center; font-size: 75%;">##################################################################</span>
-−
-<span style="text-align: center; font-size: 75%;">##################################################################</span>
 The next step would be selecting some key values in your problem which can almost reliably indicate the behavior of your code. This can be displacement or pressure of a given node, for example. To do this, you may first need to find the nodes using a helper function, like this:
-<span style="text-align: center; font-size: 75%;">    for node in node_list:</span>
+<pre>
+def FindNode(node_list, x, y, z):
-<span style="text-align: center; font-size: 75%;">        if ((node.X - x) ** 2 + (node.Y - y) ** 2 + (node.Z - z) ** 2 < 0.0000001):</span>
+    for node in node_list:
+        if ((node.X - x) ** 2 + (node.Y - y) ** 2 + (node.Z - z) ** 2 < 0.0000001):
-<span style="text-align: center; font-size: 75%;">            return node</span>
+          return node</pre>
 Also, a helper function that emits the value can be helpful:
-<span style="text-align: center; font-size: 75%;">def BenchmarkCheck(time, node1, node2):</span>
+<pre>
 def BenchmarkCheck(time, node1, node2):
-<span style="text-align: center; font-size: 75%;">benchmarking.Output(time, "Time")</span>
+    benchmarking.Output(time, "Time")
+    benchmarking.Output(node1.GetSolutionStepValue(PRESSURE), "Node 1 pressure", 1.0)</span>
-<span style="text-align: center; font-size: 75%;">benchmarking.Output(node1.GetSolutionStepValue(PRESSURE), "Node 1 pressure", 1.0)</span>
+    benchmarking.Output(node2.GetSolutionStepValue(PRESSURE), "Node 2 pressure", 1.0)</pre>
-−
-<span style="text-align: center; font-size: 75%;">benchmarking.Output(node2.GetSolutionStepValue(PRESSURE), "Node 2 pressure", 1.0)</span>
 In the main program, you first find the nodes, for example:
-<span style="text-align: center; font-size: 75%;">node_1 = FindNode(model_part.Nodes, 0.5, 0.0, 0.0)</span>
+<pre>
 node_1 = FindNode(model_part.Nodes, 0.5, 0.0, 0.0)
-<span style="text-align: center; font-size: 75%;">node_2 = FindNode(model_part.Nodes, 0.24, 0.0, 0.0)</span>
+node_2 = FindNode(model_part.Nodes, 0.24, 0.0, 0.0)</pre>
 And in the main loop you call the former function as:
-<span style="text-align: center; font-size: 75%;">BenchmarkCheck(time, node_1, node_2)</span>
+<pre>
-You may find more information about the usage of the automatic benchmarking module as well as other scripts provided / needs to be provided for automatic running of all benchmarks / building all reference data files in Kratos wiki [???].
+You may find more information about the usage of the automatic benchmarking module as well as other scripts provided / needs to be provided for automatic running of all benchmarks / building all reference data files in Kratos wiki.
 ==References==

@@ Line 122: / Line 122: @@
 This function is used to send an email with given subject and body text. It is used in the scripts provided for automatic running of all test examples, and reporting the status of each example. This function always sends the email from <span style="font-family: Monospace;">no-reply-[mailto:kratos-benchmarking@cimne.upc.es kratos-benchmarking@cimne.upc.es]</span>, and hence you might need to add this address to your address book / white list to avoid delivery of the emails to Bulk / Spam folder. The usage pattern is:
-<span style="font-family: Monospace;">benchmarking.NotifyViaEmail("Subject here!", "Body here!", [mailto:["user1@somewhere.net" ["user1@somewhere.net"],[mailto:"user2@nowhere.org"] "user2@nowhere.org"]]</span>
+<pre>
 ==Adding automatic benchmarking capability to existing test examples==

@@ Line 92: / Line 92: @@
-<nowiki>
+<pre>
-benchmarking.Output(i)</span>
+benchmarking.Output(i)
-<span style="text-align: center; font-size: 75%;">benchmarking.Output(i + j > 7)</span>
+In the first example, the value of <span style="font-family: Monospace;">i</span> has been emitted without any label or tolerances. In the second one, a boolean value has been emitted, again with no label. In the third one, the value of <span style="font-family: Monospace;">dt</span> has been emitted, specifying a label for it. And in the last one, the value of <span style="font-family: Monospace;">p</span> has been emitted, specifying a label, no absolute tolerance, but a relative tolerance of 5%.
-<span style="text-align: center; font-size: 75%;">benchmarking.Output(p, "Node 1 pressure", None, 0.05)
+<span style="font-family: Monospace;">StartTiming(), StopTiming():</span>
-</nowiki>
-−
-In the first example, the value of <span style="text-align: center; font-size: 75%;">i</span> has been emitted without any label or tolerances. In the second one, a boolean value has been emitted, again with no label. In the third one, the value of <span style="text-align: center; font-size: 75%;">dt</span> has been emitted, specifying a label for it. And in the last one, the value of <span style="text-align: center; font-size: 75%;">p</span> has been emitted, specifying a label, no absolute tolerance, but a relative tolerance of 5%.
-−
-<span style="text-align: center; font-size: 75%;">StartTiming(), StopTiming():</span>
 These functions together help you control the running time of portions of your code. These portions can be nested. Here also you can specify absolute and relative tolerance permitted. The usage is very simple:
-<span style="text-align: center; font-size: 75%;">t = benchmarking.StartTiming()</span>
+<pre>
 t = benchmarking.StartTiming()
-<span style="text-align: center; font-size: 75%;"> ...''the portion of the code to be checked...''</span>
+       ...the portion of the code to be checked...
 In the above example, no absolute tolerance specified, while a 5% relative tolerance allowed.
-<span style="text-align: center; font-size: 75%;">BuildReferenceData(), RunBenchmark():</span>
+<span style="font-family: Monospace;">BuildReferenceData(), RunBenchmark():</span>
-These two functions are only used in the scripts provided for automatic running of all benchmarks or automatic building of all reference data files. The usage is simple; just give name of the test example script, and the reference data file. The former function will run the example in benchmarking mode, storing emitted values in given reference data file, while the latter checks the emitted values against the given reference data file. Both functions assume that <span style="text-align: center; font-size: 75%;">python</span> and <span style="text-align: center; font-size: 75%;">grep</span> are available. Due to sensitivity of Kratos examples to the path they are called from, it is strongly recommended to change your working directory to the where the test examples reside, and then call the above functions.
+These two functions are only used in the scripts provided for automatic running of all benchmarks or automatic building of all reference data files. The usage is simple; just give name of the test example script, and the reference data file. The former function will run the example in benchmarking mode, storing emitted values in given reference data file, while the latter checks the emitted values against the given reference data file. Both functions assume that <span style="font-family: Monospace;">python</span> and <span style="font-family: Monospace;">grep</span> are available. Due to sensitivity of Kratos examples to the path they are called from, it is strongly recommended to change your working directory to the where the test examples reside, and then call the above functions.
-<span style="text-align: center; font-size: 75%;">NotifyViaEmail():</span>
+<span style="font-family: Monospace;">NotifyViaEmail():</span>
-This function is used to send an email with given subject and body text. It is used in the scripts provided for automatic running of all test examples, and reporting the status of each example. This function always sends the email from <span style="text-align: center; font-size: 75%;">no-reply-[mailto:kratos-benchmarking@cimne.upc.es kratos-benchmarking@cimne.upc.es]</span>, and hence you might need to add this address to your address book / white list to avoid delivery of the emails to Bulk / Spam folder. The usage pattern is:
+This function is used to send an email with given subject and body text. It is used in the scripts provided for automatic running of all test examples, and reporting the status of each example. This function always sends the email from <span style="font-family: Monospace;">no-reply-[mailto:kratos-benchmarking@cimne.upc.es kratos-benchmarking@cimne.upc.es]</span>, and hence you might need to add this address to your address book / white list to avoid delivery of the emails to Bulk / Spam folder. The usage pattern is:
-<span style="text-align: center; font-size: 75%;">benchmarking.NotifyViaEmail("Subject here!", "Body here!", [mailto:["user1@somewhere.net" ["user1@somewhere.net"],[mailto:"user2@nowhere.org"] "user2@nowhere.org"]]</span>
+<span style="font-family: Monospace;">benchmarking.NotifyViaEmail("Subject here!", "Body here!", [mailto:["user1@somewhere.net" ["user1@somewhere.net"],[mailto:"user2@nowhere.org"] "user2@nowhere.org"]]</span>
 ==Adding automatic benchmarking capability to existing test examples==

@@ Line 81: / Line 81: @@
 This function simply returns <span style="font-family: Monospace;">True</span> to indicate that the test example is being run in benchmarking mode. This can be helpful, if you only need to calculate some values for use in benchmarking only:
-<nowiki>
+<pre>
 if (benchmarking.InBenchmarkingMode()):
        ...calculate some results...
-       benchmarking.Output(...)</nowiki>
+       benchmarking.Output(...)</pre>

← Older revision	Revision as of 14:47, 9 April 2018
(No difference)

@@ Line 45: / Line 45: @@
 Table 1 lists the functions exposed by the automatic benchmarking module, along with a short description. These functions provide the interface between the module and the test examples. Also, some of these functions are used in scripts provided for automatic running of all test examples, automatic building of all reference data files or notifying the recipients from the status of the test examples. Here a brief usage example for these functions will be presenented.
 {| style="width: 100%;border-collapse: collapse;font-size:85%;"
@@ Line 52: / Line 53: @@
 |-
 |  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: left; font-family: Monospace;">InBenchmarkingMode()</span>
-|  style="border: 1pt solid black;vertical-align: top;"|Returns <code>True</code> if in benchmarking mode, False otherwise
+|  style="border: 1pt solid black;vertical-align: top;"|Returns <span style="font-family: Monospace;">True</span> if in benchmarking mode, False otherwise
 |-
-|  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: center; font-size: 75%;">Output(Var, Label = "", AbsErr = None, RelErr = None)</span>
+|  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: left; font-family: Monospace;">Output(Var, Label = "", AbsErr = None, RelErr = None)</span>
-|  style="border: 1pt solid black;vertical-align: top;"|Emits the value of <span style="text-align: center; font-size: 75%;">Var</span>, with a given label, absolute and relative error
+|  style="border: 1pt solid black;vertical-align: top;"|Emits the value of <span style="font-family: Monospace;">Var</span>, with a given label, absolute and relative error
 |-
-|  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: center; font-size: 75%;">StartTiming()</span>
+|  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: left; font-family: Monospace;">StartTiming()</span>
 |  style="border: 1pt solid black;vertical-align: top;"|Returns the current time
 |-
-|  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: center; font-size: 75%;">StopTiming(t, AbsDiff, RelDiff)</span>
+|  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: left; font-family: Monospace;">StopTiming(t, AbsDiff, RelDiff)</span>
-|  style="border: 1pt solid black;vertical-align: top;"|Emits the difference between the current time and t (returned previously by <span style="text-align: center; font-size: 75%;">StartTiming()</span>), specifying absolute and relative difference allowed
+|  style="border: 1pt solid black;vertical-align: top;"|Emits the difference between the current time and t (returned previously by <span style="font-family: Monospace;">StartTiming()</span>), specifying absolute and relative difference allowed
 |-
-|  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: center; font-size: 75%;">BuildReferenceData(ExamplePath, ReferenceFile)</span>
+|  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: left; font-family: Monospace;">>BuildReferenceData(ExamplePath, ReferenceFile)</span>
-|  style="border: 1pt solid black;vertical-align: top;"|Runs the test example given in <span style="text-align: center; font-size: 75%;">ExamplePath</span> in benchmarking mode, and stores the values emitted in <span style="text-align: center; font-size: 75%;">ReferenceFile</span>
+|  style="border: 1pt solid black;vertical-align: top;"|Runs the test example given in <span style="font-family: Monospace;">ExamplePath</span> in benchmarking mode, and stores the values emitted in <span style="font-family: Monospace;">ReferenceFile</span>
 |-
-|  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: center; font-size: 75%;">RunBenchmark(ExamplePath, ReferenceFile)</span>
+|  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: left; font-family: Monospace;">RunBenchmark(ExamplePath, ReferenceFile)</span>
-|  style="border: 1pt solid black;vertical-align: top;"|Runs the test example given in <span style="text-align: center; font-size: 75%;">ExamplePath</span> in benchmarking mode, and compares the values emitted with those in <span style="text-align: center; font-size: 75%;">ReferenceFile</span>, returns True if no difference encountered, or a message with some details on the difference found
+|  style="border: 1pt solid black;vertical-align: top;"|Runs the test example given in <span style="font-family: Monospace;">ExamplePath</span> in benchmarking mode, and compares the values emitted with those in <span style="font-family: Monospace;">ReferenceFile</span>, returns True if no difference encountered, or a message with some details on the difference found
 |-
-|  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: center; font-size: 75%;">NotifyViaEmail(Subject, Text, Recipients)</span>
+|  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: left; font-family: Monospace;">NotifyViaEmail(Subject, Text, Recipients)</span>
 |  style="border: 1pt solid black;vertical-align: top;"|Sends an email to the given list of recipients, with given subject and text
 |}
-<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">
+<div class="center" style="width: auto; margin-left: auto; margin-right: auto;font-size:75%;">
 '''Table 1''' Functions exposed by the automatic benchmarking module</div>
-<span style="text-align: center; font-size: 75%;">InBenchmarkingMode():</span>
+<span style="font-family: Monospace;">InBenchmarkingMode():</span>
-This function simply returns <span style="text-align: center; font-size: 75%;">True</span> to indicate that the test example is being run in benchmarking mode. This can be helpful, if you only need to calculate some values for use in benchmarking only:
+This function simply returns <span style="font-family: Monospace;">True</span> to indicate that the test example is being run in benchmarking mode. This can be helpful, if you only need to calculate some values for use in benchmarking only:
-<span style="text-align: center; font-size: 75%;">'''if''' (benchmarking.InBenchmarkingMode()):</span>
+<nowiki>
-<span style="text-align: center; font-size: 75%;">benchmarking.Output(...)</span>
+<span style="font-family: Monospace;">Output():</span>
-<span style="text-align: center; font-size: 75%;">Output():</span>
+This function is the mostly used part of the interface. It emits the value of <span style="font-family: Monospace;">Var</span> to the module. This value can be an integer or floating number, as well as a string or a boolean. You may optionally specify a label, which will help you when something goes wrong. You can also specify absolute or relative tolerance for numbers (integer of floting). These tolerances default to <span style="font-family: Monospace;">None</span>, which means they will not be checked. Please note that the relative tolerance is '''not''' in percents, and also you may not specify a relative tolerance for an exact value of zero. Here are some examples of usage of this function:
-<span style="text-align: center; font-size: 75%;">benchmarking.Output(i)</span>
+<nowiki>
 <span style="text-align: center; font-size: 75%;">benchmarking.Output(i + j > 7)</span>
@@ Line 96: / Line 99: @@
 <span style="text-align: center; font-size: 75%;">benchmarking.Output(dt, "Delta t")</span>
-<span style="text-align: center; font-size: 75%;">benchmarking.Output(p, "Node 1 pressure", None, 0.05)</span>
+<span style="text-align: center; font-size: 75%;">benchmarking.Output(p, "Node 1 pressure", None, 0.05)
 In the first example, the value of <span style="text-align: center; font-size: 75%;">i</span> has been emitted without any label or tolerances. In the second one, a boolean value has been emitted, again with no label. In the third one, the value of <span style="text-align: center; font-size: 75%;">dt</span> has been emitted, specifying a label for it. And in the last one, the value of <span style="text-align: center; font-size: 75%;">p</span> has been emitted, specifying a label, no absolute tolerance, but a relative tolerance of 5%.

@@ Line 51: / Line 51: @@
 |  style="border: 1pt solid black;"|'''Description'''
 |-
-|  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: left; font-family: Sans-serif;">InBenchmarkingMode()</span>
+|  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: left; font-family: Monospace;">InBenchmarkingMode()</span>
 |  style="border: 1pt solid black;vertical-align: top;"|Returns <code>True</code> if in benchmarking mode, False otherwise
 |-

@@ Line 46: / Line 46: @@
 Table 1 lists the functions exposed by the automatic benchmarking module, along with a short description. These functions provide the interface between the module and the test examples. Also, some of these functions are used in scripts provided for automatic running of all test examples, automatic building of all reference data files or notifying the recipients from the status of the test examples. Here a brief usage example for these functions will be presenented.
-{| style="width: 100%;border-collapse: collapse;"
+{| style="width: 100%;border-collapse: collapse;font-size:85%;"
 |-
-|  style="border: 1pt solid black;"|Function
+|  style="border: 1pt solid black;"|'''Function'''
-|  style="border: 1pt solid black;"|Description
+|  style="border: 1pt solid black;"|'''Description'''
 |-
-|  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: center; font-size: 75%;">InBenchmarkingMode()</span>
+|  style="border: 1pt solid black;vertical-align: top;"|InBenchmarkingMode()
-|  style="border: 1pt solid black;vertical-align: top;"|Returns <span style="text-align: center; font-size: 75%;">True</span> if in benchmarking mode, False otherwise
+|  style="border: 1pt solid black;vertical-align: top;"|Returns <code>True</code> if in benchmarking mode, False otherwise
 |-
 |  style="border: 1pt solid black;vertical-align: top;"|<span style="text-align: center; font-size: 75%;">Output(Var, Label = "", AbsErr = None, RelErr = None)</span>