Abstract
Modern science and research is unimaginable without the use of self-written and in most cases highly specialized software. By analyzing data, simulating model-related items, or simply dealing with different data sets using different formats, computer programs help the researcher to do his daily work. But even though software and its development is an essential part of scientific life, its ranking within the world of science is normally very low.
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Notes
- 1.
An explanation of electronic computer hardware, which can be programmed to process data, can be found in 7 Sect. 4.2.1 about the John von Neumann architecture.
- 2.
For more about modularization with an explanation of modules and components, see 7 Sect. 3.1.
- 3.
In a classic view, functions have some input parameters and a return value. Procedures or subroutines only have parameters and separate the code into logic parts.
- 4.
- 5.
Large, expensive, failing projects are often named «death-march projects» which nobody can stop anymore, but which it is clear will end in disaster.
- 6.
FURPS was proposed by Robert Grady and Hewlett-Packard Co. and stands for Functionality, Usability, Reliability, Performance, and Supportability (Vigenschow 2005, l.c. page 47 f.).
- 7.
The Standish Group defines all projects with less than one million dollar labor costs as «small projects» (or in the case of the European Union with less than 250,000 Euro labor costs) (The Standish Group n.d. l.c. page 13 ff.).
- 8.
The importance of the factors is in descending order.
- 9.
The number of releases can be visualized with a «heat map» over the source files, where code sequences, which are often changed, are colorized with red and others with less changes get gradually darker colors.
- 10.
Macros are replacements in the code, which a preprocessor substitutes with real, final code elements. Therefore, macros are often used for constants or fast, but short code sections, which appear regularly in the source code.
- 11.
Regular expressions are strings which define the patterns for a search criterion to be found in other strings by pattern matching (Brown 2001, l.c. page 231).
- 12.
Call-by-reference is a method which uses the real addresses of the arguments of functions, so that internal changes are directly visible outside. Call-by-reference is used to return values from functions besides the regular return argument. The opposite to call-by-reference is call-by-value, which creates a local copy of the external argument, so that changes are just local.
- 13.
Programming paradigms are general classifications of programming languages into specific categories defined by the structure and elements used in the computer programs.
- 14.
With a small change in the present version so that the global variables are from type «int» to also enable the compilation under Microsoft® Windows™, according to the further program author notes for PC users.
- 15.
Reproduced by permission of International Obfuscated C Code Contest, 7 www.ioccc.org.
- 16.
Some general hints can also be taken from the Microsoft® Design Guidelines for Class Library Developers. NET Framework 1.1 (MSDN Microsoft n.d.).
- 17.
When searching the Internet, the style type can be found under the following denotations: Allman style, «East Coast» style, BSD style, ANSI C style, or also Horstmann style.
- 18.
A very famous type conversion error with catastrophic consequences happened during the launch of the ARIANE 5 rocket of the European Space Agency (ESA), which exploded during its maiden flight. The official report from the inquiry board about the «Flight 501 Failure» on July 19, 1996, describes it like this: «The inertial SRI [= Inertial Reference System] software exception was caused during execution of a data conversion from 64-bit floating point to 16-bit signed integer value. The floating point number which was converted had a value greater than what could be represented by a 16-bit signed integer. This resulted in an Operand Error. The data conversion instructions (in Ada code) were not protected from causing an Operand Error, although other conversions of comparable variables in the same place in the code were protected» (ESA n.d. l.c. page 4).
- 19.
The program memory can simply be separated into stack memory, which is allocated together with the memory for the program code when starting the program and heap memory, which is dynamically allocated during the runtime of the program, each time it is required.
- 20.
Not all 32-bit platforms support «long double».
- 21.
Also the maximum number of file pointers is different, but this is not so relevant for programmers, if they cleanly close opened file pointers after use.
- 22.
«A shallow copy means that any reference-type data members in the [... copy] will refer to the same object as the equivalent reference-type data members in the original object. A deep copy means that [...] the entire object graph [... is copied] so that the reference-type data members of the [... copy] refer to physically independent copies (clones) [...]» (Jones and Freeman 2010, l.c. page 627).
- 23.
The code is based on a solution, suggested by (Werner n.d. l.c. page 249 ff.) but is extended with substantial modifications.
- 24.
The situation is different if a complete package is developed with an external framework, such as a framework for graphical user interfaces. Then the code in question is directly related to that code with all its advantages and disadvantages. But then it makes no sense to write converter.
- 25.
A singleton pattern is a classic OOP design pattern, which uses an improved global variable to prevent the creation of a secondary object of the same type, so that there is always only one instance of the class available in an application (Alexandrescu 2003, l.c. page 181).
- 26.
Here the programming language Perl has a big advantage, as it is possible to directly embed a Perl interpreter into C code (see 7 Sect. 2.2).
- 27.
Information is the content and the meaning (semantics) of a message in textual, graphical, or audio-visual form. Ideally, information is free from irrelevant, redundant parts and transmits knowledge about functionality, functioning, principles of operation, methods, techniques, applications, flows and activities (ITWissen n.d.).
- 28.
Call-graphs are graphical presentations which show the structure how functions call each other in a program. These calls are usually not ordered according to the calling time of each function. They just show the interactions between the functions of a program. Ordered graphs are the sequence charts of UML.
- 29.
For the following, see the web pages of (van Heesch n.d.).
- 30.
Meta-information is additional information about given data to improve its comprehensibility and shareability for users (Kretzschmar and Dreyer 2004, l.c. page 83).
- 31.
By the way, all asterisks, comment delimiters, etc., do not appear in the final documentation.
- 32.
But the included images should already have the correct output size.
- 33.
A LaTeX compiler reads the LaTeX sources and usually generates a DVI file, which then must be converted into a PostScript file. PostScript is a description language for the style of a document, including the content, which can be interpreted, for example, by the GhostScript interpreter. Most printers also directly understand PostScript.
- 34.
URL is a standardized nomenclature to reference and locate Web and network resources.
- 35.
A Wiki is a hypertext web system to offer, find, change, and discuss different topics in a fast way. The idea is to offer a simple, browser-based opportunity to read and edit text.
- 36.
A revision is a change in the document. A release is a finished version in a frozen state, which is named and delivered to the target group.
- 37.
Errors are program states which cause a fault resulting in a failure of the program logic within a dedicated runtime environment (Spillner et al. 2011, l.c. page 4). They can be caused by internally wrong code sequences or by unexpected interactions from external sources.
- 38.
A Kiviat graph is a multi-vector line graph which shows how multiple variables interrelate.
- 39.
The source code at the Geodetic Observatory Wettzell is beautified using the following options: astyle –style=ansi -S -w -Y -p -C -c -N <source-code-file>, where «–style=ansi» sets the scope parenthesis style to Allman/ANSI style, «-S» defines the «switch» indent style, «-w» defines the preprocessor indent style, «-Y» defines the scope closing style, «-p» defines the operators space padding style, «-C» defines the «class»/»struct» indent style, «-c» defines the conversion of tabs into blanks, and «-N» defines changes in the original file (for more information, see (Davidson and Pattee n.d.)).
- 40.
Verification checks if the specified functionality is reached, while validation checks if the results are correct.
- 41.
For the simple Example 2.3, it would be possible, as the chessboard is limited to 99x99 positions, but it does not make sense, as there will not be new information about the quality of the functionality by doing this.
- 42.
In OOP environments, it is necessary to classify local parameters and methods with «protected» access rights, so that the derived test class can access them. In the structured programming environments, as given with C, it might be necessary to work with «extern» declarations in the test main module if functions are not accessible via the header files.
- 43.
The importance of such automated quality tests in fields found in the Geodetic Observatory Wettzell was regularly shown by a colleague, Martin Ettl. Untiringly he developed his own compact unit testing framework, which improved the quality of all the projects tremendously. The resulting Wettzell Unit Test Suite adapted structures and ideas from the test suite used by «Cppcheck» (see 7 Sect. 2.6.3) and extended them. Therefore special thanks should be given to him for that work at this point here!
- 44.
Cron jobs are timed processes, started by the operating system and defined in a «crontab»-file.
- 45.
An audit is an interactive, quality checking discourse to verify the implementation and conformance of a development to guidelines and specified functionalities.
- 46.
A technical review verifies the compliance to specifications and guidelines according to a defined protocol together with experts with long experience in the field of work. Technical problems should be found and solved. Discussion is very welcome. Informal reviews are similar but reduced in complexity and time or personnel costs. They are usually just a discussion between developers (Spillner et al. 2011, l.c. page 163 f.).
- 47.
Regular expressions are strings which define the patterns for a search criterion to be found in other strings by pattern matching (Brown 2001, l.c. page 231).
- 48.
In a multi-processing environment, a reentrant function can be interrupted by a hardware interrupt while processing and safely restarted again without any change in its behavior.
- 49.
Operating systems are a software abstraction level above the hardware to administrate resources, such as the memory, file systems, or input/output devices. They offer interfaces and services via system calls (functions from an operating system library (Tanenbaum 1995, l.c. page 22 f.)) to operate and share devices, manage users, do networking, and handle parallel tasks (Tanenbaum 1995, l.c. page 5 ff.).
- 50.
Non-preemptive scheduling, run-to-completion, or cooperative methods allow the process to run until it ends or until it returns the resources by choice.
- 51.
Real-time systems have hard time constraints with hardware restrictions especially in the controller segment, so that a specific task must be processed within a specified delay time or must start precisely at a specified start time after an interrupt. Violations are unacceptable errors (Vigenschow 2005, l.c. page 221 ff.). Several operating system extensions for different operating systems are available, which add a real-time scheduling to a standard operating system (Langmann 2010, l.c. page 284 ff.). One representative of such extensions for Linux operating systems is Real-Time Application Interface (RTAI), which enables the writing of applications with strict timing constraints (see (RTAI Team 2010)).
- 52.
Starvation is an infinite waiting of one thread or process to get access to a critical section. Deadlocks block the whole system, for example, if two processes wait for each other, so that the blockage cannot be changed by the system itself anymore (Vigenschow 2005, l.c. page 85 f.).
- 53.
Originally such charts were designed by H. L. Gantt in 1919 to evaluate the performance of industrial plants (Klar 1995, l.c. page 135 f.).
- 54.
In a race condition, the timing and therefore the time order of single instructions defines the result of an algorithm.
- 55.
Message passing is a communication between threads, using messages over a communication network.
- 56.
Automatic parallelization splits the program into parallel processable parts during compilation.
- 57.
Transactions are communications which are processed completely or not at all if there is an error.
- 58.
Cache buffers are copies of recently used memory blocks in the memory and administrated by the operating system to optimize the access performance, such as reducing the number of hard drive accesses (Tanenbaum 1995, l.c. page 382).
- 59.
Swapping is a technique used by the operating system to swap memory blocks to the background memory (e.g., hard drive space) if not enough main memory is available. If swapping starts, the processing times increase, as hard drive accesses are much slower than main memory accesses (Tanenbaum 1995, l.c. page 372 f.).
- 60.
- 61.
A complete software project in this field is a complete software system with all the necessary parts, like program files, configuration files, documentations, and so on, plus structural mechanisms to represent and organize the project life cycles.
- 62.
For more about modularization with an explanation of modules, see 7 Sect. 3.1.
- 63.
Symbolic links are references to other files in the file system.
- 64.
Git was originally designed by Linus Torvalds to support the development of the Linux operating system kernel (Loeliger 2010, l.c. page 1).
- 65.
Copying with the Subversion® command does not destroy the historical information, e.g., about the revision changes in the past.
- 66.
UTC is the coordinated universal time based on atomic standards and corrected with leap seconds according to the Earth’s rotation parameters.
- 67.
<file.ext.> must be replaced by the real filename for which the property should be enabled.
- 68.
See 7 Sect. 3.3.2 about the definition of distributed systems.
- 69.
Hash functions are methods, for example, to calculate an addresses information from the content of a string to get a direct reference and therefore a direct access to the position, where the string data are stored. The problem is, that mapping is not unique. The memory where data can be stored is limited so that an infinite number of possible contents must be mapped to a finite set of addresses. Thus, this first hash function can lead to conflicts as reference calculations of several contents result in the same address. It needs an additional exception function to solve the conflict by finding another reference with a reversible and reproducible method. A good and secure first hash function reduces the number of conflicts to a minimum.
- 70.
Virtualization is a technique to emulate a physical hardware virtually. It is used to run several «virtual», emulated machines with their own operating systems on real hardware with a specially prepared, virtualization operating system or in a special player. Each virtual machine looks like a real machine for the users of the virtual machine.
- 71.
A «hypervisor» is a virtual machine monitor, which runs on a guest system and offers everything for a virtual machine.
- 72.
Deployment of the software means handing the release out to the customer or user.
- 73.
A suitable classification consists of a major release number and a sub-release number, for example, in the form of «Ver1.56», where 1 is the major release number and 56 is the sub-release identifier. In this sense, major releases realize completely new features, while sub-releases are more or less bug-fixed versions.
- 74.
Currently the service exists as a free «e-Service» of the «e-Control Software» environment on the web page 7 http://www.econtrol-software.de. Each project has its own user rights and credentials.
- 75.
All web pages were available on December 16, 2015.
- 76.
Sequential, top-down- or waterfall-models organize the project as a strict sequence of the activities: requirement analysis, design, coding/implementation, test, system integration, deployment, and operation with maintenance (adapted from (Leffingwell and Widrig 2003, l.c. page 24 f.)). Steps to backward activities are not allowed or restricted to avoid development delaying cycles.
- 77.
The V-model is another sequential development process which aligns verification and validation activities to a similar development chain as in a classic waterfall model. If the tests fail, restricted steps backwards are allowed for fixing bugs. The graphical representation of the activities looks like a big «V» (adapted from (Spillner et al. 2011, l.c. page 33 f.)).
- 78.
The W-model is a more detailed V-model which accentuates the affiliation of the different development phase to adequate test cases, each with a test preparation, test execution, and debugging. Therefore the graphical representation looks like a big «W». Cycles are included, because of the debugging and test case specifications. They are planned early and parallel to the development documents. But the model is in principle just a sequential process with some cycles.
- 79.
The projects in a spiral model start with a series of risk-driven prototypes, followed by a waterfall-like process for the actual product development. Therefore the spiral model starts with a better requirements planning and concept validation at the beginning. The problem is the consumption of time at the beginning and before the final development (Leffingwell and Widrig 2003, l.c. page 26 ff.). But after finalization of the pretests, a usual top-down model starts.
- 80.
The graphs over time for each discipline demonstrate the expenditure of time for that individual workflow according to the iterations in the project phases. Documentation is officially not part of the Unified Software Development Process and was extended to draw attention to continuously developing software documentation.
- 81.
User stories are very short, textual descriptions of requirements, user interactions, and software features. They are organized with cards, where each card holds one story (Wolf and Bleek 2011, l.c. page 39 f.).
- 82.
Software engineering defines «use cases» as a list of action items, describing the interaction of a specific user and the used software or program as a software scenario to achieve a specific goal with the software (Fowler and Scott 2000, l.c. page 36).
- 83.
Risk in scientific projects is different to industrial. While industrial projects must result in a specific, salable product, the gain in knowledge and insight is the prior goal in science.
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Neidhardt, A.N.J. (2017). Writing Code for Scientific Software. In: Applied Computer Science for GGOS Observatories. Springer Textbooks in Earth Sciences, Geography and Environment. Springer, Cham. https://doi.org/10.1007/978-3-319-40139-3_2
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