# The Big Calculator Gone Crazy In this article I'm going to discuss a problem few people think of\. Computer simulation of various processes becomes more and more widespread\. This technology is wonderful because it allows us to save time and materials which would be otherwise spent on senseless chemical, biological, physical and other kinds of experiments\. A computer simulation model of a wing section flow may help significantly reduce the number of prototypes to be tested in a real wind tunnel\. Numerical experiments are given more and more trust nowadays\. However, dazzled by the triumph of computer simulation, nobody notices the problem of software complexity growth behind it\. People treat computer and computer programs just as a means to obtain necessary results\. I'm worried that very few know and care about the fact that software size growth leads to a non\-linear growth of the number of software bugs\. It's dangerous to exploit a computer treating it just as a big calculator\. So, that's what I think \- I need to share this idea with other people\. ![0212_CrazyCalc/image1.png](https://import.viva64.com/docx/blog/0212_CrazyCalc/image1.png) ## The Big Calculator At first I intended to entitle this article something like "If programmers can't create medicines, why can medics create programs?" Take some imaginary programmer \- he is not allowed to develop and prepare medicines\. The reason is obvious: he doesn't have the necessary education for that\. However, it's not that simple with programming\. It may seem that an imaginary medic who has learned how to program will by default be a successful and useful programmer \- especially given that a more or less acceptable programming skill is much easier to master than organic chemistry and principles of medicine preparation\. Here lies a trap\. A computer experiment requires as much care as a real one\. Lab workers are taught to wash test tubes after experiments and make sure they are sterile\. But few really care about the problem of some array accidentally remaining uninitialized\. Programmers are well aware that the more complex software is, the more complicated and subtle bugs occur in it\. In other words, I'm speaking of [non\-linear growth of the number of bugs](https://pvs-studio.com/en/blog/posts/0158/) accompanying the code size growth\. Programs performing chemical or any other scientific computations are far from being simple, aren't they? Here's where the danger is\. It's OK that a medic\-programmer makes mistakes\. Any programmer, however skillful, makes them from time to time\. What's not OK, people tend to trust these results more and more\. You calculate something and go on with your business\. Those engaged in programming as their professional activity know how dangerous this approach is\. They know what an undefined behavior is and how a program may only pretend to work well\. There are numbers of articles and books explaining how to correctly develop unit tests and ensure the correctness of computations\. Such is the world of programmers\. But the world of chemists/physicists/medics is not that way, I'm afraid\. They never write a complex program \- they simply don't think that way\. They use the computer as if it were just a Big Calculator\. This comparison was suggested by one of our readers\. Let me quote his comment in full here, so that English\-speaking readers could learn about it too, once the article is translated\. _I_ _can_ _tell_ _you_ _something_ _on_ _this_ _subject_ _from_ _my_ _own_ _experience\._ _Though_ _being_ _a_ _professional_ _programmer,_ _I_ _actually_ _come_ _of_ _a_ _family_ _of_ _physicists_ _and_ _have_ _physics_ _education\._ _At_ _the_ _moment_ _when_ _I_ _had_ _to_ _choose_ _which_ _university_ _to_ _enter,_ _the_ _call_ _of_ _blood_ _was_ _stronger_ _than_ _my_ _faith_ _in_ _the_ _bright_ _future_ _of_ _IT\._ _So,_ _I_ _entered_ _a_ _physics_ _university,_ _rather_ _prestigious_ _on_ _the_ _local_ _scale,_ _which_ _in_ _fact_ _is_ _a_ _"kindergarten"_ _supervised_ _by_ _a_ _large_ _research_ _institute_ _in_ _my_ _native_ _city_ _Nizhny_ _Novgorod\._ _People_ _who_ _know_ _the_ _subject_ _will_ _at_ _once_ _guess_ _which_ _research_ _institute_ _and_ _which_ _university_ _I_ _mean\._ _While_ _studying_ _there,_ _I_ _quite_ _naturally_ _proved_ _to_ _be_ _one_ _of_ _the_ _best_ _at_ _programming_ _\(and_ _mathematical_ _methods_ _of_ _physical_ _modeling_ _in_ _particular\)\._ _It_ _was_ _at_ _the_ _same_ _time_ _I_ _also_ _figured_ _out_ _the_ _following_ _things:_ _1\._ _Physicists_ _tend_ _to view_ _the_ _computer_ _as_ _a_ _large_ _multi\-functional_ _calculator_ _allowing_ _you_ _to_ _draw_ _a_ _graph_ _of_ _Eta_ _versus_ _Theta_ _with_ _Gamma_ _going_ _to_ _infinity\._ _As_ _one_ _can_ _naturally_ _expect,_ _they_ _are_ _mainly_ _interested_ _in_ _the_ _graph_ _itself,_ _not_ _the_ _program\._ _2\._ _As_ _a_ _consequence_ _of_ _the_ _first_ _fact,_ _a_ _programmer_ _is_ _not_ _viewed_ _as_ _a_ _profession\._ _A_ _programmer_ _is_ _just_ _the_ _guy_ _who_ _knows_ _how_ _to_ _use_ _the_ _Big_ _Calculator_ _to_ _draw_ _the_ _needed_ _graph\._ _They_ _don't_ _care_ _which_ _way_ _it_ _will_ _be_ _done_ _\-_ _at_ _all\._ _Sorry,_ _what_ _did_ _you_ _say?_ _Static_ _analysis?_ _Version_ _control?_ _Oh,_ _come_ _on,_ _guys\!_ _C\+\+_ _is_ _the_ _language_ _of_ _programmers;_ _physicists_ _write_ _in_ _FORTRAN\!_ _3\._ _As_ _a_ _consequence_ _of_ _the_ _previous_ _fact,_ _anyone_ _who's_ _going_ _to_ _devote_ _his_ _life_ _to_ _writing_ _programs_ _to_ _do_ _physical_ _modeling,_ _even_ _all\-purpose_ _ones,_ _even_ _tough_ _as_ _hell_ _ones,_ _is_ _but_ _an_ _appendix_ _to_ _the_ _Big_ _Calculator\._ _He's_ _not_ _even_ _a_ _person_ _\-_ _just_ _a_ _kind_ _of\.\.\._ _By_ _the_ _way,_ _it_ _was_ _not_ _only_ _me_ _treated_ _in_ _such_ _a_ _way_ _by_ _physicists_ _\(I_ _was_ _just_ _an_ _ordinary_ _student,_ _after_ _all\)_ _\-_ _but_ _even_ _the_ _best_ _computer_ _modeling_ _specialist_ _in_ _the_ _research_ _institute_ _who_ _taught_ _a_ _computational_ _methods_ _course_ _at_ _our_ _university_ _and_ _who,_ _when_ _I_ _turned_ _to_ _him_ _as_ _my_ _thesis_ _adviser_ _while_ _writing_ _my_ _term_ _paper,_ _said_ _to_ _me_ _almost_ _straightforward,_ _"They_ _will_ _despise_ _you,_ _so_ _be_ _prepared_ _to_ _tolerate_ _that"\._ _I_ _didn't_ _want_ _to_ _tolerate_ _that_ _and_ _after_ _graduation_ _left_ _the_ _computer_ _modeling_ _area_ _for_ _the_ _field_ _where_ _programmers_ _are_ _not_ _thought_ _to_ _be_ _untermenschen\._ _I_ _hope_ _this_ _example_ _will_ _help_ _you_ _understand_ _why_ _initiatives_ _like_ _introducing_ _static_ _analysis_ _even into relatively large \(about 20 or 30 developers\) projects on computer modeling are a hopeless job\. There simply might not be a person who knows what it is\. And if such a person does happen to be in the team, they'll most likely trample him because they don't need no trendy programmer frills of yours\. "We've been doing without them for a hundred years \- and will do for more\."_ _Here's another story for those not bored yet\. My father, though being a pensioner, still works at a very large defense engineering enterprise here, in Nyzhny Novgorod \(it's the largest in our city and one of the largest ones across the country; again, those who know the subject will guess it ;\) \)\. He's been programming in FORTRAN for his entire life\. He started at the time when punched cards were in use\. I don't blame him for not studying C\+\+\. It was already too late for him 10 years ago \- and he's still goes on pretty well\. However, there are certain security precautions at this enterprise 2/3 of the staff of which are engaged in programming one way or another:_ _1\. No Internet\. At all\. You need literature \- you go to the library\. Stack Overflow? What's that? If you need to send an e\-mail, you have to submit a written request to the boss explaining whom and what for you want to send it\. Only a few chosen ones can use the Internet "against a receipt"\. Thank God, they have an internal network at least\._ _2\. No administration rights on your computer\. Perhaps this restriction makes sense for the white\-collar mass, but I can't imagine a programmer feeling satisfied with it\._ _3\. \(Doesn't relate to the subject; just an illustration\.\) You can't even bring a cell phone with an integrated camera \(have you seen ones without it nowadays?\)\._ _As a result, even young employees write code in FORTRAN, while really skilled programmers are very few\. I know that for sure because I trained some guy of 25 whom my father had recommended as a promising programmer\._ _Here's my verdict: they are stuck in the 80\-s there\. Even given that they have pretty good salaries, I wouldn't go there for the world\._ _These are just two examples from the intellectual elite's life\. I don't mean to discredit anyone \- they do their job well enough, but my heart is bleeding as I watch which windmills my father has to fight sometimes\. \(Thank God, I've managed to persuade him to start using git recently\.\) No OOP in a million\-line project, no static analysis \- nothing\._ _It's just has to do with the human's trait to be very conservative about areas which are not one's strong points\._ _Ilja Mayzus\. [The original comment](https://habr.com/en/company/pvs-studio/blog/191688/#comment_6660364)\._ The core of this story is the ideology of treating the computer as a Big Calculator\. In that case, you don't need to know any more about it than its younger brother, the pocket calculator, deserves\. And it's the way it is actually used in many areas\. Let's digress for a while and have a look inside the world of physics\. Let's see how another theory finds a confirmation\. To do this, I'll again have to quote a large extract from Bryan Greene's book "The Elegant Universe: Superstrings, Hidden Dimensions, and the Quest for the Ultimate Theory" \[1\]: _We_ _all_ _huddled_ _around_ _Morrison's_ _computer_ _in_ _the_ _office_ _he_ _and_ _I_ _shared\._ _Aspinwall_ _told_ _Morrison_ _how_ _to_ _bring_ _his_ _program_ _up_ _on_ _the_ _screen_ _and_ _showed_ _us_ _the_ _precise_ _form_ _for_ _the_ _required_ _input\._ _Morrison_ _appropriately_ _formatted_ _the_ _results_ _we_ _had_ _generated_ _the_ _previous_ _night,_ _and_ _we_ _were_ _set_ _to_ _go\._ _The_ _particular_ _calculation_ _we_ _were_ _performing_ _amounts,_ _roughly_ _speaking,_ _to_ _determining_ _the_ _mass_ _of_ _a_ _certain_ _particle_ _species—a_ _specific_ _vibrational_ _pattern_ _of_ _a_ _string—when_ _moving_ _through_ _a_ _universe_ _whose_ _Calabi\-Yau_ _component_ _we_ _had_ _spent_ _all_ _fall_ _identifying\._ _We_ _hoped,_ _in_ _line_ _with_ _the_ _strategy_ _discussed_ _earlier,_ _that_ _this_ _mass_ _would_ _agree_ _identically_ _with_ _a_ _similar_ _calculation_ _done_ _on_ _the_ _Calabi\-Yau_ _shape_ _emerging_ _from_ _the_ _space\-tearing_ _flop_ _transition\._ _The_ _latter_ _was_ _the_ _relatively_ _easy_ _calculation,_ _and_ _we_ _had_ _completed_ _it_ _weeks_ _before;_ _the_ _answer_ _turned_ _out_ _to_ _be_ _3,_ _in_ _the_ _particular_ _units_ _we_ _were_ _using\._ _Since_ _we_ _were_ _now_ _doing_ _the_ _purported_ _mirror_ _calculation_ _numerically_ _on_ _a_ _computer,_ _we_ _expected_ _to_ _get_ _something_ _extremely_ _close_ _to_ _but_ _not_ _exactly_ _3,_ _something_ _like 3\.000001_ _or_ _2\.999999,_ _with_ _the_ _tiny_ _difference_ _arising_ _from_ _rounding_ _errors\._ _Morrison_ _sat_ _at_ _the_ _computer_ _with_ _his_ _finger_ _hovering_ _over_ _the_ _enter_ _button\._ _With_ _the_ _tension_ _mounting_ _he_ _said,_ _"Here_ _goes,"_ _and_ _set_ _the_ _calculation_ _in_ _motion\._ _In_ _a_ _couple_ _of_ _seconds_ _the_ _computer_ _returned_ _its_ _answer:_ _8\.999999\._ _My_ _heart_ _sank\._ _Could_ _it_ _be_ _that_ _space\-tearing_ _flop_ _transitions_ _shatter_ _the_ _mirror_ _relation,_ _likely_ _indicating_ _that_ _they_ _cannot_ _actually_ _occur?_ _Almost_ _immediately,_ _though,_ _we_ _all_ _realized_ _that_ _something_ _funny_ _must_ _be_ _going_ _on\._ _If_ _there_ _was_ _a_ _real_ _mismatch_ _in_ _the_ _physics_ _following_ _from_ _the_ _two_ _shapes,_ _it_ _was_ _extremely_ _unlikely_ _that_ _the_ _computer_ _calculation_ _should_ _yield_ _an_ _answer_ _so_ _close_ _to_ _a_ _whole_ _number\._ _If our_ _ideas_ _were_ _wrong,_ _there_ _was_ _no_ _reason_ _in_ _the_ _world_ _to_ _expect_ _anything_ _but_ _a_ _random_ _collection_ _of_ _digits\._ _We_ _had_ _gotten_ _a_ _wrong_ _answer,_ _but_ _one_ _that_ _suggested,_ _perhaps,_ _that_ _we_ _had_ _just_ _made_ _some_ _simple_ _arithmetic_ _error\._ _Aspinwall_ _and_ _I_ _went_ _to_ _the_ _blackboard,_ _and_ _in_ _a_ _moment_ _we_ _found_ _our_ _mistake:_ _we_ _had_ _dropped_ _a_ _factor_ _of_ _3_ _in_ _the_ _"simpler"_ _calculation_ _we_ _had_ _done_ _weeks_ _before;_ _the_ _true_ _result was 9\. The computer answer was therefore just what we wanted_\. _Of_ _course,_ _the_ _after\-the\-fact_ _agreement_ _was_ _only_ _marginally_ _convincing\._ _When_ _you_ _know_ _the_ _answer_ _you_ _want,_ _it_ _is_ _often_ _all_ _too_ _easy_ _to_ _figure_ _out_ _a_ _way_ _of_ _getting_ _it\._ _We_ _needed_ _to_ _do_ _another_ _example\._ _Having_ _already_ _written_ _all_ _of_ _the_ _necessary_ _computer_ _code,_ _this_ _was_ _not_ _hard_ _to_ _do\._ _We_ _calculated_ _another_ _particle_ _mass_ _on_ _the_ _upper_ _Calabi\-Yau_ _shape,_ _being_ _careful_ _this_ _time_ _to_ _make_ _no_ _errors\._ _We_ _found_ _the_ _answer:_ _12\._ _Once_ _again,_ _we_ _huddled_ _around_ _the_ _computer_ _and_ _set_ _it_ _on_ _its_ _way\._ _Seconds_ _later_ _it_ _returned_ _11\.999999\._ _Agreement\._ _We_ _had_ _shown_ _that_ _the_ _supposed_ _mirror_ _is_ _the_ _mirror,_ _and_ _hence_ _space\-tearing_ _flop_ _transitions_ _are_ _part_ _of_ _the_ _physics_ _of_ _string_ _theory\._ _At_ _this_ _I_ _jumped_ _out_ _of_ _my_ _chair_ _and_ _ran_ _an_ _unrestrained_ _victory_ _lap_ _around_ _the_ _office\._ _Morrison_ _beamed_ _from_ _behind_ _the_ _computer\._ _Aspinwall's_ _reaction,_ _though,_ _was_ _rather_ _different\._ _"That's_ _great,_ _but_ _I_ _knew_ _it_ _would_ _work,"_ _he_ _calmly_ _said\._ _"And_ _where's_ _my_ _beer?"_ I truly believe they are geniuses\. But let's imagine for a moment that it were some ordinary students who used this approach to calculate an integral\. I don't think programmers would take it seriously then\. And what if the program generated 3 right away? The bug would be taken as the final evidence? I think it would clear up later, during a re\-check by themselves or their scientist colleagues\. Still, the "ideal spherical programmer in vacuum" is scared to death by this fact\. This is how things are in reality\. It's not only personal computers used in such a way \- it's also cluster systems exploited for scientific computations\. And what's most scary, people trust the results produced by programs\. In the future we are going to deal with even more computations of this kind, and the price of having software bugs will become steeper too\. Isn't it time to change something? Yes, nobody can forbid me to stick a plaster on a cut myself; I guess I can recommend some medicine to take when you've caught a cold\. But not more than that\. I cannot drill a tooth or write out a prescription\. Don't you find it reasonable that developers creating a software system whose responsibility extends beyond certain scope should also confirm their skill? I know there exist various certifications\. But I'm talking of a different thing now\. Certification is intended to ensure that program code conforms to certain standards\. It partially prevents slopwork, in an indirect way\. But the range of areas where certification is a strict requirement is quite narrow\. It obviously does not cover the whole set of areas and situations where careless use of the Big Calculator may do much harm\. ## Example of the Danger I guess many of you find my worries too abstract\. That's why I suggest examining a few real\-life examples\. There is the open\-source package [Trans\-Proteomic Pipeline](https://en.wikipedia.org/wiki/Trans-Proteomic_Pipeline) \(TPP\) designed to solve various tasks in biology\. No doubt, it is used \- by its developers and perhaps some third\-party organizations\. I believe that any bug in it is already a potential issue\. And does it have bugs? Yes, it does; and still more are appearing\. We checked this project one year ago and reported it in the blog\-post "[Analysis of the Trans\-Proteomic Pipeline \(TPP\) project](https://pvs-studio.com/en/blog/posts/cpp/0156/)"\. What has changed since then? Nothing\. The project is going on to develop and accumulate new bugs\. The Big Calculator ideology has won\. The developers are not writing a high\-quality project with the minimum number of bugs possible\. They simply solve their tasks; otherwise they would have reacted in some way to the last year article and considered introducing some static analysis tools\. I don't mean they must necessarily choose PVS\-Studio; there are numbers of other static code analyzers\. The point is that their responsible application goes on collecting most trivial bugs\. Let's see what fresh ones they've got\. ### 1\. Some bungler goes on writing incorrect loops In the previous article I mentioned incorrect loop conditions\. The new package version has them too\. ```cpp double SpectraSTPeakList::calcDot(SpectraSTPeakList* other) { .... for (i = this->m_bins->begin(), j = other->m_bins->begin(); i != this->m_bins->end(), j != other->m_bins->end(); i++, j++) { d = (*i) * (*j); dot += d; } .... } ``` PVS\-Studio's diagnostic message: V521 Such expressions using the ',' operator are dangerous\. Make sure the expression is correct\. spectrastpeaklist\.cpp 504 In the check "i \!\= this\-\>m\_bins\-\>end\(\), j \!\= other\-\>m\_bins\-\>end\(\)", the expression before the comma does not check anything\. The ',' operator is used to execute expressions both to the right and to the left of it in the left\-to\-right order and **return the value of the right expression**\. This is what the correct check should look like: ```cpp i != this->m_bins->end() && j != other->m_bins->end() ``` The same defect can be also found in the following fragments: * spectrastpeaklist\.cpp 516 * spectrastpeaklist\.cpp 529 * spectrastpeaklist\.cpp 592 * spectrastpeaklist\.cpp 608 * spectrastpeaklist\.cpp 625 * spectrastpeaklist\.cpp 696 ### 2\. Null pointer dereferencing This bug won't lead to outputting incorrect computation results \- it will cause a crash instead, which is much better\. However, it would be strange not to mention these bugs\. ```cpp void ASAPRatio_getDataStrctRatio(dataStrct *data, ....) { .... int *outliers, *pepIndx=NULL; .... //pepIndx doesn't change .... if(data->dataCnts[i] == 1 && pepIndx[i] == 0) data->dataCnts[i] = 0; .... } ``` PVS\-Studio's diagnostic message: V522 Dereferencing of the null pointer 'pepIndx' might take place\. asapcgidisplay2main\.cxx 534 The same defect can be also found in the following fragments: * Pointer 'peptides'\. asapcgidisplay2main\.cxx 556 * Pointer 'peptides'\. asapcgidisplay2main\.cxx 557 * Pointer 'peptides'\. asapcgidisplay2main\.cxx 558 * Pointer 'peptides'\. asapcgidisplay2main\.cxx 559 * Pointer 'peptides'\. asapcgidisplay2main\.cxx 560 * Pointer 'pepIndx'\. asapcgidisplay2main\.cxx 569 ### 3\. Uncleared arrays ```cpp static void clearTagNames() { std::vectorptrs; for (tagname_set::iterator i = tagnames.begin(); i!=tagnames.end();i++) { ptrs.push_back(*i); } for (tagname_set::iterator j = attrnames.begin(); j!=attrnames.end();j++) { ptrs.push_back(*j); } tagnames.empty(); attrnames.empty(); for (size_t n=ptrs.size();n--;) { delete [] (char *)(ptrs[n]); // cast away const } } ``` In this code the analyzer has caught two uncleared arrays at once: V530 The return value of function 'empty' is required to be utilized\. tag\.cxx 72 V530 The return value of function 'empty' is required to be utilized\. tag\.cxx 73 You should call the clear\(\) function instead of empty\(\)\. ### 4\. Uninitialized class objects ```cpp class ExperimentCycleRecord { public: ExperimentCycleRecord() { ExperimentCycleRecord(0,0,0,True,False); } ExperimentCycleRecord(long lExperiment, long lCycleStart, long lCycleEnd, Boolean bSingleCycle, Boolean bRangleCycle) { .... } .... } ``` PVS\-Studio's diagnostic message: V603 The object was created but it is not being used\. If you wish to call constructor, 'this\-\>ExperimentCycleRecord::ExperimentCycleRecord\(\.\.\.\.\)' should be used\. mascotconverter\.cxx 101 The ExperimentCycleRecord\(\) constructor does not do what it is intended to; it doesn't initialize anything\. The developer might be an excellent chemist, but if he doesn't know how to use the C\+\+ language properly, his computations using uninitialized memory aren't worth a damn\. It's like using a dirty test tube\. Instead of calling another constructor, the line "ExperimentCycleRecord\(0,0,0,True,False\);" creates a temporary object which will be destroyed after that\. This error pattern is discussed in detail in the article "[Wade not in unknown waters\. Part one](https://pvs-studio.com/en/blog/posts/cpp/0127/)"\. The same defect can be also found in the following fragments: * asapratiopeptideparser\.cxx 57 * asapratiopeptidecgidisplayparser\.cxx 36 * cruxdiscrimfunction\.cxx 36 * discrimvalmixturedistr\.cxx 34 * mascotdiscrimfunction\.cxx 47 * mascotscoreparser\.cxx 37 * tandemdiscrimfunction\.cxx 35 * tandemkscoredf\.cxx 37 * tandemnativedf\.cxx 37 ### 5\. Comments breaching execution logic ```cpp int main(int argc, char** argv) { .... if (getIsInteractiveMode()) //p->writePepSHTML(); //p->printResult(); // regression test? if (testType!=NO_TEST) { TagListComparator("InterProphetParser",testType, outfilename,testFileName); .... } ``` PVS\-Studio's diagnostic message: V628 It's possible that the line was commented out improperly, thus altering the program's operation logics\. interprophetmain\.cxx 175 After the 'if' operator, a few lines executing some operations were commented out\. As a result, the program logic changed quite differently than expected\. The programmer didn't want any actions to be done after executing the condition\. Instead, the 'if' operator affects the code below\. As a consequence, the tests' output now depends not only on the "testType\!\=NO\_TEST" condition, but on the "getIsInteractiveMode\(\)" condition as well\. That is, the test may not test anything\. That's why I [strongly recommend](https://pvs-studio.com/en/blog/posts/cpp/a0080/) not to rely fully on one testing methodology alone \(for example, TDD\)\. ### 6\. Misprints Misprints are to be found everywhere and all the time\. It's not that bad if you get fewer hit points after an explosion in a game than you ought to, because of such a bug\. But what do incorrect data mean when computing chemical reactions? ```cpp void ASAPRatio_getProDataStrct(proDataStrct *data, char **pepBofFiles) { .... if (data->indx == -1) { data->ratio[0] = -2.; data->ratio[0] = 0.; data->inv_ratio[0] = -2.; data->inv_ratio[1] = 0.; return; } .... } ``` PVS\-Studio's diagnostic message: V519 The 'data\-\>ratio\[0\]' variable is assigned values twice successively\. Perhaps this is a mistake\. Check lines: 130, 131\. asapcgidisplay2main\.cxx 131 One and the same variable is by mistake assigned two different values\. The correct code is this one: ```cpp data->ratio[0] = -2.; data->ratio[1] = 0.; ``` This fragment was then copied\-and\-pasted into other parts of the program: * asapcgidisplay2main\.cxx 338 * asapcgidisplay2main\.cxx 465 * asapratioproteincgidisplayparser\.cxx 393 * asapratioproteincgidisplayparser\.cxx 518 ### 7\. Comparing signed and unsigned values Comparing signed and unsigned values properly requires some skill\. Ordinary calculators don't deal with unsigned values, but the C\+\+ language does\. ```cpp size_type size() const; void computeDegenWts() { .... int have_cluster = 0; .... if ( have_cluster > 0 && ppw_ref.size() - have_cluster > 0 ) .... } ``` PVS\-Studio's diagnostic message: V555 The expression 'ppw\_ref\.size\(\) \- have\_cluster \> 0' will work as 'ppw\_ref\.size\(\) \!\= have\_cluster'\. proteinprophet\.cpp 6767 The programmer wanted the check "ppw\_ref\.size\(\) \> have\_cluster" to be executed\. But he got something very different instead\. To make it clearer, let's assume we have the 'size\_t' type which is 32\-bit\. Suppose the function "ppw\_ref\.size\(\)" returns 10 while the variable have\_cluster equals 15\. The function ppw\_ref\.size\(\) returns the unsigned type 'size\_t'\. According to the C\+\+ rules, the right operand in the subtraction operation must also have the type 'size\_t' before subtraction is executed\. It's alright for now: we have 10u on the left and 15u on the right\. Here goes the subtraction: 10u \- 15u And here's where we get a trouble\. Those very C\+\+ rules tell us that the result of subtraction between two unsigned variables must also be unsigned\. It means that 10u \- 15u \= FFFFFFFBu\. As you know, 4294967291 is greater than 0\. The Big Calculator Riot is successful\. Writing a correct theoretical algorithm is only half of the job\. You also need to write a correct code\. A similar bug can be found in the following fragment: ```cpp double SpectraSTPeakList::calcXCorr() { .... for (int tau = -75; tau <= 75; tau++) { float dot = 0.0; for (unsigned int b = 0; b < numBins; b++) { if (b + tau >= 0 && b + tau < (int)numBins) { dot += (*m_bins)[b] * theoBins[b + tau] / 10000.0; } } .... .... } ``` PVS\-Studio's diagnostic message: V547 Expression 'b \+ tau \>\= 0' is always true\. Unsigned type value is always \>\= 0\. spectrastpeaklist\.cpp 2058 As you can see, the variable 'tau' takes values within the range \[\-75, 75\]\. To avoid array overrun, the check b \+ tau \>\= 0 is used\. I guess you've already got the point that this check won't work\. The variable 'b' has the 'unsigned' modifier\. It means that the "b \+ tau" expression's result is unsigned too\. And an unsigned value is always greater than or equal to 0\. ### 8\. Strange loop ```cpp const char* ResidueMass::getStdModResidues(....) { .... for (rmap::const_iterator i = p.first; i != p.second; ++i) { const cResidue &r = (*i).second; if (r.m_masses[0].m_nterm) { n_term_aa_mod = true; } else if (r.m_masses[0].m_cterm) { c_term_aa_mod = true; } return r.m_residue.c_str(); } if(! strcmp(mod, "+N-formyl-met (Protein)")) { return "n"; } if (! strcmp(mod, "13C6-15N2 (K)")) { return "K"; } if (! strcmp(mod, "13C6-15N4 (R)")) { return "R"; .... } ``` PVS\-Studio's diagnostic message: V612 An unconditional 'return' within a loop\. residuemass\.cxx 1442 There is the 'return' operator inside the loop and it's called in any case\. The loop can execute only once, after which the function terminates\. It's either a misprint here or some condition is missing before the 'return' operator\. ### 9\. Rough calculations ```cpp double RTCalculator::getUsedForGradientRate() { if (rts_.size() > 0) return used_count_ / rts_.size(); return 0.; } ``` PVS\-Studio's diagnostic message: V636 The 'used\_count\_ / rts\_\.size\(\)' expression was implicitly casted from 'int' type to 'double' type\. Consider utilizing an explicit type cast to avoid the loss of a fractional part\. An example: double A \= \(double\)\(X\) / Y;\. rtcalculator\.cxx 6406 Since the function returns values of the double type, I find it reasonable to suppose the following\. When the variable 'used\_count\_' is assigned the value 5 and the function rts\_\.size\(\) returns 7, the approximate result is 0,714\. However, the function getUsedForGradientRate\(\) will return 0 in this case\. The variable 'used\_count\_' has the 'int' type\. The rts\_\.size\(\) function also returns an 'int' value\. An integer division occurs, and the result is obvious: it's zero\. Then zero is implicitly cast to double, but it doesn't matter at this point\. To fix the defect, the code should be rewritten in the following way: ```cpp return static_cast(used_count_) / rts_.size(); ``` Other defects of this kind: * cgi\_pep3d\_xml\.cxx 3203 * cgi\_pep3d\_xml\.cxx 3204 * asapratiopeptideparser\.cxx 4108 ### 10\. Great and mighty Copy\-Paste The function setPepMaxProb\(\) contains a few large similarly looking blocks\. In this fragment one can feel that specific smell of the Copy\-Paste technique\. Using it naturally results in an error\. I had to SIGNIFICANTLY abridge the sample text\. The bug is very noticeable in the abridged code, but it's almost impossible to see it in the original code\. Yeah, it's an advertisement of static analysis tools in general and [PVS\-Studio](https://pvs-studio.com/en/pvs-studio/) in particular\. ```cpp void setPepMaxProb( bool use_nsp, bool use_fpkm, bool use_joint_probs, bool compute_spectrum_cnts ) { double prob = 0.0; double max2 = 0.0; double max3 = 0.0; double max4 = 0.0; double max5 = 0.0; double max6 = 0.0; double max7 = 0.0; .... if ( pep3 ) { ... if ( use_joint_probs && prob > max3 ) ... } .... if ( pep4 ) { ... if ( use_joint_probs && prob > max4 ) ... } .... if ( pep5 ) { ... if ( use_joint_probs && prob > max5 ) ... } .... if ( pep6 ) { ... if ( use_joint_probs && prob > max6 ) ... } .... if ( pep7 ) { ... if ( use_joint_probs && prob > max6 ) ... } .... } ``` V525 The code containing the collection of similar blocks\. Check items 'max3', 'max4', 'max5', 'max6', 'max6' in lines 4664, 4690, 4716, 4743, 4770\. proteinprophet\.cpp 4664 PVS\-Studio's diagnostic message: V525 The code containing the collection of similar blocks\. Check items 'max3', 'max4', 'max5', 'max6', 'max6' in lines 4664, 4690, 4716, 4743, 4770\. proteinprophet\.cpp 4664 Unfortunately, the V525 diagnostic produces many false positives and therefore referred to the third\-level warnings\. But if one overcomes one's laziness and study this class of warnings, one may find numbers of such nice bugs\. ### 11\. Pointer is not initialized sometimes ```cpp int main(int argc, char** argv) { .... ramp_fileoffset_t *pScanIndex; .... if ( (pFI=rampOpenFile(mzXmlPath_.c_str()))==NULL) { .... } else { .... pScanIndex = readIndex(pFI, indexOffset, &iAnalysisLastScan); .... } .... if (pScanIndex != NULL) free(pScanIndex); return 0; } ``` PVS\-Studio's diagnostic message: V614 Potentially uninitialized pointer 'pScanIndex' used\. sqt2xml\.cxx 476 This program may crash at the end if the function rampOpenFile\(\) returns NULL\. It's not critical yet unpleasant\. Here's another variable that may remain uninitialized: * Potentially uninitialized pointer 'fp\_' used\. dta\-xml\.cpp 307 ### 12\. Virtual destructor missing ```cpp class DiscriminantFunction { public: DiscriminantFunction(int charge); virtual Boolean isComputable(SearchResult* result) = 0; virtual double getDiscriminantScore(SearchResult* result) = 0; virtual void error(int charge); protected: int charge_; double const_; }; // class class CometDiscrimFunction : public DiscriminantFunction; class CruxDiscrimFunction : public DiscriminantFunction; class InspectDiscrimFunction : public DiscriminantFunction; ..... class DiscrimValMixtureDistr : public MixtureDistr { .... DiscriminantFunction* discrim_func_; .... }; DiscrimValMixtureDistr::~DiscrimValMixtureDistr() { delete[] posinit_; delete[] neginit_; delete discrim_func_; } ``` PVS\-Studio's diagnostic message: V599 The virtual destructor is not present, although the 'DiscriminantFunction' class contains virtual functions\. discrimvalmixturedistr\.cxx 206 A number of classes are inherited from the DiscriminantFunction class\. For example, such is the class DiscrimValMixtureDistr\. Its destructor frees memory; therefore, it's very desirable that you call it\. Unfortunately, the DiscriminantFunction class's destructor is not declared as a virtual one \- with all the ensuing consequences\. ### 13\. Miscellaneous There are numbers of small defects which won't have serious consequences but are still not very pleasant to have in your code\. There are also strange fragments, but I can't say for sure if they are incorrect\. Here's one of them: ```cpp Boolean MixtureModel::iterate(int counter) { .... if (done_[charge] < 0) { done_[charge]; } else if (priors_[charge] > 0.0) { done_[charge] += extraitrs_; } .... } ``` PVS\-Studio's diagnostic message: V607 Ownerless expression 'done\_\[charge\]'\. mixturemodel\.cxx 1558 What is it? Incomplete code? Or maybe the programmer just wanted to point it out that nothing should be done if the "done\_\[charge\] < 0" condition is true? And here you are an incorrect way of freeing memory\. Any critical consequences are unlikely, but still the code smells\. ```cpp string Field::getText(....) { .... char* pepString = new char[peplen + 1]; .... delete pepString; .... } ``` PVS\-Studio's diagnostic message: V611 The memory was allocated using 'new T\[\]' operator but was released using the 'delete' operator\. Consider inspecting this code\. It's probably better to use 'delete \[\] pepString;'\. pepxfield\.cxx 1023 The correct way of doing this is to write "delete \[\] pepString"\. There are many other defects of this kind: * cruxdiscrimvalmixturedistr\.cxx 705 * cruxdiscrimvalmixturedistr\.cxx 715 * mascotdiscrimvalmixturedistr\.cxx 426 * mascotdiscrimvalmixturedistr\.cxx 550 * mascotdiscrimvalmixturedistr\.cxx 624 * phenyxdiscrimvalmixturedistr\.cxx 692 * probiddiscrimvalmixturedistr\.cxx 487 * probiddiscrimvalmixturedistr\.cxx 659 * tandemdiscrimvalmixturedistr\.cxx 731 * tandemdiscrimvalmixturedistr\.cxx 741 And here's an incorrect implementation of the "\-\-" operator\. It doesn't seem to be used anywhere, otherwise the bug would quickly reveal itself\. ```cpp CharIndexedVectorIterator operator++(int) { // postincrement CharIndexedVectorIterator _Tmp = *this; ++m_itr; return (_Tmp); } CharIndexedVectorIterator& operator--() { // predecrement ++m_itr; return (*this); } ``` PVS\-Studio's diagnostic message: V524 It is odd that the body of '\-\-' function is fully equivalent to the body of '\+\+' function\. charindexedvector\.hpp 81 The operators "\-\-" and "\+\+" are implemented in the same way\. They must have been copied\-and\-pasted then: * charindexedvector\.hpp 87 * charindexedvector\.hpp 159 * charindexedvector\.hpp 165 Let's stop here\. It all is not very interesting, and the article is big enough\. As usual, I'm urging the developers not to limit themselves to fixing only the mentioned defects\. [Download](https://pvs-studio.com/en/pvs-studio/download/) and check the project with PVS\-Studio yourself\. I could have missed many errors\. We can even grant you a free registration key for some time\. ## Summary Unfortunately, the article has appeared a bit tangled\. What did the author want to say, after all? I'll try to repeat in a very brief form my ideas I want to share with you\. 1. We are currently using more and more programs to perform scientific and engineering computations and simulate various processes, and we grow to trust them\. 1. Programs get very complicated\. Professional programmers understand it very well that one cannot approach the task of creating a software package for computer simulation in the same way as using a software calculator\. The growth of software complexity leads to an exponential increase of the number of errors \[[2](https://pvs-studio.com/en/blog/posts/0158/)\]\. 1. It appears that physicists/biologists/medics cannot simply calculate something in the usual manner\. One cannot ignore the software complexity increase and the consequences of incorrect computations arising from imperfect knowledge of a programming language\. 1. In this article I've given arguments to prove that this is the real state of things\. The first quotation tells us that people tend to treat the computer as an ordinary calculator\. The second quotation just reaffirms this idea\. The error samples discussed after that are meant to demonstrate that people really make mistakes when treating computer simulation software in such a way\. So, my anxiety has solid ground\. So, what shall we do? First of all, I'd like you to realize this problem and tell your colleagues from related areas\. It's been clear to programmers for a long time that the software complexity growth and silly mistakes in large projects may easily turn into a source of great harm\. On the other hand, those people who treat programming and computers just as a tool don't know that and don't bother to think about it\. So, we need to draw their attention to this problem\. Here you are an analogy\. Imagine a man who has got him a cudgel and starts hunting some animals\. The cudgel in his hands gradually turns into a stone axe, then a sword, and finally a gun\. But he still uses it just to stun hares by hitting them on the head\. It's not only that this way of using the weapon is absolutely inefficient; it has also become much more dangerous now \(he can accidentally shoot himself or his fellow men\)\. Hunters from the "programmers" tribe quickly adapt themselves to these changes\. The rest don't have time for that \- they are busy hunting hares\. After all, it's all about the hares\. We need to tell these people that they have to learn, whether they like it or not\. It'll improve everyone's life\. And waving your gun around is no good\. ## References 1. Bryan Greene "The Elegant Universe: Superstrings, Hidden Dimensions, and the Quest for the Ultimate Theory\. ISBN 978\-0375708114 1. Andrey Karpov\. [Feelings confirmed by numbers](https://pvs-studio.com/en/blog/posts/0158/)\.