I am using the Kernel Density Estimator toolbox form http://www.ics.uci.edu/~ihler/code/kde.html . But I am getting the following error when I try to execute the demo files -
>> demo_kde_3
KDE Example #3 : Product sampling methods (single, anecdotal run)
Attempt to reference field of non-structure array.
Error in double (line 10)
if (npd.N > 0) d = 1; % return 1 if the density exists
Error in repmat (line 49)
nelems = prod(double(siz));
Error in kde (line 39)
if (size(ks,1) == 1) ks = repmat(ks,[size(points,1),1]); end;
Error in demo_kde_3 (line 8)
p = kde([.1,.45,.55,.8],.05); % create a mixture of 4 gaussians for
testing
Can anyone suggest what might be wrong? I am new to Matlab and having a hard time to figure out the problem.
Thank You,
Try changing your current directory away from the #kde folder; you may have to add the #kde folder to your path when you do this. For example run:
cd('c:\');
addpath('full\path\to\the\folder\#kde');
You may also need to add
addpath('full\path\to\the\folder\#kde\examples');
Then see if it works.
It looks like function repmat (a mathworks function) is picking up the #kde class's version of the double function, causing an error. Usually, only objects of the class #kde can invoke that functions which are in the #kde folder.
I rarely use the #folder form of class definitions, so I'm not completely sure of the semantics; I'm curious if this has any effect on the error.
In general, I would not recommend using the #folder class format for any development that you do. The mathworks overhauled their OO paradigm a few versions ago to a much more familiar (and useful) format. Use help classdef to see more. This #kde code seems to predate this upgrade.
MATLAB gives you the code line where the error occurs. As double and repmat belong to MATLAB, the bug probably is in kde.m line 39. Open that file in MATLAB debugger, set a breakpoint on that line (so the execution stops immediately before the execution of that specific line), and then when the code is stopped there, check the situation. Try the entire code line in console (copy-paste or type it, do not single-step, as causing an uncatched error while single-stepping ends the execution of code in debugger), it should give you an error (but doesn't stop execution). Then try pieces of the code of that code line, what works as it should and what not, eg. does the result of size(points, 1) make any sense.
However, debugging unfamiliar code is not an easy task, especially if you're a beginner in MATLAB. But if you learn and understand the essential datatypes of MATLAB (arrays, cell arrays and structs) and the different ways they can be addressed, and apply that knowledge to the situation on the line 39 of kde.m, hopefully you can fix the bug.
Repmat calls double and expects the built-in double to be called.
However I would guess that this is not part of that code:
if (npd.N > 0) d = 1; % return 1 if the density exists
So if all is correct this means that the buil-tin function double has been overloaded, and that this is the reason why the code crashes.
EDIT:
I see that #Pursuit has already addressed the issue but I will leave my answer in place as it describes the method of detection a bit more.
Related
EDIT: The original question had unnecessary details
I have a source file which I do value analysis in Frama-C, some of the code is highlighted as dead code in the normalized window, no the original source code.
Can I obtain a slice of the original code that removes the dead code?
Short answer: there's nothing in the current Frama-C version that will let you do that directly. Moreover, if your original code contains macros, Frama-C will not even see the real original code, as it relies on an external preprocessor (e.g. cpp) to do macro expansion.
Longer answer: Each statement in the normalized (aka CIL) Abstract Syntax Tree (AST, the internal representation of C code within Frama-C) contains information about the location (start point and end point) of the original statement where it stems from, and this information is also available in the original AST (aka Cabs). It might thus be possible for someone with a good knowledge of Frama-C's inner workings (e.g. a reader of the developer's manual), to build a correspondance between both, and to use that to detect dead statement in Cabs. Going even further, one could bypass Cabs, and identify zones in the original text of the program which are dead code. Note however that it would be a tedious and quite error prone (notably because a single original statement can be expanded in several normalized ones) task.
Given your clarifications, I stand by #Virgile's answer; but for people interested in performing some simplistic dead code elimination within Frama-C, the script below, gifted by a colleague who has no SO account, could be helpful.
(* remove_dead_code.ml *)
let main () =
!Db.Value.compute ();
Slicing.Api.Project.reset_slicing ();
let selection = ref Slicing.Api.Select.empty_selects in
let o = object (self)
inherit Visitor.frama_c_inplace
method !vstmt_aux stmt =
if Db.Value.is_reachable_stmt stmt then
selection :=
Slicing.Api.Select.select_stmt ~spare:true
!selection
stmt
(Extlib.the self#current_kf);
Cil.DoChildren
end in
Visitor.visitFramacFileSameGlobals o (Ast.get ());
Slicing.Api.Request.add_persistent_selection !selection;
Slicing.Api.Request.apply_all_internal ();
Slicing.Api.Slice.remove_uncalled ();
ignore (Slicing.Api.Project.extract "no-dead")
let () = Db.Main.extend main
Usage:
frama-c -load-script remove_dead_code.ml file.c -then-last -print -ocode output.c
Note that this script does not work in all cases and could have further improvements (e.g. to handle initializers), but for some quick-and-dirty hacking, it can still be helpful.
I was going through swirl() again as a refresher, and I've noticed that the author of swirl says the command ?matrix is the correct form to calling for a help screen. But, when I run ?matrix(), it still works? Is there a difference between having and not having a pair of parenthesis?
It's not specific to the swirl environment (about which I was entirely unaware until 5 minutes ago) That is standard for R. The help page for the ? shortcut says:
Arguments
topic
Usually, a name or character string specifying the topic for which help is sought.
Alternatively, a function call to ask for documentation on a corresponding S4 method: see the section on S4 method documentation. The calls pkg::topic and pkg:::topic are treated specially, and look for help on topic in package pkg.
It something like the second option that is being invoked with the command:
?matrix()
Since ?? is actually a different shortcut one needs to use this code to bring up that page, just as one needs to use quoted strings for help with for, if, next or any of the other reserved words in R:
?'?' # See ?Reserved
This is not based on a "fuzzy logic" search in hte help system. Using help instead of ? gets a different response:
> help("str()")
No documentation for ‘str()’ in specified packages and libraries:
you could try ‘??str()’
You can see the full code for the ? function by typing ? at the command line, but I am just showing how it starts the language level processing of the expressions given to it:
`?`
function (e1, e2)
{
if (missing(e2)) {
type <- NULL
topicExpr <- substitute(e1)
}
#further output omitted
By running matrix and in general any_function you get the source code of it.
Consider the following code:
File C.jl
module C
export printLength
printLength = function(arr)
println(lentgh(arr))
end
end #module
File Main.jl
using C
main = function()
arr = Array(Int64, 4)
printLength(arr)
end
main()
Let's try to execute it.
$ julia Main.jl
ERROR: lentgh not defined
in include at /usr/bin/../lib64/julia/sys.so
in process_options at /usr/bin/../lib64/julia/sys.so
in _start at /usr/bin/../lib64/julia/sys.so
while loading /home/grzes/julia_sucks/Main.jl, in expression starting on line 8
Obviously, it doesn't compile, because lentgh is misspelled. The problem is the message I received. expression starting on line 8 is simply main(). Julia hopelessly fails to point the invalid code fragment -- it just points to the invocation of main, but the erroneous line is not even in that file! Now imagine a real project where an error hides really deep in the call stack. Julia still wouldn't tell anything more than that the problem started on the entry point of the execution. It is impossible to work like that...
Is there a way to force Julia to give a little more precise messages?
In this case it's almost certainly a consequence of inlining: your printLength function is so short, it's almost certainly inlined into the call site, which is why you get the line number 8.
Eventually, it is expected that inlining won't cause problems for backtraces. At the moment, your best bet---if you're running julia's pre-release 0.4 version---is to start julia as julia --inline=no and run your tests again.
I am using custom LLVM pass where if I encounter a store to
where the compiler converts the value to a Constant; e.g. there is an explicit store:
X[gidx] = 10;
Then LLVM will generate this error:
aoc: ../../../Instructions.cpp:1056: void llvm::StoreInst::AssertOK(): Assertion `getOperand(0)->getType() == cast<PointerType>(getOperand(1)->getType())->getElementType() && "Ptr must be a pointer to Val type!"' failed.
The inheritance order goes as: Value<-User<-Constant, so this shouldn't be an issue, but it is. Using an a cast on the ConstantInt or ConstantFP has no effect on this error.
So I've tried this bloated solution:
Value *new_value;
if(isa<ConstantInt>(old_value) || isa<ConstantFP>(old_value)){
Instruction *allocInst = builder.CreateAlloca(old_value->getType());
builder.CreateStore(old_value, allocInst);
new_value = builder.CreateLoad(allocResultInst);
}
However this solution creates its own register errors when different type are involved, so I'd like to avoid it.
Does anyone know how to convert a Constant to a Value? It must be a simple issue that I'm not seeing. I'm developing on Ubuntu 12.04, LLVM 3, AMD gpu, OpenCL kernels.
Thanks ahead of time.
EDIT:
The original code that produces the first error listed is simply:
builder.CreateStore(old_value, store_addr);
EDIT2:
This old_value is declared as
Value *old_value = current_instruction->getOperand(0);
So I'm grabbing the value to be stored, in this case "10" from the first code line.
You didn't provide the code that caused this first assertion, but its wording is pretty clear: you are trying to create a store where the value operand and the pointer operand do not agree on their types. It would be useful for the question if you'd provide the code that generated that error.
Your second, so-called "bloated" solution, is the correct way to store old_value into the stack and then load it again. You write:
However this solution creates its own register errors when different type are involved
These "register errors" are the real issue you should be addressing.
In any case, the whole premise of "converting a constant to a value" is flawed - as you have correctly observed, all constants are values. There's no point storing a value into the stack with the sole purpose of loading it again, and indeed the standard LLVM pass "mem2reg" will completely remove such a sequence, replacing all uses of the load with the original value.
folks!
I pass a struct full of data to my kernel, and I run into the following difficulty using it (very stripped down):
[edit: mac osx / xcode 3.2 on mac book pro; this compile is obviously for cpu]
typedef struct
{
float xoom;
int sizex;
} varholder;
float zX, xd;
__kernel void Harlan( __global varholder * vh )
{
int X = get_global_id(0), Y = get_global_id(1);
zX = ( ( X - vh->sizex/2 ) / vh->xoom + vh->sizex/2 ); // (a)
xd = zX; // (b) BOOM!!
}
after executing line (a), the line marked (b), a simple assignment, gives "LLVM compiler failed to compile a function".
if, however, we do not execute line (a), then line (b) is fine.
So, through my fiddling around a LOT with this, it seems as if it is the assignment statement (a), which uses a passed-in parameter, that messes up the future access of the variable zX. However, of course I need to be able to use the results of calculations further down the line.
I have zX and xd declared at the file level because my helper functions need them.
Any thoughts?
Thanks!
David
p.s. I'm now registered so will be able to upvote and accept answers, which I am sadly unable to do for the last person who helped me (used same username to register, but can't seem to vote on the old post; sorry!).
No, say it ain't so!
I am sincerely hoping that this is not a "correct" answer to my own question. I found on another forum (though not the same question asked!) the following, and I am afraid that it refers to what I'm trying to do:
(quote)
You're doing something the standard prohibits. Section 6.5 says:
'All program scope variables must be declared in the __constant address space.'
In other words, program scope variables cannot be mutable.
(end quote)
... well, tcha!!!! What an astoundingly inconvenient restriction! I'm sure there's reasoning behind it.
[edit: Not At All inconvenient! it was in fact astonishingly easy to work around, given a fresh start the next morning. (And no alcohol.)]
You guys & dolls all knew this, right, and didn't have the heart to tell me?...