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serializing an arbitrary data structure into a flat buffer (raw contiguousmemory block)

 
 
Alfonso Morra
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      10-03-2005
Hi,

I am writing a messaging library which will allow me to send a generic
message structure with custom "payloads".

In many cases, a message must store a non-linear data structure (i.e.
"payload") using pointers. Examples of these are binary trees, hash
tables etc. Thus, the message itself contains only a pointer to the
actual data. When the message is sent to the same processor, these
pointers point to the original locations, which are within the address
space of the same processor. However, when such a message is sent to
other processors, these pointers will point to invalid locations.

I need a way to ``serialize'' (or pack) my message structures into a
contiguous raw memory block (and then be able to de-serialize or
"unpack" them at the other end.

I just need a simple example, using a simple structure that contains
pointers (say a ptr to another struct, or a char*) so that I can build
on from that.

Searches on Google over the last few days have yielded nothig useful.

Thanks

 
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Zara
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Posts: n/a
 
      10-03-2005
Alfonso Morra wrote:
> Hi,
>
> I am writing a messaging library which will allow me to send a generic
> message structure with custom "payloads".
>
> In many cases, a message must store a non-linear data structure (i.e.
> "payload") using pointers. Examples of these are binary trees, hash
> tables etc. Thus, the message itself contains only a pointer to the
> actual data. When the message is sent to the same processor, these
> pointers point to the original locations, which are within the address
> space of the same processor. However, when such a message is sent to
> other processors, these pointers will point to invalid locations.
>
> I need a way to ``serialize'' (or pack) my message structures into a
> contiguous raw memory block (and then be able to de-serialize or
> "unpack" them at the other end.
>
> I just need a simple example, using a simple structure that contains
> pointers (say a ptr to another struct, or a char*) so that I can build
> on from that.
>
> Searches on Google over the last few days have yielded nothig useful.
>
> Thanks
>

A typical solution would be to store first all common data for the
message structure. Next, an "integer" (whichever integral type you
prefer) with the count of elements contained. Then, for every element,
the common part of it, followed by a count element, followed bu every
sub-element... Thus you will have no pointers and all (relevant) data
contained in the message.

In some cases, when elements have different structures, you may need to
prefix them with a type tag and/or a size field.

For instance:

<Total-size><message structure fields><number of elements>
{for every element}
<Element size><element type tag><element fields><number of
sub-elements>
{for every sub-element}
...
<some kind of element checksum>
<some kind of total checksum>
 
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Alfonso Morra
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Posts: n/a
 
      10-03-2005


Zara wrote:

> Alfonso Morra wrote:
>
>> Hi,
>>
>> I am writing a messaging library which will allow me to send a generic
>> message structure with custom "payloads".
>>
>> In many cases, a message must store a non-linear data structure (i.e.
>> "payload") using pointers. Examples of these are binary trees, hash
>> tables etc. Thus, the message itself contains only a pointer to the
>> actual data. When the message is sent to the same processor, these
>> pointers point to the original locations, which are within the address
>> space of the same processor. However, when such a message is sent to
>> other processors, these pointers will point to invalid locations.
>>
>> I need a way to ``serialize'' (or pack) my message structures into a
>> contiguous raw memory block (and then be able to de-serialize or
>> "unpack" them at the other end.
>>
>> I just need a simple example, using a simple structure that contains
>> pointers (say a ptr to another struct, or a char*) so that I can build
>> on from that.
>>
>> Searches on Google over the last few days have yielded nothig useful.
>>
>> Thanks
>>

> A typical solution would be to store first all common data for the
> message structure. Next, an "integer" (whichever integral type you
> prefer) with the count of elements contained. Then, for every element,
> the common part of it, followed by a count element, followed bu every
> sub-element... Thus you will have no pointers and all (relevant) data
> contained in the message.
>
> In some cases, when elements have different structures, you may need to
> prefix them with a type tag and/or a size field.
>
> For instance:
>
> <Total-size><message structure fields><number of elements>
> {for every element}
> <Element size><element type tag><element fields><number of
> sub-elements>
> {for every sub-element}
> ...
> <some kind of element checksum>
> <some kind of total checksum>


Thanks - but this is not what I'm looking for. Your code looks like some
kind of markup language. What I want is a byte stream (i.e. binary data).

For those reading - I am not concerned with endianess and other low
level details (its not necessary for my purposes).

 
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Zara
Guest
Posts: n/a
 
      10-03-2005
Alfonso Morra wrote:
>
>
> Zara wrote:
>
>> Alfonso Morra wrote:
>>
>>> Hi,
>>>
>>> I am writing a messaging library which will allow me to send a
>>> generic message structure with custom "payloads".
>>>

(...)
>>>
>>> I need a way to ``serialize'' (or pack) my message structures into a
>>> contiguous raw memory block (and then be able to de-serialize or
>>> "unpack" them at the other end.
>>>
>>>

(...)
>>
>> For instance:
>>
>> <Total-size><message structure fields><number of elements>
>> {for every element}
>> <Element size><element type tag><element fields><number of
>> sub-elements>
>> {for every sub-element}
>> ...
>> <some kind of element checksum>
>> <some kind of total checksum>

>
> Thanks - but this is not what I'm looking for. Your code looks like some
> kind of markup language. What I want is a byte stream (i.e. binary data).
>
> For those reading - I am not concerned with endianess and other low
> level details (its not necessary for my purposes).
>


Well, although my instance is full of < and >, it is not a mark-up
language. Suppose this:

struct node {
char *name;
node * next;
};

struct structure {
char *string;
node *list;
} my_structure;

and let it be:

my_structure
"Root node"
list---------->node 1
"It's me"
next------------>node 2
"It's I"
next->NULL

the message, in binary, could look something like:

00 23 00 09 52 6f 6f 54 20 6e 6f 64 65 00 02 00
0a 01 00 07 49 54 27 53 20 6d 65 00 09 01 00 06
49 54 27 53 20 49

Which has all of the data contained in it, except the checksums (I don`t
feel like putting them in), and it supposes a little-endian, ASCII machine.

Now, if you bother with looking at it, you will see it fits with your
specs, and is described by my former message

Regards

 
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Alfonso Morra
Guest
Posts: n/a
 
      10-03-2005


Zara wrote:

> Alfonso Morra wrote:
>
>>
>>
>> Zara wrote:
>>
>>> Alfonso Morra wrote:
>>>
>>>> Hi,
>>>>
>>>> I am writing a messaging library which will allow me to send a
>>>> generic message structure with custom "payloads".
>>>>

> (...)
>
>>>>
>>>> I need a way to ``serialize'' (or pack) my message structures into a
>>>> contiguous raw memory block (and then be able to de-serialize or
>>>> "unpack" them at the other end.
>>>>
>>>>

> (...)
>
>>>
>>> For instance:
>>>
>>> <Total-size><message structure fields><number of elements>
>>> {for every element}
>>> <Element size><element type tag><element fields><number of
>>> sub-elements>
>>> {for every sub-element}
>>> ...
>>> <some kind of element checksum>
>>> <some kind of total checksum>

>>
>>
>> Thanks - but this is not what I'm looking for. Your code looks like
>> some kind of markup language. What I want is a byte stream (i.e.
>> binary data).
>>
>> For those reading - I am not concerned with endianess and other low
>> level details (its not necessary for my purposes).
>>

>
> Well, although my instance is full of < and >, it is not a mark-up
> language. Suppose this:
>
> struct node {
> char *name;
> node * next;
> };
>
> struct structure {
> char *string;
> node *list;
> } my_structure;
>
> and let it be:
>
> my_structure
> "Root node"
> list---------->node 1
> "It's me"
> next------------>node 2
> "It's I"
> next->NULL
>
> the message, in binary, could look something like:
>
> 00 23 00 09 52 6f 6f 54 20 6e 6f 64 65 00 02 00
> 0a 01 00 07 49 54 27 53 20 6d 65 00 09 01 00 06
> 49 54 27 53 20 49
>
> Which has all of the data contained in it, except the checksums (I don`t
> feel like putting them in), and it supposes a little-endian, ASCII machine.
>
> Now, if you bother with looking at it, you will see it fits with your
> specs, and is described by my former message
>
> Regards
>


You've completely lost me now. I have no idea how you arived at the hex
dump from your two structures. What I'm really after is a simple example
(or a link to a site where I can see an example of serializing a simple
struct containing pointers). I have searchedGoogle over the last three
days - to no avail.

It does not have to be anything too complicated. Simply so that I can
build on it and use it as the starting point for serializing my
stuctures - although I have a rough idea of what you're doing, I am
unfortunately, unable to build on your examples thus far.

 
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Michael Wojcik
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Posts: n/a
 
      10-04-2005

In article <dhqll3$h5i$(E-Mail Removed)-infra.bt.com>, Alfonso Morra <(E-Mail Removed)> writes:
>
> In many cases, a message must store a non-linear data structure (i.e.
> "payload") using pointers. Examples of these are binary trees, hash
> tables etc. Thus, the message itself contains only a pointer to the
> actual data. When the message is sent to the same processor, these
> pointers point to the original locations, which are within the address
> space of the same processor. However, when such a message is sent to
> other processors, these pointers will point to invalid locations.
>
> I need a way to ``serialize'' (or pack) my message structures into a
> contiguous raw memory block (and then be able to de-serialize or
> "unpack" them at the other end.


This is not a trivial problem, but it's not a particularly difficult
one, either.

In some cases the original data structure, or a suitable facsimile,
can be reconstructed from the data alone. This is often the case
with hash tables, sorted lists, binary trees, and so forth. The
sending side simply sends the nodes and the receiving side inserts
them into the appropriate data structure.

In the general case, however, you need a mechanism for preserving
associations between pieces of data. Pointers are such a mechanism,
but they (almost always[1]) represent a system-specific, and usually
process-specific, mapping, and in any case the information that a
portable C program can extract from them is limited.

So the obvious solution is to have your serialization process replace
the pointers with some portable representation of the associations
between items. One very simple approach is to serialize all of the
items into a single block of malloc'd memory (using a pointer to
unsigned char), and replace the pointers with offsets into that
block. The deserializer extracts items, remembering the locations it
has extracted them to, and converts from offsets back into pointers.

A better scheme is probably to label each item with a unique
identifier and replace each pointer with the identifier of the object
it points to. This is essentially the same as the "offset" scheme
except that it makes the mapping explicit (offsets are really just
unique IDs). That increases the information available to the
deserializer, which makes it more robust - it's easier for it to
detect malformed input. Transporting data and converting it among
representations are fragile, vulnerable operations, and you want to
make them as robust as possible.

> I just need a simple example, using a simple structure that contains
> pointers (say a ptr to another struct, or a char*) so that I can build
> on from that.


It's difficult to provide a robust, portable, short example, because
this is not a problem that lends itself to short, portable code.
Portable data representations require marshalling and unmarshalling
from and to the local system's representation. Furthermore, to
really handle the general case, you have to keep a map from object
addresses to IDs while serializing (so that each pointer can be
converted to its ID), and a reverse map while deserializing.

Here's an outline for the serializer:

- Walk the data, creating a unique ID for each item and mapping
it to the item's address. You'll have to choose what data structure
to use for the map; a hash table (keyed by address) is an obvious
choice, but might not be worth the overhead and complexity.

- As each item is serialized, prefix it with its ID (and, presumably,
type information and any other metadata your system needs to provide).

- In the serialized representation, replace each pointer field with
the ID of the pointed-to object.

This two-pass approach is simpler than a single pass, which would
have to remember the locations in the serialized data of pointer/ID
fields that referred to objects that hadn't yet been assigned an ID,
so you could fill those in later.

The deserializer would use a similar two-pass process, first
allocating areas for each item and building a map between area and ID
in the process, then deserializing each item into its area and
setting pointer fields using the map.


1. There are esoteric architectures which use "fat" pointers that
contain more information than simply an offset into address space,
but that's an implementation detail that's not useful in portable C
programming.

--
Michael Wojcik http://www.velocityreviews.com/forums/(E-Mail Removed)

Against all odds, over a noisy telephone line, tapped by the tax authorities
and the secret police, Alice will happily attempt, with someone she doesn't
trust, whom she can't hear clearly, and who is probably someone else, to
fiddle her tax return and to organise a coup d'etat, while at the same time
minimising the cost of the phone call. -- John Gordon
 
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