Distributed Array Access Communication Cost - chapel

I'm finishing up implementing a sort of "Terasort Lite" program in Chapel, based on a distributed bucket sort, and I'm noticing what seems to be significant performance bottlenecks around access to a block-distributed array. A rough benchmark shows Chapel takes ~7 seconds to do the whole sort of 3.5MB with 5 locales, while the original MPI+C program does it in around 8.2ms with 5 processes. My local machine has 16 cores, so I don't need to oversubscribe MPI to get 5 processes working.
The data to be sorted are loaded into a block-distributed array across each of the locales so that each locale has an even (and contiguous) share of the unsorted records. In an MPI+C bucket sort, each process would have its records in memory and sort those local records. To that end, I've written a locale-aware implementation of qsort (based on the C stdlib implementation), and this is where I see extreme performance bottlenecks. The overall bucket sort procedure takes a reference to a block distributed array, and qsort is called with the local subdomain: qsort(records[records.localSubdomain()]) from within the coforall block and on loc do clause.
My main question is how Chapel maintains coherence on distributed arrays, and whether any type of coherence actions across locales are what's obliterating my performance. I've checked, and each locale's qsort call is only ever accessing array indices within its local subdomain; I would expect that this means that no communication is required, since each locale accesses only the portion of the domain that it owns. Is this a reasonable expectation, or is this simultaneous access to private portions of a distributed array causing communication overhead?
For context, I am running locally on one physical machine using the UDP GASNET communication substrate, and the documentation notes that this is not expected to give good performance. Nonetheless, I do plan to move the code to a cluster with InfiniBand, so I'd still like to know if I should approach the problem a different way to get better performance. Please let me know if there's any other information that would help this question be answered. Thank you!

Thanks for your question. I can answer some of the questions here.
First, I'd like to point out some other distributed sort implementations in Chapel:
The distributed sort in Arkouda
distributedPartitioningSortWithScratchSpace I have not worked on this in a while but if I recall correctly it is a distributed sample sort backed by a not-in-place radix sort and I think it is tested so it should run
I have other partial work trying to port over ips4o but that algorithm is pretty complicated and I didn't get all the way through and it's not running yet.
Generally I would expect a radix sort to outperform a quick sort for the local problems unless they are very small.
Now to your questions:
My main question is how Chapel maintains coherence on distributed arrays, and whether any type of coherence actions across locales are what's obliterating my performance.
There is a cache for remote data that is on by default. It can be disabled with --no-cache-remote when compiling but I suspect it is not the problem here. In particular, it mainly does any coherence activities on some sort of memory fence (which includes on statement, task end, use of sync/atomic variables). But, you can turn it off and see if that changes things.
Distributed arrays and domains currently use an eager privatization strategy. That means that once they are created, some elements of the data structure is replicated across all locales. Since this involves all locales, it can cause performance problems when running multilocale.
You can check for communication within your kernel with the CommDiagnostics module or with the local block. The CommDiagnostics module will allow you to count or trace communication events while the local block will halt your program if communication is attempted within it.
Another possibility is that the compiler is not generating communication but it is running slower because it has trouble optimizing when the data might be remote. The indicator that this is the problem would be that the performance you get when compiling with CHPL_COMM=none is significantly faster than when running with 1 locale with gasnet and UDP. (You could alternatively use --local and --no-local flags to compare). Some ways to potentially help that:
instead of records[records.localSubdomain()], you could try records.localSlice(records.localSubdomain()) but that uses an undocumented feature. I do not know why it is undocumented, though.
using a local block within your computation should solve this as well but note that we generally try to solve the problem in other ways since the local block is a big hammer.
Slicing has more overhead than we would like. See e.g. https://github.com/chapel-lang/chapel/issues/13317 . As I said, there might also be privatization costs (I don't remember what the current situation of slicing and privatization is, off-hand). In my experience, for local sorting code, you are better off passing a start and end argument as ints, or maybe a range; but slicing to get the local part of the array is certainly more important in the distributed setting.
Lastly, you mentioned that you're trying to analyze the performance when running oversubscribed. If you haven't already seen it, check out this documentation about oversubscription that recommends a setting.

Related

Compiling an application for use in highly radioactive environments

We are compiling an embedded C++ application that is deployed in a shielded device in an environment bombarded with ionizing radiation. We are using GCC and cross-compiling for ARM. When deployed, our application generates some erroneous data and crashes more often than we would like. The hardware is designed for this environment, and our application has run on this platform for several years.
Are there changes we can make to our code, or compile-time improvements that can be made to identify/correct soft errors and memory-corruption caused by single event upsets? Have any other developers had success in reducing the harmful effects of soft errors on a long-running application?
Working for about 4-5 years with software/firmware development and environment testing of miniaturized satellites*, I would like to share my experience here.
*(miniaturized satellites are a lot more prone to single event upsets than bigger satellites due to its relatively small, limited sizes for its electronic components)
To be very concise and direct: there is no mechanism to recover from detectable, erroneous
situation by the software/firmware itself without, at least, one
copy of minimum working version of the software/firmware somewhere for recovery purpose - and with the hardware supporting the recovery (functional).
Now, this situation is normally handled both in the hardware and software level. Here, as you request, I will share what we can do in the software level.
...recovery purpose.... Provide ability to update/recompile/reflash your software/firmware in real environment. This is an almost must-have feature for any software/firmware in highly ionized environment. Without this, you could have redundant software/hardware as many as you want but at one point, they are all going to blow up. So, prepare this feature!
...minimum working version... Have responsive, multiple copies, minimum version of the software/firmware in your code. This is like Safe mode in Windows. Instead of having only one, fully functional version of your software, have multiple copies of the minimum version of your software/firmware. The minimum copy will usually having much less size than the full copy and almost always have only the following two or three features:
capable of listening to command from external system,
capable of updating the current software/firmware,
capable of monitoring the basic operation's housekeeping data.
...copy... somewhere... Have redundant software/firmware somewhere.
You could, with or without redundant hardware, try to have redundant software/firmware in your ARM uC. This is normally done by having two or more identical software/firmware in separate addresses which sending heartbeat to each other - but only one will be active at a time. If one or more software/firmware is known to be unresponsive, switch to the other software/firmware. The benefit of using this approach is we can have functional replacement immediately after an error occurs - without any contact with whatever external system/party who is responsible to detect and to repair the error (in satellite case, it is usually the Mission Control Centre (MCC)).
Strictly speaking, without redundant hardware, the disadvantage of doing this is you actually cannot eliminate all single point of failures. At the very least, you will still have one single point of failure, which is the switch itself (or often the beginning of the code). Nevertheless, for a device limited by size in a highly ionized environment (such as pico/femto satellites), the reduction of the single point of failures to one point without additional hardware will still be worth considering. Somemore, the piece of code for the switching would certainly be much less than the code for the whole program - significantly reducing the risk of getting Single Event in it.
But if you are not doing this, you should have at least one copy in your external system which can come in contact with the device and update the software/firmware (in the satellite case, it is again the mission control centre).
You could also have the copy in your permanent memory storage in your device which can be triggered to restore the running system's software/firmware
...detectable erroneous situation.. The error must be detectable, usually by the hardware error correction/detection circuit or by a small piece of code for error correction/detection. It is best to put such code small, multiple, and independent from the main software/firmware. Its main task is only for checking/correcting. If the hardware circuit/firmware is reliable (such as it is more radiation hardened than the rests - or having multiple circuits/logics), then you might consider making error-correction with it. But if it is not, it is better to make it as error-detection. The correction can be by external system/device. For the error correction, you could consider making use of a basic error correction algorithm like Hamming/Golay23, because they can be implemented more easily both in the circuit/software. But it ultimately depends on your team's capability. For error detection, normally CRC is used.
...hardware supporting the recovery Now, comes to the most difficult aspect on this issue. Ultimately, the recovery requires the hardware which is responsible for the recovery to be at least functional. If the hardware is permanently broken (normally happen after its Total ionizing dose reaches certain level), then there is (sadly) no way for the software to help in recovery. Thus, hardware is rightly the utmost importance concern for a device exposed to high radiation level (such as satellite).
In addition to the suggestion for above anticipating firmware's error due to single event upset, I would also like to suggest you to have:
Error detection and/or error correction algorithm in the inter-subsystem communication protocol. This is another almost must have in order to avoid incomplete/wrong signals received from other system
Filter in your ADC reading. Do not use the ADC reading directly. Filter it by median filter, mean filter, or any other filters - never trust single reading value. Sample more, not less - reasonably.
NASA has a paper on radiation-hardened software. It describes three main tasks:
Regular monitoring of memory for errors then scrubbing out those errors,
robust error recovery mechanisms, and
the ability to reconfigure if something no longer works.
Note that the memory scan rate should be frequent enough that multi-bit errors rarely occur, as most ECC memory can recover from single-bit errors, not multi-bit errors.
Robust error recovery includes control flow transfer (typically restarting a process at a point before the error), resource release, and data restoration.
Their main recommendation for data restoration is to avoid the need for it, through having intermediate data be treated as temporary, so that restarting before the error also rolls back the data to a reliable state. This sounds similar to the concept of "transactions" in databases.
They discuss techniques particularly suitable for object-oriented languages such as C++. For example
Software-based ECCs for contiguous memory objects
Programming by Contract: verifying preconditions and postconditions, then checking the object to verify it is still in a valid state.
And, it just so happens, NASA has used C++ for major projects such as the Mars Rover.
C++ class abstraction and encapsulation enabled rapid development and testing among multiple projects and developers.
They avoided certain C++ features that could create problems:
Exceptions
Templates
Iostream (no console)
Multiple inheritance
Operator overloading (other than new and delete)
Dynamic allocation (used a dedicated memory pool and placement new to avoid the possibility of system heap corruption).
Here are some thoughts and ideas:
Use ROM more creatively.
Store anything you can in ROM. Instead of calculating things, store look-up tables in ROM. (Make sure your compiler is outputting your look-up tables to the read-only section! Print out memory addresses at runtime to check!) Store your interrupt vector table in ROM. Of course, run some tests to see how reliable your ROM is compared to your RAM.
Use your best RAM for the stack.
SEUs in the stack are probably the most likely source of crashes, because it is where things like index variables, status variables, return addresses, and pointers of various sorts typically live.
Implement timer-tick and watchdog timer routines.
You can run a "sanity check" routine every timer tick, as well as a watchdog routine to handle the system locking up. Your main code could also periodically increment a counter to indicate progress, and the sanity-check routine could ensure this has occurred.
Implement error-correcting-codes in software.
You can add redundancy to your data to be able to detect and/or correct errors. This will add processing time, potentially leaving the processor exposed to radiation for a longer time, thus increasing the chance of errors, so you must consider the trade-off.
Remember the caches.
Check the sizes of your CPU caches. Data that you have accessed or modified recently will probably be within a cache. I believe you can disable at least some of the caches (at a big performance cost); you should try this to see how susceptible the caches are to SEUs. If the caches are hardier than RAM then you could regularly read and re-write critical data to make sure it stays in cache and bring RAM back into line.
Use page-fault handlers cleverly.
If you mark a memory page as not-present, the CPU will issue a page fault when you try to access it. You can create a page-fault handler that does some checking before servicing the read request. (PC operating systems use this to transparently load pages that have been swapped to disk.)
Use assembly language for critical things (which could be everything).
With assembly language, you know what is in registers and what is in RAM; you know what special RAM tables the CPU is using, and you can design things in a roundabout way to keep your risk down.
Use objdump to actually look at the generated assembly language, and work out how much code each of your routines takes up.
If you are using a big OS like Linux then you are asking for trouble; there is just so much complexity and so many things to go wrong.
Remember it is a game of probabilities.
A commenter said
Every routine you write to catch errors will be subject to failing itself from the same cause.
While this is true, the chances of errors in the (say) 100 bytes of code and data required for a check routine to function correctly is much smaller than the chance of errors elsewhere. If your ROM is pretty reliable and almost all the code/data is actually in ROM then your odds are even better.
Use redundant hardware.
Use 2 or more identical hardware setups with identical code. If the results differ, a reset should be triggered. With 3 or more devices you can use a "voting" system to try to identify which one has been compromised.
You may also be interested in the rich literature on the subject of algorithmic fault tolerance. This includes the old assignment: Write a sort that correctly sorts its input when a constant number of comparisons will fail (or, the slightly more evil version, when the asymptotic number of failed comparisons scales as log(n) for n comparisons).
A place to start reading is Huang and Abraham's 1984 paper "Algorithm-Based Fault Tolerance for Matrix Operations". Their idea is vaguely similar to homomorphic encrypted computation (but it is not really the same, since they are attempting error detection/correction at the operation level).
A more recent descendant of that paper is Bosilca, Delmas, Dongarra, and Langou's "Algorithm-based fault tolerance applied to high performance computing".
Writing code for radioactive environments is not really any different than writing code for any mission-critical application.
In addition to what has already been mentioned, here are some miscellaneous tips:
Use everyday "bread & butter" safety measures that should be present on any semi-professional embedded system: internal watchdog, internal low-voltage detect, internal clock monitor. These things shouldn't even need to be mentioned in the year 2016 and they are standard on pretty much every modern microcontroller.
If you have a safety and/or automotive-oriented MCU, it will have certain watchdog features, such as a given time window, inside which you need to refresh the watchdog. This is preferred if you have a mission-critical real-time system.
In general, use a MCU suitable for these kind of systems, and not some generic mainstream fluff you received in a packet of corn flakes. Almost every MCU manufacturer nowadays have specialized MCUs designed for safety applications (TI, Freescale, Renesas, ST, Infineon etc etc). These have lots of built-in safety features, including lock-step cores: meaning that there are 2 CPU cores executing the same code, and they must agree with each other.
IMPORTANT: You must ensure the integrity of internal MCU registers. All control & status registers of hardware peripherals that are writeable may be located in RAM memory, and are therefore vulnerable.
To protect yourself against register corruptions, preferably pick a microcontroller with built-in "write-once" features of registers. In addition, you need to store default values of all hardware registers in NVM and copy-down those values to your registers at regular intervals. You can ensure the integrity of important variables in the same manner.
Note: always use defensive programming. Meaning that you have to setup all registers in the MCU and not just the ones used by the application. You don't want some random hardware peripheral to suddenly wake up.
There are all kinds of methods to check for errors in RAM or NVM: checksums, "walking patterns", software ECC etc etc. The best solution nowadays is to not use any of these, but to use a MCU with built-in ECC and similar checks. Because doing this in software is complex, and the error check in itself could therefore introduce bugs and unexpected problems.
Use redundancy. You could store both volatile and non-volatile memory in two identical "mirror" segments, that must always be equivalent. Each segment could have a CRC checksum attached.
Avoid using external memories outside the MCU.
Implement a default interrupt service routine / default exception handler for all possible interrupts/exceptions. Even the ones you are not using. The default routine should do nothing except shutting off its own interrupt source.
Understand and embrace the concept of defensive programming. This means that your program needs to handle all possible cases, even those that cannot occur in theory. Examples.
High quality mission-critical firmware detects as many errors as possible, and then handles or ignores them in a safe manner.
Never write programs that rely on poorly-specified behavior. It is likely that such behavior might change drastically with unexpected hardware changes caused by radiation or EMI. The best way to ensure that your program is free from such crap is to use a coding standard like MISRA, together with a static analyser tool. This will also help with defensive programming and with weeding out bugs (why would you not want to detect bugs in any kind of application?).
IMPORTANT: Don't implement any reliance of the default values of static storage duration variables. That is, don't trust the default contents of the .data or .bss. There could be any amount of time between the point of initialization to the point where the variable is actually used, there could have been plenty of time for the RAM to get corrupted. Instead, write the program so that all such variables are set from NVM in run-time, just before the time when such a variable is used for the first time.
In practice this means that if a variable is declared at file scope or as static, you should never use = to initialize it (or you could, but it is pointless, because you cannot rely on the value anyhow). Always set it in run-time, just before use. If it is possible to repeatedly update such variables from NVM, then do so.
Similarly in C++, don't rely on constructors for static storage duration variables. Have the constructor(s) call a public "set-up" routine, which you can also call later on in run-time, straight from the caller application.
If possible, remove the "copy-down" start-up code that initializes .data and .bss (and calls C++ constructors) entirely, so that you get linker errors if you write code relying on such. Many compilers have the option to skip this, usually called "minimal/fast start-up" or similar.
This means that any external libraries have to be checked so that they don't contain any such reliance.
Implement and define a safe state for the program, to where you will revert in case of critical errors.
Implementing an error report/error log system is always helpful.
It may be possible to use C to write programs that behave robustly in such environments, but only if most forms of compiler optimization are disabled. Optimizing compilers are designed to replace many seemingly-redundant coding patterns with "more efficient" ones, and may have no clue that the reason the programmer is testing x==42 when the compiler knows there's no way x could possibly hold anything else is because the programmer wants to prevent the execution of certain code with x holding some other value--even in cases where the only way it could hold that value would be if the system received some kind of electrical glitch.
Declaring variables as volatile is often helpful, but may not be a panacea.
Of particular importance, note that safe coding often requires that dangerous
operations have hardware interlocks that require multiple steps to activate,
and that code be written using the pattern:
... code that checks system state
if (system_state_favors_activation)
{
prepare_for_activation();
... code that checks system state again
if (system_state_is_valid)
{
if (system_state_favors_activation)
trigger_activation();
}
else
perform_safety_shutdown_and_restart();
}
cancel_preparations();
If a compiler translates the code in relatively literal fashion, and if all
the checks for system state are repeated after the prepare_for_activation(),
the system may be robust against almost any plausible single glitch event,
even those which would arbitrarily corrupt the program counter and stack. If
a glitch occurs just after a call to prepare_for_activation(), that would imply
that activation would have been appropriate (since there's no other reason
prepare_for_activation() would have been called before the glitch). If the
glitch causes code to reach prepare_for_activation() inappropriately, but there
are no subsequent glitch events, there would be no way for code to subsequently
reach trigger_activation() without having passed through the validation check or calling cancel_preparations first [if the stack glitches, execution might proceed to a spot just before trigger_activation() after the context that called prepare_for_activation() returns, but the call to cancel_preparations() would have occurred between the calls to prepare_for_activation() and trigger_activation(), thus rendering the latter call harmless.
Such code may be safe in traditional C, but not with modern C compilers. Such compilers can be very dangerous in that sort of environment because aggressive they strive to only include code which will be relevant in situations that could come about via some well-defined mechanism and whose resulting consequences would also be well defined. Code whose purpose would be to detect and clean up after failures may, in some cases, end up making things worse. If the compiler determines that the attempted recovery would in some cases invoke undefined behavior, it may infer that the conditions that would necessitate such recovery in such cases cannot possibly occur, thus eliminating the code that would have checked for them.
This is an extremely broad subject. Basically, you can't really recover from memory corruption, but you can at least try to fail promptly. Here are a few techniques you could use:
checksum constant data. If you have any configuration data which stays constant for a long time (including hardware registers you have configured), compute its checksum on initialization and verify it periodically. When you see a mismatch, it's time to re-initialize or reset.
store variables with redundancy. If you have an important variable x, write its value in x1, x2 and x3 and read it as (x1 == x2) ? x2 : x3.
implement program flow monitoring. XOR a global flag with a unique value in important functions/branches called from the main loop. Running the program in a radiation-free environment with near-100% test coverage should give you the list of acceptable values of the flag at the end of the cycle. Reset if you see deviations.
monitor the stack pointer. In the beginning of the main loop, compare the stack pointer with its expected value. Reset on deviation.
What could help you is a watchdog. Watchdogs were used extensively in industrial computing in the 1980s. Hardware failures were much more common then - another answer also refers to that period.
A watchdog is a combined hardware/software feature. The hardware is a simple counter that counts down from a number (say 1023) to zero. TTL or other logic could be used.
The software has been designed as such that one routine monitors the correct operation of all essential systems. If this routine completes correctly = finds the computer running fine, it sets the counter back to 1023.
The overall design is so that under normal circumstances, the software prevents that the hardware counter will reach zero. In case the counter reaches zero, the hardware of the counter performs its one-and-only task and resets the entire system. From a counter perspective, zero equals 1024 and the counter continues counting down again.
This watchdog ensures that the attached computer is restarted in a many, many cases of failure. I must admit that I'm not familiar with hardware that is able to perform such a function on today's computers. Interfaces to external hardware are now a lot more complex than they used to be.
An inherent disadvantage of the watchdog is that the system is not available from the time it fails until the watchdog counter reaches zero + reboot time. While that time is generally much shorter than any external or human intervention, the supported equipment will need to be able to proceed without computer control for that timeframe.
This answer assumes you are concerned with having a system that works correctly, over and above having a system that is minimum cost or fast; most people playing with radioactive things value correctness / safety over speed / cost
Several people have suggested hardware changes you can make (fine - there's lots of good stuff here in answers already and I don't intend repeating all of it), and others have suggested redundancy (great in principle), but I don't think anyone has suggested how that redundancy might work in practice. How do you fail over? How do you know when something has 'gone wrong'? Many technologies work on the basis everything will work, and failure is thus a tricky thing to deal with. However, some distributed computing technologies designed for scale expect failure (after all with enough scale, failure of one node of many is inevitable with any MTBF for a single node); you can harness this for your environment.
Here are some ideas:
Ensure that your entire hardware is replicated n times (where n is greater than 2, and preferably odd), and that each hardware element can communicate with each other hardware element. Ethernet is one obvious way to do that, but there are many other far simpler routes that would give better protection (e.g. CAN). Minimise common components (even power supplies). This may mean sampling ADC inputs in multiple places for instance.
Ensure your application state is in a single place, e.g. in a finite state machine. This can be entirely RAM based, though does not preclude stable storage. It will thus be stored in several place.
Adopt a quorum protocol for changes of state. See RAFT for example. As you are working in C++, there are well known libraries for this. Changes to the FSM would only get made when a majority of nodes agree. Use a known good library for the protocol stack and the quorum protocol rather than rolling one yourself, or all your good work on redundancy will be wasted when the quorum protocol hangs up.
Ensure you checksum (e.g. CRC/SHA) your FSM, and store the CRC/SHA in the FSM itself (as well as transmitting in the message, and checksumming the messages themselves). Get the nodes to check their FSM regularly against these checksum, checksum incoming messages, and check their checksum matches the checksum of the quorum.
Build as many other internal checks into your system as possible, making nodes that detect their own failure reboot (this is better than carrying on half working provided you have enough nodes). Attempt to let them cleanly remove themselves from the quorum during rebooting in case they don't come up again. On reboot have them checksum the software image (and anything else they load) and do a full RAM test before reintroducing themselves to the quorum.
Use hardware to support you, but do so carefully. You can get ECC RAM, for instance, and regularly read/write through it to correct ECC errors (and panic if the error is uncorrectable). However (from memory) static RAM is far more tolerant of ionizing radiation than DRAM is in the first place, so it may be better to use static DRAM instead. See the first point under 'things I would not do' as well.
Let's say you have an 1% chance of failure of any given node within one day, and let's pretend you can make failures entirely independent. With 5 nodes, you'll need three to fail within one day, which is a .00001% chance. With more, well, you get the idea.
Things I would not do:
Underestimate the value of not having the problem to start off with. Unless weight is a concern, a large block of metal around your device is going to be a far cheaper and more reliable solution than a team of programmers can come up with. Ditto optical coupling of inputs of EMI is an issue, etc. Whatever, attempt when sourcing your components to source those rated best against ionizing radiation.
Roll your own algorithms. People have done this stuff before. Use their work. Fault tolerance and distributed algorithms are hard. Use other people's work where possible.
Use complicated compiler settings in the naive hope you detect more failures. If you are lucky, you may detect more failures. More likely, you will use a code-path within the compiler which has been less tested, particularly if you rolled it yourself.
Use techniques which are untested in your environment. Most people writing high availability software have to simulate failure modes to check their HA works correctly, and miss many failure modes as a result. You are in the 'fortunate' position of having frequent failures on demand. So test each technique, and ensure its application actual improves MTBF by an amount that exceeds the complexity to introduce it (with complexity comes bugs). Especially apply this to my advice re quorum algorithms etc.
Since you specifically ask for software solutions, and you are using C++, why not use operator overloading to make your own, safe datatypes? For example:
Instead of using uint32_t (and double, int64_t etc), make your own SAFE_uint32_t which contains a multiple (minimum of 3) of uint32_t. Overload all of the operations you want (* + - / << >> = == != etc) to perform, and make the overloaded operations perform independently on each internal value, ie don't do it once and copy the result. Both before and after, check that all of the internal values match. If values don't match, you can update the wrong one to the value with the most common one. If there is no most-common value, you can safely notify that there is an error.
This way it doesn't matter if corruption occurs in the ALU, registers, RAM, or on a bus, you will still have multiple attempts and a very good chance of catching errors. Note however though that this only works for the variables you can replace - your stack pointer for example will still be susceptible.
A side story: I ran into a similar issue, also on an old ARM chip. It turned out to be a toolchain which used an old version of GCC that, together with the specific chip we used, triggered a bug in certain edge cases that would (sometimes) corrupt values being passed into functions. Make sure your device doesn't have any problems before blaming it on radio-activity, and yes, sometimes it is a compiler bug =)
Disclaimer: I'm not a radioactivity professional nor worked for this kind of application. But I worked on soft errors and redundancy for long term archival of critical data, which is somewhat linked (same problem, different goals).
The main problem with radioactivity in my opinion is that radioactivity can switch bits, thus radioactivity can/will tamper any digital memory. These errors are usually called soft errors, bit rot, etc.
The question is then: how to compute reliably when your memory is unreliable?
To significantly reduce the rate of soft errors (at the expense of computational overhead since it will mostly be software-based solutions), you can either:
rely on the good old redundancy scheme, and more specifically the more efficient error correcting codes (same purpose, but cleverer algorithms so that you can recover more bits with less redundancy). This is sometimes (wrongly) also called checksumming. With this kind of solution, you will have to store the full state of your program at any moment in a master variable/class (or a struct?), compute an ECC, and check that the ECC is correct before doing anything, and if not, repair the fields. This solution however does not guarantee that your software can work (simply that it will work correctly when it can, or stops working if not, because ECC can tell you if something is wrong, and in this case you can stop your software so that you don't get fake results).
or you can use resilient algorithmic data structures, which guarantee, up to a some bound, that your program will still give correct results even in the presence of soft errors. These algorithms can be seen as a mix of common algorithmic structures with ECC schemes natively mixed in, but this is much more resilient than that, because the resiliency scheme is tightly bounded to the structure, so that you don't need to encode additional procedures to check the ECC, and usually they are a lot faster. These structures provide a way to ensure that your program will work under any condition, up to the theoretical bound of soft errors. You can also mix these resilient structures with the redundancy/ECC scheme for additional security (or encode your most important data structures as resilient, and the rest, the expendable data that you can recompute from the main data structures, as normal data structures with a bit of ECC or a parity check which is very fast to compute).
If you are interested in resilient data structures (which is a recent, but exciting, new field in algorithmics and redundancy engineering), I advise you to read the following documents:
Resilient algorithms data structures intro by Giuseppe F.Italiano, Universita di Roma "Tor Vergata"
Christiano, P., Demaine, E. D., & Kishore, S. (2011). Lossless fault-tolerant data structures with additive overhead. In Algorithms and Data Structures (pp. 243-254). Springer Berlin Heidelberg.
Ferraro-Petrillo, U., Grandoni, F., & Italiano, G. F. (2013). Data structures resilient to memory faults: an experimental study of dictionaries. Journal of Experimental Algorithmics (JEA), 18, 1-6.
Italiano, G. F. (2010). Resilient algorithms and data structures. In Algorithms and Complexity (pp. 13-24). Springer Berlin Heidelberg.
If you are interested in knowing more about the field of resilient data structures, you can checkout the works of Giuseppe F. Italiano (and work your way through the refs) and the Faulty-RAM model (introduced in Finocchi et al. 2005; Finocchi and Italiano 2008).
/EDIT: I illustrated the prevention/recovery from soft-errors mainly for RAM memory and data storage, but I didn't talk about computation (CPU) errors. Other answers already pointed at using atomic transactions like in databases, so I will propose another, simpler scheme: redundancy and majority vote.
The idea is that you simply do x times the same computation for each computation you need to do, and store the result in x different variables (with x >= 3). You can then compare your x variables:
if they all agree, then there's no computation error at all.
if they disagree, then you can use a majority vote to get the correct value, and since this means the computation was partially corrupted, you can also trigger a system/program state scan to check that the rest is ok.
if the majority vote cannot determine a winner (all x values are different), then it's a perfect signal for you to trigger the failsafe procedure (reboot, raise an alert to user, etc.).
This redundancy scheme is very fast compared to ECC (practically O(1)) and it provides you with a clear signal when you need to failsafe. The majority vote is also (almost) guaranteed to never produce corrupted output and also to recover from minor computation errors, because the probability that x computations give the same output is infinitesimal (because there is a huge amount of possible outputs, it's almost impossible to randomly get 3 times the same, even less chances if x > 3).
So with majority vote you are safe from corrupted output, and with redundancy x == 3, you can recover 1 error (with x == 4 it will be 2 errors recoverable, etc. -- the exact equation is nb_error_recoverable == (x-2) where x is the number of calculation repetitions because you need at least 2 agreeing calculations to recover using the majority vote).
The drawback is that you need to compute x times instead of once, so you have an additional computation cost, but's linear complexity so asymptotically you don't lose much for the benefits you gain. A fast way to do a majority vote is to compute the mode on an array, but you can also use a median filter.
Also, if you want to make extra sure the calculations are conducted correctly, if you can make your own hardware you can construct your device with x CPUs, and wire the system so that calculations are automatically duplicated across the x CPUs with a majority vote done mechanically at the end (using AND/OR gates for example). This is often implemented in airplanes and mission-critical devices (see triple modular redundancy). This way, you would not have any computational overhead (since the additional calculations will be done in parallel), and you have another layer of protection from soft errors (since the calculation duplication and majority vote will be managed directly by the hardware and not by software -- which can more easily get corrupted since a program is simply bits stored in memory...).
One point no-one seems to have mentioned. You say you're developing in GCC and cross-compiling onto ARM. How do you know that you don't have code which makes assumptions about free RAM, integer size, pointer size, how long it takes to do a certain operation, how long the system will run for continuously, or various stuff like that? This is a very common problem.
The answer is usually automated unit testing. Write test harnesses which exercise the code on the development system, then run the same test harnesses on the target system. Look for differences!
Also check for errata on your embedded device. You may find there's something about "don't do this because it'll crash, so enable that compiler option and the compiler will work around it".
In short, your most likely source of crashes is bugs in your code. Until you've made pretty damn sure this isn't the case, don't worry (yet) about more esoteric failure modes.
You want 3+ slave machines with a master outside the radiation environment. All I/O passes through the master which contains a vote and/or retry mechanism. The slaves must have a hardware watchdog each and the call to bump them should be surrounded by CRCs or the like to reduce the probability of involuntary bumping. Bumping should be controlled by the master, so lost connection with master equals reboot within a few seconds.
One advantage of this solution is that you can use the same API to the master as to the slaves, so redundancy becomes a transparent feature.
Edit: From the comments I feel the need to clarify the "CRC idea." The possibilty of the slave bumping it's own watchdog is close to zero if you surround the bump with CRC or digest checks on random data from the master. That random data is only sent from master when the slave under scrutiny is aligned with the others. The random data and CRC/digest are immediately cleared after each bump. The master-slave bump frequency should be more than double the watchdog timeout. The data sent from the master is uniquely generated every time.
How about running many instances of your application. If crashes are due to random memory bit changes, chances are some of your app instances will make it through and produce accurate results. It's probably quite easy (for someone with statistical background) to calculate how many instances do you need given bit flop probability to achieve as tiny overall error as you wish.
What you ask is quite complex topic - not easily answerable. Other answers are ok, but they covered just a small part of all the things you need to do.
As seen in comments, it is not possible to fix hardware problems 100%, however it is possible with high probabily to reduce or catch them using various techniques.
If I was you, I would create the software of the highest Safety integrity level level (SIL-4). Get the IEC 61513 document (for the nuclear industry) and follow it.
Someone mentioned using slower chips to prevent ions from flipping bits as easily. In a similar fashion perhaps use a specialized cpu/ram that actually uses multiple bits to store a single bit. Thus providing a hardware fault tolerance because it would be very unlikely that all of the bits would get flipped. So 1 = 1111 but would need to get hit 4 times to actually flipped. (4 might be a bad number since if 2 bits get flipped its already ambiguous). So if you go with 8, you get 8 times less ram and some fraction slower access time but a much more reliable data representation. You could probably do this both on the software level with a specialized compiler(allocate x amount more space for everything) or language implementation (write wrappers for data structures that allocate things this way). Or specialized hardware that has the same logical structure but does this in the firmware.
Perhaps it would help to know does it mean for the hardware to be "designed for this environment". How does it correct and/or indicates the presence of SEU errors ?
At one space exploration related project, we had a custom MCU, which would raise an exception/interrupt on SEU errors, but with some delay, i.e. some cycles may pass/instructions be executed after the one insn which caused the SEU exception.
Particularly vulnerable was the data cache, so a handler would invalidate the offending cache line and restart the program. Only that, due to the imprecise nature of the exception, the sequence of insns headed by the exception raising insn may not be restartable.
We identified the hazardous (not restartable) sequences (like lw $3, 0x0($2), followed by an insn, which modifies $2 and is not data-dependent on $3), and I made modifications to GCC, so such sequences do not occur (e.g. as a last resort, separating the two insns by a nop).
Just something to consider ...
If your hardware fails then you can use mechanical storage to recover it. If your code base is small and have some physical space then you can use a mechanical data store.
There will be a surface of material which will not be affected by radiation. Multiple gears will be there. A mechanical reader will run on all the gears and will be flexible to move up and down. Down means it is 0 and up means it is 1. From 0 and 1 you can generate your code base.
Use a cyclic scheduler. This gives you the ability to add regular maintenance times to check the correctness of critical data. The problem most often encountered is corruption of the stack. If your software is cyclical you can reinitialize the stack between cycles. Do not reuse the stacks for interrupt calls, setup a separate stack of each important interrupt call.
Similar to the Watchdog concept is deadline timers. Start a hardware timer before calling a function. If the function does not return before the deadline timer interrupts then reload the stack and try again. If it still fails after 3/5 tries you need reload from ROM.
Split your software into parts and isolate these parts to use separate memory areas and execution times (Especially in a control environment). Example: signal acquisition, prepossessing data, main algorithm and result implementation/transmission. This means a failure in one part will not cause failures through the rest of the program. So while we are repairing the signal acquisition the rest of tasks continues on stale data.
Everything needs CRCs. If you execute out of RAM even your .text needs a CRC. Check the CRCs regularly if you using a cyclical scheduler. Some compilers (not GCC) can generate CRCs for each section and some processors have dedicated hardware to do CRC calculations, but I guess that would fall out side of the scope of your question. Checking CRCs also prompts the ECC controller on the memory to repair single bit errors before it becomes a problem.
Use watchdogs for bootup no just once operational. You need hardware help if your bootup ran into trouble.
Firstly, design your application around failure. Ensure that as part of normal flow operation, it expects to reset (depending on your application and the type of failure either soft or hard). This is hard to get perfect: critical operations that require some degree of transactionality may need to be checked and tweaked at an assembly level so that an interruption at a key point cannot result in inconsistent external commands.
Fail fast as soon as any unrecoverable memory corruption or control flow deviation is detected. Log failures if possible.
Secondly, where possible, correct corruption and continue. This means checksumming and fixing constant tables (and program code if you can) often; perhaps before each major operation or on a timed interrupt, and storing variables in structures that autocorrect (again before each major op or on a timed interrupt take a majority vote from 3 and correct if is a single deviation). Log corrections if possible.
Thirdly, test failure. Set up a repeatable test environment that flips bits in memory psuedo-randomly. This will allow you to replicate corruption situations and help design your application around them.
Given supercat's comments, the tendencies of modern compilers, and other things, I'd be tempted to go back to the ancient days and write the whole code in assembly and static memory allocations everywhere. For this kind of utter reliability I think assembly no longer incurs a large percentage difference of the cost.
Here are huge amount of replies, but I'll try to sum up my ideas about this.
Something crashes or does not work correctly could be result of your own mistakes - then it should be easily to fix when you locate the problem. But there is also possibility of hardware failures - and that's difficult if not impossible to fix in overall.
I would recommend first to try to catch the problematic situation by logging (stack, registers, function calls) - either by logging them somewhere into file, or transmitting them somehow directly ("oh no - I'm crashing").
Recovery from such error situation is either reboot (if software is still alive and kicking) or hardware reset (e.g. hw watchdogs). Easier to start from first one.
If problem is hardware related - then logging should help you to identify in which function call problem occurs and that can give you inside knowledge of what is not working and where.
Also if code is relatively complex - it makes sense to "divide and conquer" it - meaning you remove / disable some function calls where you suspect problem is - typically disabling half of code and enabling another half - you can get "does work" / "does not work" kind of decision after which you can focus into another half of code. (Where problem is)
If problem occurs after some time - then stack overflow can be suspected - then it's better to monitor stack point registers - if they constantly grows.
And if you manage to fully minimize your code until "hello world" kind of application - and it's still failing randomly - then hardware problems are expected - and there needs to be "hardware upgrade" - meaning invent such cpu / ram / ... -hardware combination which would tolerate radiation better.
Most important thing is probably how you get your logs back if machine fully stopped / resetted / does not work - probably first thing bootstap should do - is a head back home if problematic situation is entcovered.
If it's possible in your environment also to transmit a signal and receive response - you could try out to construct some sort of online remote debugging environment, but then you must have at least of communication media working and some processor/ some ram in working state. And by remote debugging I mean either GDB / gdb stub kind of approach or your own implementation of what you need to get back from your application (e.g. download log files, download call stack, download ram, restart)
I've really read a lot of great answers!
Here is my 2 cent: build a statistical model of the memory/register abnormality, by writing a software to check the memory or to perform frequent register comparisons. Further, create an emulator, in the style of a virtual machine where you can experiment with the issue. I guess if you vary junction size, clock frequency, vendor, casing, etc would observe a different behavior.
Even our desktop PC memory has a certain rate of failure, which however doesn't impair the day to day work.

Is there a fast in-memory queue I can use that swaps items as it reaches a certain size?

I've been using c/c++/cuda for less than a week and not familiar with all the options available in terms of libraries(sorry if my question is too wacky or impossible). Here's my problem, I have a process that takes data and analyzes it then does 1 of 3 things, (1) saves the results, (2) discards the results or (3) breaks the data down and sends it back to be processed.
Often option (3) creates a lot of data and I very quickly exceed the memory available to me(my server is 16 gigs) so the way I got around that was to setup a queue server(rabbitmq) that I would send and receive work from(it swaps the queue once it reaches a certain size of memory). This worked perfectly when I used small servers with faster nics to transfer the data, but lately I have been learning and converting my code from Java to c/c++ and running it on a GPU which has made the queues a big bottleneck. The bottleneck was obviously the network io(profiling on cheap systems showed high cpu usage and similar on old gpu's but new faster cpus/gpus are not getting utilized as much and network IO is steady at 300-400/mbs). So I decided to try to eliminate the network totally and run the queue server locally on the server which made it faster but I suspect it could be even more faster if I used a solution that didn't rely on external network services(even if I am running them locally). It may not work but I want to experiment.
So my question is, is there anything that I can use like a queue that I can remove entries as I read them but also swaps the queue to disk once it reaches a certain size(but keeps the in-memory queue always full so I don't have to wait to read from disk)? When learning about Cuda, there are many examples of researchers running analysis on huge datasets, any ideas of how they keep data coming in at the fastest rate for the system to process(I imagine they aren't bound by disk/network otherwise faster gpu's wouldn't really give them magnitudes increase in performance)?
Does anything like this exist?
p.s. if it helps, so far I have experimented with rabbitmq(too slow for my situation), apollo mq(good but still network based), reddis(really liked it but cannot exceed physical memory), playing with mmap(), and I've also compressed my data to get better throughput. I know general solutions but I'm wondering if there's something native to c/c++, cuda or a library I can use(ideally, I would have a queue in Cuda global memory that swapped to the host memory that swapped to the disk so the GPU's would always be at full speed but that maybe wishful thinking). If there's anything else you can think of let me know and I'd enjoy experimenting with it(if it helps, I develop on a Mac and run it on linux).
Let me suggest something quite different.
Building a custom solution would not be excessively hard for an experienced programmer, but it is probably impossible for an inexperienced or even intermediate programmer to produce something robust and reliable.
Have you considered a DBMS?
For small data sets it will all be cached in memory. As it grows, the DBMS will have some very sophisticated caching/paging techniques. You get goodies like sorting/prioritisation, synchronisation/sharing for free.
A really well-written custom solution will be much faster than a DBMS, but will have huge costs in developing and maintaining the custom solution. Spend a bit of time optimising and tuning the DBMS and it starts looking pretty fast and will be very robust.
It may not fit your needs, but I'd suggest having a long hard look at a DBMS before you reject it.
There's an open source implementation of the Standard Template Library containers that's created to address exactly this problem.
STXXL nearly transparently swaps data to the disk for any of the standard STL containers. It's very well-written and well-maintained, and is very easy to adapt/migrate your code to given its similarity to the STL.
Another option is to use the existing STL containers but specify a disk-backed allocator. All the STL containers have a template parameter for the STL allocator, which specifies how the memory for entries is stored. There's a good disk-backed STL allocator that's on the tip of my tongue, but I can't seem to find via Google (I'll update this if/when I do).
Edit: I see Roger had actually already mentioned this in the comments.

What is the defacto standard for sharing variables between programs in different languages?

I've never had formal training in this area so I'm wondering what do they teach in school (if they do).
Say you have two programs in written in two different languages: C++ and Python or some other combination and you want to share a constantly updated variable on the same machine, what would you use and why? The information need not be secured but must be isochronous should be reliable.
Eg. Program A will get a value from a hardware device and update variable X every 0.1ms, I'd like to be able to access this X from Program B as often as possible and obtain the latest values. Program A and B are written and compiled in two different (robust) languages. How do I access X from program B? Assume I have the source code from A and B and I do not want to completely rewrite or port either of them.
The method's I've seen used thus far include:
File Buffer - Read and write to a
single file (eg C:\temp.txt).
Create a wrapper - From A to B or B
to A.
Memory Buffer - Designate a specific
memory address (mutex?).
UDP packets via sockets - Haven't
tried it yet but looks good.
Firewall?
Sorry for just throwing this out there, I don't know what the name of this technique is so I have trouble searching.
Well you can write XML and use some basic message queuing (like rabbitMQ) to pass messages around
Don't know if this will be helpful, but I'm also a student, and this is what I think you mean.
I've used marshalling to get a java class and import it into a C# program.
With marshalling you use xml to transfer code in a way so that it can be read by other coding environments.
When asking particular questions, you should aim at providing as much information as possible. You have added a use case, but the use case is incomplete.
Your particular use case seems like a very small amount of data that has to be available at a high frequency 10kHz. I would first try to determine whether I can actually make both pieces of code part of a single process, rather than two different processes. Depending on the languages (missing from the question) it might even be simple, or turn the impossible into possible --depending on the OS (missing from the question), the scheduler might not be fast enough switching from one process to another, and it might impact the availability of the latest read. Switching between threads is usually much faster.
If you cannot turn them into a single process, then you will have to use some short of IPC (Inter Process Communication). Due to the frequency I would rule out most heavy weight protocols (avoid XML, CORBA) as the overhead will probably be too high. If the receiving end needs only access to the latest value, and that access may be less frequent than 0.1 ms, then you don't want to use any protocol that includes queueing as you do not want to read the next element in the queue, you only care about the last, if you did not read the element when it was good, avoid the cost of processing it when it is already stale --i.e. it does not make sense to loop extracting from the queue and discarding.
I would be inclined to use shared memory, or a memory mapped shared file (they are probably quite similar, depends on the platform missing from the question). Depending on the size of the element and the exact hardware architecture (missing from the question) you may be able to avoid locking with a mutex. As an example in current intel processors, read/write access to 32 bit integers from memory is guaranteed to be atomic if the variable is correctly aligned, so in that case you would not be locking.
At my school they teach CORBA. They shouldn't, it's an ancient hideous language from the eon of mainframes, it's a classic case of design-by-committee, every feature possible that you don't want is included, and some that you probably do (asynchronous calls?) aren't. If you think the c++ specification is big, think again.
Don't use it.
That said though, it does have a nice, easy-to-use interface for doing simple things.
But don't use it.
It almost always pass through C binding.

performance penalty of message passing as opposed to shared data

There is a lot of buzz these days about not using locks and using Message passing approaches like Erlang. Or about using immutable datastructures like in Functional programming vs. C++/Java.
But what I am concerned with is the following:
AFAIK, Erlang does not guarantee Message delivery. Messages might be lost. Won't the algorithm and code bloat and be complicated again if you have to worry about loss of messages? Whatever distributed algorithm you use must not depend on guaranteed delivery of messages.
What if the Message is a complicated object? Isn't there a huge performance penalty in copying and sending the messages vs. say keeping it in a shared location (like a DB that both processes can access)?
Can you really totally do away with shared states? I don't think so. For e.g. in a DB, you have to access and modify the same record. You cannot use message passing there. You need to have locking or assume Optimistic concurrency control mechanisms and then do rollbacks on errors. How does Mnesia work?
Also, it is not the case that you always need to worry about concurrency. Any project will also have a large piece of code that doesn't have to do anything with concurrency or transactions at all (but they do have performance and speed as a concern). A lot of these algorithms depend on shared states (that's why pass-by-reference or pointers are so useful).
Given this fact, writing programs in Erlang etc is a pain because you are prevented from doing any of these things. May be, it makes programs robust, but for things like Solving a Linear Programming problem or Computing the convex hulll etc. performance is more important and forcing immutability etc. on the algorithm when it has nothing to do with Concurrency/Transactions is a poor decision. Isn't it?
That's real life : you need to account for this possibility regardless of the language / platform. In a distributed world (the real world), things fail: live with it.
Of course there is a cost: nothing is free in our universe. But shouldn't you use another medium (e.g. file, db) instead of shuttling "big objects" in communication pipes? You can always use "message" to refer to "big objects" stored somewhere.
Of course not: the idea behind functional programming / Erlang OTP is to "isolate" as much as possible the areas were "shared state" is manipulated. Futhermore, having clearly marked places where shared state is mutated helps testability & traceability.
I believe you are missing the point: there is no such thing as a silver bullet. If your application cannot be successfully built using Erlang then don't do it. You can always some other part of the overall system in another fashion i.e. use a different language / platform. Erlang is no different from another language in this respect: use the right tool for the right job.
Remember: Erlang was designed to help solve concurrent, asynchronous and distributed problems. It isn't optimized for working efficiently on a shared block of memory for example... unless you count interfacing with nif functions working on shared blocks part of the game :-)
Real-world systems are always hybrids anyway: I don't believe the modern paradigms try, in practice, to get rid of mutable data and shared state.
The objective, however, is not to need concurrent access to this shared state. Programs can be divided into the concurrent and the sequential, and use message-passing and the new paradigms for the concurrent parts.
Not every code will get the same investment: There is concern that threads are fundamentally "considered harmful". Something like Apache may need traditional concurrent threads and a key piece of technology like that may be carefully refined over a period of years so it can blast away with fully concurrent shared state. Operating system kernels are another example where "solve the problem no matter how expensive it is" may make sense.
There is no benefit to fast-but-broken: But for new code, or code that doesn't get so much attention, it may be the case that it simply isn't thread-safe, and it will not handle true concurrency, and so the relative "efficiency" is irrelevant. One way works, and one way doesn't.
Don't forget testability: Also, what value can you place on testing? Thread-based shared-memory concurrency is simply not testable. Message-passing concurrency is. So now you have the situation where you can test one paradigm but not the other. So, what is the value in knowing that the code has been tested? The danger in not even knowing if the other code will work in every situation?
A few comments on the misunderstanding you have of Erlang:
Erlang guarantees that messages will not be lost, and that they will arrive in the order sent. A basic error situation is that machine A can not speak to machine B. When that happens process monitors and links will trigger, and system node-down messages will be sent to the processes that registered for it. Nothing will be silently dropped. Processes will "crash" and supervisors (if any) tries to restart them.
Objects can not be mutated, so they are always copied. One way to secure immutability is by copying values to other erlang process' heaps. Another way is to allocate objects in a shared heap, message references to them and simply not have any operations that mutate them. Erlang does the first for performance! Realtime suffers if you need to stop all processes to garbage collect a shared heap. Ask Java.
There is shared state in Erlang. Erlang is not proud of it, but it is pragmatic about it. One example is the local process registry which is a global map that maps a name to a process so that system processes can be restarted and claim their old name. Erlang just tries to avoid shared state if it possibly can. ETS tables that are public are another example.
Yes, sometimes Erlang is too slow. This happens all languages. Sometimes Java is too slow. Sometimes C++ is too slow. Just because a tight loop in a game had to drop down to assembly to kick off some serious SIMD-based vector mathematics you can't deduce that everything should be written in assembly because it is the only language that is fast when it matters. What matters is being able to write systems that have good performance, and Erlang manages quite well. See benchmarks on yaws or rabbitmq.
Your facts are not facts about Erlang. Even if you think Erlang programming is a pain, you will find other people create some awesome software thanks to it. You should attempt writing an IRC server in Erlang, or something else very concurrent. Even if you're never going to use Erlang again, you would have learned to think about concurrency another way. But of course, you will, because Erlang is awesome easy.
Those that do not understand Erlang are doomed to re-implement it badly.
Okay, the original was about Lisp, but... its true!
There are some implicit assumption in your questions - you assume that all the data can fit
on one machine and that the application is intrinsically localised to one place.
What happens if the application is so large it cannot fit on one machine? What happens if the application outgrows one machine?
You don't want to have one way to program an application if it fits on one machine and
a completely different way of programming it as soon as it outgrows one machine.
What happens if you want make a fault-tolerant application? To make something fault-tolerant you need at least two physically separated machines and no sharing.
When you talk about sharing and data bases you omit to mention that things like mySQL
cluster achieve fault-tolerence precisely by maintaining synchronised copies of the
data in physically separated machines - there is a lot of message passing and
copying that you don't see on the surface - Erlang just exposes this.
The way you program should not suddenly change to accommodate fault-tolerance and scalability.
Erlang was designed primarily for building fault-tolerant applications.
Shared data on a multi-core has it's own set of problems - when you access shared data
you need to acquire a lock - if you use a global lock (the easiest approach) you can end up
stopping all the cores while you access the shared data. Shared data access on a multicore
can be problematic due to caching problems, if the cores have local data caches then accessing "far away" data (in some other processors cache) can be very expensive.
Many problems are intrinsically distributed and the data is never available in one place
at the same time so - these kind of problems fit well with the Erlang way of thinking.
In a distributed setting "guaranteeing message delivery" is impossible - the destination machine might have crashed. Erlang cannot thus guarantee message delivery -
it takes a different approach - the system will tell you if it failed to deliver a message
(but only if you have used the link mechanism) - then you can write you own custom error
recovery.)
For pure number crunching Erlang is not appropriate - but in a hybrid system Erlang
is good at managing how computations get distributed to available processors, so we see a lot of systems where Erlang manages the distribution and fault-tolerent aspects of the problem, but the problem itself is solved in a different language.
and other languages are used
For e.g. in a DB, you have to access and modify the same record
But that is handled by the DB. As a user of the database, you simply execute your query, and the database ensures it is executed in isolation.
As for performance, one of the most important things about eliminating shared state is that it enables new optimizations. Shared state is not particularly efficient. You get cores fighting over the same cache lines, and data has to be written through to memory where it could otherwise stay in a register or in CPU cache.
Many compiler optimizations rely on absence of side effects and shared state as well.
You could say that a stricter language guaranteeing these things requires more optimizations to be performant than something like C, but it also makes these optimizations much much easier for the compiler to implement.
Many concerns similar to concurrency issues arise in singlethreaded code. Modern CPUs are pipelined, execute instructions out of order, and can run 3-4 of them per cycle. So even in a single-threaded program, it is vital that the compiler and CPU is able to determine which instructions can be interleaved and executed in parallel.
For correctness, shared is the way to go, and keep the data as normalized as possible. For immediacy, send messages to inform of changes, but always back them up with polling. Messages get dropped, duplicated, re-ordered, delayed - don't rely on them.
If speed is what you're worried about, first do it single-thread and tune the daylights out of it. Then if you've got multiple cores and know how to split up the work, use parallelism.
Erlang provides supervisors and gen_server callbacks for synchronous calls, so you will know about it if a message isn't delivered: either the gen_server call returns a timeout, or your whole node will be brought down and up if the supervisor is triggered.
usually if the processes are on the same node, message-passing languages optimise away the data copying, so it's almost like shared memory, except if the object is changed used by both afterward, which can not be done using shared memory either anyways
There is some state which is kept by processes by passing it around to themselves in the recursive tail-calls, also some state can be of course passed through messages. I don't use mnesia much, but it is a transactional database, so once you have passed the operation to mnesia (and it has returned) you are pretty much guaranteed it will go through..
Which is why it is easy to tie such applications into erlang with the use of ports or drivers. The easiest are the ports, it's much like a unix pipe, though I think performance isn't that great...and as said, message-passing usually ends up just being pointer passing anyways as the VM/compiler optimise the memory copy out.

BerkeleyDB Concurrency

What's the optimal level of concurrency that the C++ implementation of BerkeleyDB can reasonably support?
How many threads can I have hammering away at the DB before throughput starts to suffer because of resource contention?
I've read the manual and know how to set the number of locks, lockers, database page size, etc. but I'd just like some advice from someone who has real-world experience with BDB concurrency.
My application is pretty simple, I'll be doing gets and puts of records that are about 1KB each. No cursors, no deleting.
It depends on what kind of application you are building. Create a representative test scenario, and start hammering away. Then you will know the definitive answer.
Besides your use case, it also depends on CPU, memory, front-side bus, operating system, cache settings, etcetera.
Seriously, just test your own scenario.
If you need some numbers (that actually may mean nothing in your scenario):
Oracle Berkeley DB:
Performance Metrics and
Benchmarks
Performance Metrics
& Benchmarks:
Berkeley DB
I strongly agree with Daan's point: create a test program, and make sure the way in which it accesses data mimics as closely as possible the patterns you expect your application to have. This is extremely important with BDB because different access patterns yield very different throughput.
Other than that, these are general factors I found to be of major impact on throughput:
Access method (which in your case i guess is BTREE).
Level of persistency with which you configured DBD (for example, in my case the 'DB_TXN_WRITE_NOSYNC' environment flag improved write performance by an order of magnitude, but it compromises persistency)
Does the working set fit in cache?
Number of Reads Vs. Writes.
How spread out your access is (remember that BTREE has a page level locking - so accessing different pages with different threads is a big advantage).
Access pattern - meanig how likely are threads to lock one another, or even deadlock, and what is your deadlock resolution policy (this one may be a killer).
Hardware (disk & memory for cache).
This amounts to the following point:
Scaling a solution based on DBD so that it offers greater concurrency has two key ways of going about it; either minimize the number of locks in your design or add more hardware.
Doesn't this depend on the hardware as well as number of threads and stuff?
I would make a simple test and run it with increasing amounts of threads hammering and see what seems best.
What I did when working against a database of unknown performance was to measure turnaround time on my queries. I kept upping the thread count until turn-around time dropped, and dropping the thread count until turn-around time improved (well, it was processes in my environment, but whatever).
There were moving averages and all sorts of metrics involved, but the take-away lesson was: just adapt to how things are working at the moment. You never know when the DBAs will improve performance or hardware will be upgraded, or perhaps another process will come along to load down the system while you're running. So adapt.
Oh, and another thing: avoid process switches if you can - batch things up.
Oh, I should make this clear: this all happened at run time, not during development.
The way I understand things, Samba created tdb to allow "multiple concurrent writers" for any particular database file. So if your workload has multiple writers your performance may be bad (as in, the Samba project chose to write its own system, apparently because it wasn't happy with Berkeley DB's performance in this case).
On the other hand, if your workload has lots of readers, then the question is how well your operating system handles multiple readers.