Increase RAM available for Knime? - knime

Is there an easy way to increase the RAM available in Knime through a config file or through menu options?
I am constantly running into "heap-space" errors during execution and it by default limits the number of categorical variables to 1,000, as well as difficulty displaying charts with more than n values (~10,000).
Example error:
ERROR Decision Tree Learner 0:65 Execute failed: Java heap space
Thanks!

Sure, you can edit knime.ini (in the knime or knime_<version> folder) and change the row starting with -Xmx (I think by default it is 2048m, two GiB). Though do not use so much memory that would cause the OS to swap as Java do not play very well with swapping.
(Displaying too many variables might still be slow, maybe you could aggregate them somehow.)

Related

Can QEMU catch accesses to non-existing RAM on a Cortex-M processor?

is it possible to have QEMU report read or write accesses to non-existing RAM for a Cortex-M machine? Maybe a log function or a special option when building QEMU?
After all, it gets passed the address map - so it shouldn't be too difficult to detect this situation (of course this incurs a run-time cost).
All I found in the sources was
"Trying to execute code outside RAM or ROM at 0x"
but nothing comparable for reading or writing.
Any help will be highly appreciated.
M'
If you're looking at a QEMU with the "Trying to execute code outside RAM or ROM" message then it's a pretty old one and you should probably be looking at a newer version, especially if you're digging into its source code.
Anyway, it is in theory possible but it isn't currently an implemented feature. You could probably get 90% of the way there by enabling the DEBUG_UNASSIGNED printf()s in softmmu/memory.c. A proper solution would require implementing suitable tracepoints instead.

Limiting the size of the Regular Expression Cache in JRuby

We are finding that the Regular Expression Cache in our JRuby application is out of control - it just keeps growing and growing until the app is grinding to a halt.
It eventually does garbage collect, but transaction time is becomes far too high (90 secs instead of 1-2 secs) long before that.
Is there a way to either stop this Regexp Cache from growing so much or limit the size of the cache?
first of all, since you already mentioned looking at the source at Very large retained heap size for org.jruby.RubyRegexp$RegexpCache in JRuby Rails App you probably realised there's no such support implemented.
would say you have 2-3 options to decide :
implement support for limiting or completely disabling the cache within JRuby's RubyRegexp
introduce a "hack" that will check available memory and clear out some of the cache RubyRegexp caches e.g. from another thread (at least until a PR is accepted into JRuby)
look into tuning or using a different GC (including some JVM options) so that the app performs more predictably ... this is application dependent and can no be answered (in general) without knowing the specifics
one hint related to how the JVM keeps soft references -XX:SoftRefLRUPolicyMSPerMB=250 it's 1000 (1 seconds) by default thus decreasing it means they will live shorter ... but it might just all relate to when they're collected (depends on GC and Java version I guess) so in the end you might find out to be fixing the symptom and not the real cause (as noted things such these can not be generalized esp. knowing very little about the app and/or JVM OPTS used)

In-memory function calls

What are in-memory function calls? Could someone please point me to some resource discussing this technique and its advantages. I need to learn more about them and at the moment do not know where to go. Google does not seem to help as it takes me to the domain of cognition and nervous system etc..
Assuming your explanatory comment is correct (I'd have to see the original source of your question to know for sure..) it's probably a matter of either (a) function binding times or (b) demand paging.
Function Binding
When a program starts, the linker/loader finds all function references in the executable file that aren't resolvable within the file. It searches all the linked libraries to find the missing functions, and then iterates. At least the Linux ld.so(8) linker/loader supports two modes of operation: LD_BIND_NOW forces all symbol references to be resolved at program start up. This is excellent for finding errors and it means there's no penalty for the first use of a function vs repeated use of a function. It can drastically increase application load time. Without LD_BIND_NOW, functions are resolved as they are needed. This is great for small programs that link against huge libraries, as it'll only resolve the few functions needed, but for larger programs, this might require re-loading libraries from disk over and over, during the lifetime of the program, and that can drastically influence response time as the application is running.
Demand Paging
Modern operating system kernels juggle more virtual memory than physical memory. Each application thinks it has access to an entire machine of 4 gigabytes of memory (for 32-bit applications) or much much more memory (for 64-bit applications), regardless of the actual amount of physical memory installed in the machine. Each page of memory needs a backing store, a drive space that will be used to store that page if the page must be shoved out of physical memory under memory pressure. If it is purely data, the it gets stored in a swap partition or swap file. If it is executable code, then it is simply dropped, because it can be reloaded from the file in the future if it needs to be. Note that this doesn't happen on a function-by-function basis -- instead, it happens on pages, which are a hardware-dependent feature. Think 4096 bytes on most 32 bit platforms, perhaps more or less on other architectures, and with special frameworks, upwards of 2 megabytes or 4 megabytes. If there is a reference for a missing page, the memory management unit will signal a page fault, and the kernel will load the missing page from disk and restart the process.

Reliably monitor a serial port (Nortel CS1000)

I have a custom python script that monitors the call logs from a Nortel phone system. This phone system is under extremely high volume throughout the day and it's starting to appear that some records may be getting lost.
Some of you may dislike this, but I'm not interested in sharing the source code or current method in any way. I would rather consider this from a "new project" approach.
I'm looking for insight into the easiest and safest way to reliably monitor heavy data output through a serial port on Linux. I'm not limiting this to any particular set of tools or languages, I want to find out what works best to do this one critical job. I'm comfortable enough parsing the data and inserting it into mysql that we could just assume the data could be dropped to a text file.
Thank you
Well, the way that I would approach this this to have 2 threads (or processes) working.
Thread 1: The read thread
This thread does nothing but read data from the raw serial port and put the data into a local buffer/queue (In memory is preferred for speed). It should do nothing else. Depending on the clock speed of the serial connection, this should be pretty easy to do.
Thread2: The processing thread
This thread just sleeps until there is data in the local buffer to process, then reads and processes it. That's it.
The reason for splitting it apart in two, is so that if one is busy (a block in MySQL for the processing thread) it won't affect the other. After all, while the serial port is buffered by the OS, the buffer size is limited.
But then again, any local program is likely going to be way faster than the serial port can send data. Serial transfer is actually quite slow relative to the clock speed of the processor (115.2kbps is about the limit on standard hardware). So unless you're CPU speed bound (such as on an Arduino), I can't see normal conditions affecting it too much. So your choice of language really shouldn't be of too much concern (assuming modern hardware). Stick to what you know.

What are the advantages of memory-mapped files?

I've been researching memory mapped files for a project and would appreciate any thoughts from people who have either used them before, or decided against using them, and why?
In particular, I am concerned about the following, in order of importance:
concurrency
random access
performance
ease of use
portability
I think the advantage is really that you reduce the amount of data copying required over traditional methods of reading a file.
If your application can use the data "in place" in a memory-mapped file, it can come in without being copied; if you use a system call (e.g. Linux's pread() ) then that typically involves the kernel copying the data from its own buffers into user space. This extra copying not only takes time, but decreases the effectiveness of the CPU's caches by accessing this extra copy of the data.
If the data actually have to be read from the disc (as in physical I/O), then the OS still has to read them in, a page fault probably isn't any better performance-wise than a system call, but if they don't (i.e. already in the OS cache), performance should in theory be much better.
On the downside, there's no asynchronous interface to memory-mapped files - if you attempt to access a page which isn't mapped in, it generates a page fault then makes the thread wait for the I/O.
The obvious disadvantage to memory mapped files is on a 32-bit OS - you can easily run out of address space.
I have used a memory mapped file to implement an 'auto complete' feature while the user is typing. I have well over 1 million product part numbers stored in a single index file. The file has some typical header information but the bulk of the file is a giant array of fixed size records sorted on the key field.
At runtime the file is memory mapped, cast to a C-style struct array, and we do a binary search to find matching part numbers as the user types. Only a few memory pages of the file are actually read from disk -- whichever pages are hit during the binary search.
Concurrency - I had an implementation problem where it would sometimes memory map the file multiple times in the same process space. This was a problem as I recall because sometimes the system couldn't find a large enough free block of virtual memory to map the file to. The solution was to only map the file once and thunk all calls to it. In retrospect using a full blown Windows service would of been cool.
Random Access - The binary search is certainly random access and lightning fast
Performance - The lookup is extremely fast. As users type a popup window displays a list of matching product part numbers, the list shrinks as they continue to type. There is no noticeable lag while typing.
Memory mapped files can be used to either replace read/write access, or to support concurrent sharing. When you use them for one mechanism, you get the other as well.
Rather than lseeking and writing and reading around in a file, you map it into memory and simply access the bits where you expect them to be.
This can be very handy, and depending on the virtual memory interface can improve performance. The performance improvement can occur because the operating system now gets to manage this former "file I/O" along with all your other programmatic memory access, and can (in theory) leverage the paging algorithms and so forth that it is already using to support virtual memory for the rest of your program. It does, however, depend on the quality of your underlying virtual memory system. Anecdotes I have heard say that the Solaris and *BSD virtual memory systems may show better performance improvements than the VM system of Linux--but I have no empirical data to back this up. YMMV.
Concurrency comes into the picture when you consider the possibility of multiple processes using the same "file" through mapped memory. In the read/write model, if two processes wrote to the same area of the file, you could be pretty much assured that one of the process's data would arrive in the file, overwriting the other process' data. You'd get one, or the other--but not some weird intermingling. I have to admit I am not sure whether this is behavior mandated by any standard, but it is something you could pretty much rely on. (It's actually agood followup question!)
In the mapped world, in contrast, imagine two processes both "writing". They do so by doing "memory stores", which result in the O/S paging the data out to disk--eventually. But in the meantime, overlapping writes can be expected to occur.
Here's an example. Say I have two processes both writing 8 bytes at offset 1024. Process 1 is writing '11111111' and process 2 is writing '22222222'. If they use file I/O, then you can imagine, deep down in the O/S, there is a buffer full of 1s, and a buffer full of 2s, both headed to the same place on disk. One of them is going to get there first, and the other one second. In this case, the second one wins. However, if I am using the memory-mapped file approach, process 1 is going to go a memory store of 4 bytes, followed by another memory store of 4 bytes (let's assume that't the maximum memory store size). Process 2 will be doing the same thing. Based on when the processes run, you can expect to see any of the following:
11111111
22222222
11112222
22221111
The solution to this is to use explicit mutual exclusion--which is probably a good idea in any event. You were sort of relying on the O/S to do "the right thing" in the read/write file I/O case, anyway.
The classing mutual exclusion primitive is the mutex. For memory mapped files, I'd suggest you look at a memory-mapped mutex, available using (e.g.) pthread_mutex_init().
Edit with one gotcha: When you are using mapped files, there is a temptation to embed pointers to the data in the file, in the file itself (think linked list stored in the mapped file). You don't want to do that, as the file may be mapped at different absolute addresses at different times, or in different processes. Instead, use offsets within the mapped file.
Concurrency would be an issue.
Random access is easier
Performance is good to great.
Ease of use. Not as good.
Portability - not so hot.
I've used them on a Sun system a long time ago, and those are my thoughts.