This is perhaps a very obvious question due simple computer science rules, but is there a good explanation of why it varies so much from time to time? Reading a small file can sometimes take a few milliseconds and other times it can take a few seconds. Of course this depends on how you read the file, and also what language you read it in (i.e the programming language).
Maybe there isn't a obvious answer for this? I'm not sure, I havn't read much about it, so that is why I'm asking the question.
One thing that can cause varying read time is whether the file is in memory or not.
Disk is a much slower read than from memory. So if a file has been read and placed in memory, it will be much quicker to read from that file afterwards, until it gets kicked out of memory.
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I have this molecular dynamics program that writes atom position and velocities to a file at every n steps of simulation. The actual writing is taking like 90% of the running time! (checked by eiminating the writes) So I desperately need to optimize that.
I see that some fortrans have an extension to change the write buffer size (called i/o block size) and the "number of blocks" at the OPEN statement, but it appears that gfortran doesn't. Also I read somewhere that gfortran uses 8192 bytes write buffer.
I even tried to do an FSTAT (right after opening, is that right?) to see what is the block size and number of blocks it is using but it returns -1 on both. (compiling for windows 64 bit)
Isn't there a way to enlarge the write buffer for a file in gfortran? Will it be diferent compiling for linux than for windows?
I'd really really rather stay in fortran but as a desperate measure isn't there a way to do so by adding some c routine?
thanks!
IanH question is key. Unformatted IO is MUCH faster than formatted. The conversion from base 2 to base 10 is very CPU intensive. If you don't need the values to be human readable, then use unformatted IO. If you want to be able to read the values in another language, then use access='stream'.
Another approach would be to add your own buffering. Replace the write statement with a call to a subroutine. Have that subroutine store values and write only when it has received M values. You'll also have to have a "flush" call to the subroutine to cause it to write the last values, if they are fewer them M.
If gcc C is faster at IO, you could mix Fortran and C with Fortran's ISO_C_Binding: https://stackoverflow.com/questions/tagged/fortran-iso-c-binding. There are examples of the use of the ISO C Binding in the gfortran manual under "Mixed Language Programming".
If you spend 90% of your runtime writing coords/vels every n timesteps, the obvious quick fix would be to instead write data every, say, n/100 timestep. But I'm sure you already thought of that yourself.
But yes, gfortran has a fixed 8k buffer, whose size cannot be changed except by modifying the libgfortran source and rebuilding it. The reason for the buffering is to amortize the syscall overhead; (simplistic) tests on Linux showed that 8k is sufficient and more than that goes far into diminishing returns territory. That being said, if you have some substantiated claims that bigger buffers are useful on some I/O patterns and/or OS, there's no reason why the buffer can't be made larger in a future release.
As for you performance issues, as already mentioned, unformatted is a lot faster than formatted I/O. Additionally, gfortran has rather high per-IO-statement overhead. You can amortize that by writing arrays (or, array sections) rather than individual elements (this matters mostly for unformatted, for formatted IO there is so much to do that this doesn't help that much).
I am thinking that if cost of IO is comparable or even larger than the effort of simulation, then it probably isn't such a good idea to store all these data to disk the first place. It is better to do whatever processing you intend to do directly during the simulation, instead of saving lots of intermediate data them later read them in again to do the processing.
Moreover, MD is an inherently highly parallelizable problem, and with IO you will severely cripple the efficiency of parallelization! I would avoid IO whenever possible.
For individual trajectories, normally you just need to store the initial condition of each trajectory, along with its key statistics, or important snapshots at a small number of time values. When you need one specific trajectory plotted you can regenerate the exact same trajectory or section of trajectory from the initial condition or the closest snapshot, and with similar cost as reading it from the disk.
This question strikes me as almost silly, but I just want to sanity check myself. For a variety of reasons, I'm welding together a bunch of files into a single megafile before packing this as a resource in my iOS app. I'm then using NSFileHandle to open the file, seek to the right place, and read out just the bytes I want.
Is there any performance difference between doing it this way and reading loose files? Or, supposing I could choose to use just one monolithic megafile, versus, say, 10 medium-sized (but still joined) files, is there any performance difference between "opening" the large versus a smaller file?
Since I know exactly where to seek to, and I'm reading just the bytes I want, I don't see how there could be a difference. But, hey -- Stranger things have proved to be. Thanks in advance!
There could be a difference if it was an extremely large number of files. Every open file uses up resources in memory (file handles, and the like), and on some storage devices, a file will take up an entire block even if it doesn't fill it. That can lead to wasted space in extreme cases. But in practice, it probably won't be a problem. To know for sure, you can profile your code and see if it's faster one way vs. the other, and see what sort of space it takes up on a typical device.
I am trying to speed up my file I/O using MPI-2, but there doesn't appear to be any way to read/write formatted files. Many of my I/O files are formatted for ease of pre and post-processing.
Any suggestions for an MPI-2 solution for formatted I/O?
The usual answer to using MPI-IO while generating some sort of portable, sensible file format is to use HDF5 or NetCDF4 . There's a real learning curve to both (but also lots of tutorials out there) but the result is you hve portable, self-describing files that there are a zillion tools for accessing, manipulating, etc.
If by `formatted' output you mean plain human-readable text, then as someone who does a lot of this stuff, I wouldn't be doing my job if I didn't urge you enough to start moving away from that approach. We all by and large start that way, dumping plain text so we can quickly see what's going on; but it's just not a good approach for doing production runs. The files are bloated, the I/O is way slower (I routinely see 6x slowdown in using ascii as vs binary, partly because you're writing out small chunks at a time and partly because of the string conversions), and for what? If there's so little data being output that you actually can feasibly read and understand the output, you don't need parallel I/O; if there are so many numbers that you can't really plausibly flip through them all and understand what's going on, then what's the point?
I'm thinking of optimizing a program via taking a linear array and writing each element to a arbitrary location (random-like from the perspective of the CPU) in another array. I am only doing simple writes and not reading the elements back.
I understand that a scatted read for a classical CPU can be quite slow as each access will cause a cache miss and thus a processor wait. But I was thinking that a scattered write could technically be fast because the processor isn't waiting for a result, thus it may not have to wait for the transaction to complete.
I am unfortunately unfamiliar with all the details of the classical CPU memory architecture and thus there may be some complications that may cause this also to be quite slow.
Has anyone tried this?
(I should say that I am trying to invert a problem I have. I currently have an linear array from which I am read arbitrary values -- a scattered read -- and it is incredibly slow because of all the cache misses. My thoughts are that I can invert this operation into a scattered write for a significant speed benefit.)
In general you pay a high penalty for scattered writes to addresses which are not already in cache, since you have to load and store an entire cache line for each write, hence FSB and DRAM bandwidth requirements will be much higher than for sequential writes. And of course you'll incur a cache miss on every write (a couple of hundred cycles typically on modern CPUs), and there will be no help from any automatic prefetch mechanism.
I must admit, this sounds kind of hardcore. But I take the risk and answer anyway.
Is it possible to divide the input array into pages, and read/scan each page multiple times. Every pass through the page, you only process (or output) the data that belongs in a limited amount of pages. This way you only get cache-misses at the start of each input page loop.
When creating applications (Java, run on a normal computer). How important is program size for users? For example, would it be necessary to replace .png's with .jpg's, convert .wav's to .midi's, or strip down libraries to save space, or do users generally not care if my program is 5mb when it could be 50kb if stripped down?
Thanks.
That depends on the delivery mechanism.
Size is generally only relevant in terms of the bandwidth required to download it. If you download it often, then it matters a lot. If its only once, it matters less and you have to weigh up the time involved in reducing that vs how much space you save.
After that, nobody cares until you get into gigabytes. Well, mobile applications will probably start caring at about 10MB+.
Users definitely care (after all, not only does space cost money, but affects program load time). However, the question becomes how much do you optimize. I suggest the 80/20 rule. 80% of your benefit comes from the first 20% of the effort.
If you use a utility like TreePie you might be able to see what parts of a large application are consuming most of your resources. If you find it's just a few large images, or one big DLL with a bunch of embedded resources, it's probably worth taking a look at reducing the size, if it's easy.
But there's a cost/benefit tradeoff. I just saw a terrabyte drive for $100 the other day. Saving the user 1 gig is about 10 cents in terms of storage space, and perhaps some hard to quantify amount of time spent loading every time they load. If you have 100,000 users, it probably worth your time to optimize a bit, but if you're writing custom software for one user it's probably not worth it unless they're complaining.
As mentioned by Graham Lee, a great deal of this is very dependant on your users. If you are writing something that needs to be optimized to fit on the chip of a 68000 processor, then you'd better believe that program size matters. Assuming you're not programming 30 years ago, you probably won't run across that particular issue.
But in general, you should be making your application as small as possible while still achieving the quality you want. That is to say, if your application is likely to be viewed on an 640x480 screen, then you don't need hi-res 6mg pngs for all your images. On the other hand, if your application is designed to be blown up on a big screen at conferences, then you probably want to upsize your images.
Another option that is very common is creating installers with separate options ranging from full to minimal. That way you can allow your users to decide whether size matters to them. It allows you to create the pretty pretty version of your app, and a scaled back version that doesn't include tutorials or mp3 files of a soothing woman's voice telling you that you've push the wrong button.
Know your users. And if you don't, then let them decide for themselves.
Consider yourself, what would you use? Would you rather save space with 5KB programs or waste it with 5MB programs?
I think that smaller is better, especially if the program doesn't use/need much graphics and can be optimized.
I would say not important at all, unless it's obscenely large.
I would argue that startup time is far more important to users that application size.
However if you include a lot of media files with your system it is logical to optimise this data as much as possible. But don't compromise the quality - switching to jpeg might be okay for photos, but it sucks for technical diagrams. A .wav could be an .aac or .mp3, but not if you're writing a professional audio application.