I'm implementing finite difference algorithm from uFDTD book. Many FDM equations involve operations on adjoined vector elements.
For example, an update equation for electric field
ez[m] = ez[m] + (hy[m] - hy[m-1]) * imp0
uses adjoined vector values hy[m] and hy[m-1].
How can I implement these operations in PETSc efficiently? Is there something beyond local vector loops and scatterers?
If my goal was efficiency, I would call a stencil engine. There are many many many papers, and sometimes even open source code, for example, Devito. The idea is that PETSc manages the data structure and parallelism. Then you can feed the local data brick to your favorite stencil computer.
I have my program which requires maximum use of GPU.
So, does blockDim.x * blockIdx.x + threadIdx.x; is able to access all the threads? or it is a must to use .y and .z also ?
is that mandatory?
The CUDA threads hierarchy is just a convenience abstraction and there's no requirement for using one, two or three dimensions, nor you will lose performances if you just use one dimension instead of all three of them. You will be able to use all the threads you launched with a set of indices as long as you specified the correct grid dimension.
2.2. Thread Hierarchy
For convenience, threadIdx is a 3-component vector, so that threads can be identified using a one-dimensional, two-dimensional, or three-dimensional thread index, forming a one-dimensional, two-dimensional, or three-dimensional thread block. This provides a natural way to invoke computation across the elements in a domain such as a vector, matrix, or volume.
Read more at: http://docs.nvidia.com/cuda/cuda-c-programming-guide/index.html#thread-hierarchy
The way you get access to threads depends on the way you declare your grid and block dimensions. if it's a one dimensional grid and one dimensional block you can have access to all threads by only .x. That is arbitrary and program dependent. you can define your grid 1 or 2 dimensional and for blocks up to 3.
I have a program that uses opencv and oclMat.
When I tried to run this my PC gets slow and sometimes get freezed.
I guess there are two much memory in GPU. So, my question is how can I release the memory allocated by opencv ocl mat. I execute 4 kernels. Something like this:
I create the oclmat and call the kernel and pass the matrices to the kernel.The result is a ocl mat which is used in the following kernel. M3,M4,M8,M9,M5,M10 are matrices that hold data inside the kernel. I am not using local memory(as the target device does not support local memory). SO, I am using the above mentioned ocl mat as data holder. All the temporary calculated data inside the kernel is stored in those matrix. They work the way a local memory would have worked here.I do not need them in the next kernel. SO I want to free them. What is the process to do that?
oclmat M1,M2,M3,M4
kernel1 (M1,M2,M3,M4)
oclmat M5,M6
kernel2(M4,M5,M6)
oclmat M7,M8,M9
kernel3(M6,M7,M8,M9)
oclmat M10,M11
kernel2(M9,M10,M11)
How do I use scikit-learn to train a model on a large csv data (~75MB) without running into memory problems?
I'm using IPython notebook as the programming environment, and pandas+sklearn packages to analyze data from kaggle's digit recognizer tutorial.
The data is available on the webpage , link to my code , and here is the error message:
KNeighborsClassifier is used for the prediction.
Problem:
"MemoryError" occurs when loading large dataset using read_csv
function. To bypass this problem temporarily, I have to restart the
kernel, which then read_csv function successfully loads the file, but
the same error occurs when I run the same cell again.
When the read_csv function loads the file successfully, after making changes to the dataframe, I can pass the features and labels to the KNeighborsClassifier's fit() function. At this point, similar memory error occurs.
I tried the following:
Iterate through the CSV file in chunks, and fit the data accordingly, but the problem is that the predictive model is overwritten every time for a chunk of data.
What do you think I can do to successfully train my model without running into memory problems?
Note: when you load the data with pandas it will create a DataFrame object where each column has an homogeneous datatype for all the rows but 2 columns can have distinct datatypes (e.g. integer, dates, strings).
When you pass a DataFrame instance to a scikit-learn model it will first allocate a homogeneous 2D numpy array with dtype np.float32 or np.float64 (depending on the implementation of the models). At this point you will have 2 copies of your dataset in memory.
To avoid this you could write / reuse a CSV parser that directly allocates the data in the internal format / dtype expected by the scikit-learn model. You can try numpy.loadtxt for instance (have a look at the docstring for the parameters).
Also if you data is very sparse (many zero values) it will be better to use a scipy.sparse datastructure and a scikit-learn model that can deal with such an input format (check the docstrings to know). However the CSV format itself is not very well suited for sparse data and I am not sure there exist a direct CSV-to-scipy.sparse parser.
Edit: for reference KNearestNeighborsClassifer allocate temporary distances array with shape (n_samples_predict, n_samples_train) which is very wasteful when only (n_samples_predict, n_neighbors) is needed instead. This issue can be tracked here:
https://github.com/scikit-learn/scikit-learn/issues/325
Several times now, I've encountered this term in matlab, fortran ... some other ... but I've never found an explanation what does it mean, and what it does? So I'm asking here, what is vectorization, and what does it mean for example, that "a loop is vectorized" ?
Many CPUs have "vector" or "SIMD" instruction sets which apply the same operation simultaneously to two, four, or more pieces of data. Modern x86 chips have the SSE instructions, many PPC chips have the "Altivec" instructions, and even some ARM chips have a vector instruction set, called NEON.
"Vectorization" (simplified) is the process of rewriting a loop so that instead of processing a single element of an array N times, it processes (say) 4 elements of the array simultaneously N/4 times.
I chose 4 because it's what modern hardware is most likely to directly support for 32-bit floats or ints.
The difference between vectorization and loop unrolling:
Consider the following very simple loop that adds the elements of two arrays and stores the results to a third array.
for (int i=0; i<16; ++i)
C[i] = A[i] + B[i];
Unrolling this loop would transform it into something like this:
for (int i=0; i<16; i+=4) {
C[i] = A[i] + B[i];
C[i+1] = A[i+1] + B[i+1];
C[i+2] = A[i+2] + B[i+2];
C[i+3] = A[i+3] + B[i+3];
}
Vectorizing it, on the other hand, produces something like this:
for (int i=0; i<16; i+=4)
addFourThingsAtOnceAndStoreResult(&C[i], &A[i], &B[i]);
Where "addFourThingsAtOnceAndStoreResult" is a placeholder for whatever intrinsic(s) your compiler uses to specify vector instructions.
Terminology:
Note that most modern ahead-of-time compilers are able to auto vectorize very simple loops like this, which can often be enabled via a compile option (on by default with full optimization in modern C and C++ compilers, like gcc -O3 -march=native). OpenMP #pragma omp simd is sometimes helpful to hint the compiler, especially for "reduction" loops like summing an FP array where vectorization requires pretending that FP math is associative.
More complex algorithms still require help from the programmer to generate good vector code; we call this manual vectorization, often with intrinsics like x86 _mm_add_ps that map to a single machine instruction as in SIMD prefix sum on Intel cpu or How to count character occurrences using SIMD. Or even use SIMD for short non-looping problems like Most insanely fastest way to convert 9 char digits into an int or unsigned int or How to convert a binary integer number to a hex string?
The term "vectorization" is also used to describe a higher level software transformation where you might just abstract away the loop altogether and just describe operating on arrays instead of the elements that comprise them. e.g. writing C = A + B in some language that allows that when those are arrays or matrices, unlike C or C++. In lower-level languages like that, you could describe calling BLAS or Eigen library functions instead of manually writing loops as a vectorized programming style. Some other answers on this question focus on that meaning of vectorization, and higher-level languages.
Vectorization is the term for converting a scalar program to a vector program. Vectorized programs can run multiple operations from a single instruction, whereas scalar can only operate on pairs of operands at once.
From wikipedia:
Scalar approach:
for (i = 0; i < 1024; i++)
{
C[i] = A[i]*B[i];
}
Vectorized approach:
for (i = 0; i < 1024; i+=4)
{
C[i:i+3] = A[i:i+3]*B[i:i+3];
}
Vectorization is used greatly in scientific computing where huge chunks of data needs to be processed efficiently.
In real programming application , i know it's used in NUMPY(not sure of other else).
Numpy (package for scientific computing in python) , uses vectorization for speedy manipulation of n-dimensional array ,which generally is slower if done with in-built python options for handling arrays.
although tons of explanation are out there , HERE'S WHAT VECTORIZATION IS DEFINED AS IN NUMPY DOCUMENTATION PAGE
Vectorization describes the absence of any explicit looping, indexing, etc., in the code - these things are taking place, of course, just “behind the scenes” in optimized, pre-compiled C code. Vectorized code has many advantages, among which are:
vectorized code is more concise and easier to read
fewer lines of code generally means fewer bugs
the code more closely resembles standard mathematical notation
(making it easier, typically, to correctly code mathematical
constructs)
vectorization results in more “Pythonic” code. Without
vectorization, our code would be littered with inefficient and
difficult to read for loops.
Vectorization, in simple words, means optimizing the algorithm so that it can utilize SIMD instructions in the processors.
AVX, AVX2 and AVX512 are the instruction sets (intel) that perform same operation on multiple data in one instruction. for eg. AVX512 means you can operate on 16 integer values(4 bytes) at a time. What that means is that if you have vector of 16 integers and you want to double that value in each integers and then add 10 to it. You can either load values on to general register [a,b,c] 16 times and perform same operation or you can perform same operation by loading all 16 values on to SIMD registers [xmm,ymm] and perform the operation once. This lets speed up the computation of vector data.
In vectorization we use this to our advantage, by remodelling our data so that we can perform SIMD operations on it and speed up the program.
Only problem with vectorization is handling conditions. Because conditions branch the flow of execution. This can be handled by masking. By modelling the condition into an arithmetic operation. eg. if we want to add 10 to value if it is greater then 100. we can either.
if(x[i] > 100) x[i] += 10; // this will branch execution flow.
or we can model the condition into arithmetic operation creating a condition vector c,
c[i] = x[i] > 100; // storing the condition on masking vector
x[i] = x[i] + (c[i] & 10) // using mask
this is very trivial example though... thus, c is our masking vector which we use to perform binary operation based on its value. This avoid branching of execution flow and enables vectorization.
Vectorization is as important as Parallelization. Thus, we should make use of it as much possible. All modern days processors have SIMD instructions for heavy compute workloads. We can optimize our code to use these SIMD instructions using vectorization, this is similar to parrallelizing our code to run on multiple cores available on modern processors.
I would like to leave with the mention of OpenMP, which lets yo vectorize the code using pragmas. I consider it as a good starting point. Same can be said for OpenACC.
It refers to a the ability to do single mathematical operation on a list -- or "vector" -- of numbers in a single step. You see it often with Fortran because that's associated with scientific computing, which is associated with supercomputing, where vectorized arithmetic first appeared. Nowadays almost all desktop CPUs offer some form of vectorized arithmetic, through technologies like Intel's SSE. GPUs also offer a form of vectorized arithmetic.
By Intel people I think is easy to grasp.
Vectorization is the process of converting an algorithm from operating
on a single value at a time to operating on a set of values at one
time. Modern CPUs provide direct support for vector operations where a
single instruction is applied to multiple data (SIMD).
For example, a CPU with a 512 bit register could hold 16 32- bit
single precision doubles and do a single calculation.
16 times faster than executing a single instruction at a time. Combine
this with threading and multi-core CPUs leads to orders of magnitude
performance gains.
Link https://software.intel.com/en-us/articles/vectorization-a-key-tool-to-improve-performance-on-modern-cpus
In Java there is a option to this be included in JDK 15 of 2020 or late at JDK 16 at 2021. See this official issue.
hope you are well!
vectorization refers to all the techniques that convert scaler implementation, in which a single operation processes a single entity at a time to vector implementation in which a single operation processes multiple entities at the same time.
Vectorization refers to a technique with the help of which we optimize the code to work with huge chunks of data efficiently. application of vectorization seen in scientific applications like NumPy, pandas also you can use this technique while working with Matlab, image processing, NLP, and much more. Overall it optimizes the runtime and memory allocation of the program.
Hope you may get your answer!
Thank you. 🙂
I would define vectorisation a feature of a given language where the responsibility on how to iterate over the elements of a certain collection can be delegated from the programmer (e.g. explicit loop of the elements) to some method provided by the language (e.g. implicit loop).
Now, why do we ever want to do that ?
Code readeability. For some (but not all!) cases operating over the entire collection at once rather than to its elements is easier to read and quicker to code;
Some interpreted languages (R, Python, Matlab.. but not Julia for example) are really slow in processing explicit loops. In these cases vectorisation uses under the hood compiled instructions for these "element order processing" and can be several orders of magnitude faster than processing each programmer-specified loop operation;
Most modern CPUs (and, nowadays, GPUs) have build-in parallelization that is exploitable when we use the vectorisation method provided by the language rather than our self-implemented order of operations of the elements;
In a similar way our programming language of choice will likely use for some vectorisation operations (e.g. matrix operations) software libraries (e.g. BLAS/LAPACK) that exploit multi-threading capabilities of the CPU, another form of parallel computation.
Note that for points 3 and 4 some languages (Julia notably) allow these hardware parallelizations to be exploited also using programmer-defined order processing (e.g. for loops), but this happens automatically and under the hood when using the vectorisation method provided by the language.
Now, while vectorisation has many advantages, sometimes an algorithm is more intuitively expressed using an explicit loop than vectorisation (where perhaps we need to resort to complex linear algebra operations, identity and diagonal matrices... all to retain our "vectorised" approach), and if using an explicit ordering form has no computational disadvantages, this one should be preferred.
See the two answers above. I just wanted to add that the reason for wanting to do vectorization is that these operations can easily be performed in paraell by supercomputers and multi-processors, yielding a big performance gain. On single processor computers there will be no performance gain.