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Questions tagged [memory-management]

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1answer
52 views

Understading memory sharing in a GPGPU using a lattice example

I am new in the GPUs world, I used them in Matlab ambient so I didn't need to appreciate the subtleties of these devices. I know that a GPU can be divided into multiprocessors (also called Streaming ...
2
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0answers
56 views

OpenMP inconsistently segfaulting

I parallelized my code with openMP, and now have this bug in my code that's really odd. If it's the first time I run on a computer, it segfaults, but if I run the program again it runs fine. I've ...
0
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1answer
57 views

Efficient way to store array where elements are added and removed frequently

At any point in time I have a list of N points, points will be added and removed making the number of total points change over time. If I just use an array to store this information, I'm concerned ...
0
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3answers
106 views

How to store a TB size array in C++ on a cluster

I want to do a huge simulation that requires ~ 1 TB of data to describe a bunch of interacting particles (each has different interactions). Is it possible to store this data in an array in C++, so ...
0
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0answers
52 views

Petsc matrix with DM objects takes too much memory

I have been learning petsc recently and made a simple solver for stokes equation on 3D staggered grid. My code is running on server with 200GB ram, but if I run a solver on 256^3 grid, memory used by ...
4
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2answers
2k views
2
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0answers
56 views

Processing time steps in chunks with Fortran [closed]

My PDE simulation program written in Fortran has to make about 2 million variable time steps. But with each time step it slows down more and more, so that if it initially makes 1000 time steps per ...
1
vote
1answer
113 views

Doing computations on a very large numpy array: streaming the calculation vs out-of-core memory

I am trying to perform a calculation in numpy that depends on several parameters, and involved the creation of many intermediate arrays. These intermediate steps involve integrals over more parameters....
0
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0answers
16 views

Cost functions to judge time/memory/accuracy tradeoffs

I am working on an interesting algorithm: Its absolute error is exponential in a parameter $j \in \mathbb{N}$, and for a given $j$, I have complete freedom to choose between an $\mathcal{O}(1)$ time-...
1
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1answer
68 views

Minimizing the used memory in diffusion simulation using Python

I am recently dealing with a diffusion simulation project and I have come up with the following code: ...
1
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1answer
145 views

Finite difference - Explicit / Implicit / Crank Nicolson - Does the implicit method require the least memory?

Examine a dynamic 2D heat equation $\dot{u} = \Delta u$ with zero boundary temperature. A standard finite difference approach is used on a rectangle using a $n\times n$ grid. For the resulting linear ...
1
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0answers
113 views

Why is the method of im2col with GEMM is more efficient than the method of direction implementation with SIMD in CNN

The convolutional layers are most computationally intense parts of Convolutional neural networks (CNNs).Currently the common approach to impement convolutional layers is to expand the image into a ...
1
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2answers
65 views

Access optimized data structure for representing integer lattice

Consider the integer lattice in $2d$, namely the set $\mathbb{Z}^2 = \{(x,y): x,y\in \mathbb{Z}\}$, and let $u:\mathbb{Z}^2 \to \mathbb{R} $ be a function defined on some bounded subset of $\mathbb{Z}^...
0
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1answer
97 views

Use of GPU with respect to CPU

I have research work where I need to compute a matrix inversion. The matrix has a size $31300\times31300$. I am using a universal java matrix package to invert this matrix. But as the dimension of the ...
0
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1answer
86 views

Compare 64gb dd3 ram with 2gb Quadro M1000M gpu on Lenovo P50

I frequently work with Keras and tensorflow-gpu on my Lenovo P50 workstation which has 64GB ram and a 2GB Nvidia QUadro M1000M GPU. Today while training my model on GPU, it ran into memory error and ...
1
vote
1answer
114 views

Reordering algorithm for minimization of ram usage of a skyline matrix

The stiffness matrix of $Ax=B$ system of linear equations, where $A$ is an $n\times n$ symmetric matrix stored in the form of symmetric skyline matrix, that is associated with a finite element model ...
0
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1answer
178 views

Why does multithreaded code Segfault in 64-bit but not 32-bit [closed]

I have written some multithreaded code using PyOpenCL, which works fine under the following conditions: GPU 32-bit floating point values (Intel Iris GPU can only handle single precision values) CPU ...
1
vote
1answer
326 views

Why does PETSc matrix memory allocation improve performance so much?

Context In the Portable, Extensible Toolkit for Scientific Computing (PETSc), the user often creates matrices and vectors. These objects are then used as input for other routines like iterative ...
1
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0answers
271 views

Memory requirement to find eigenvalues and -vectors of large sparse matrix

How can I estimate how much memory will be needed to find eigenvalues and eigenvectors of a given large sparse matrix? I have a real symmetric matrix with roughly $5 \times 10^4$ rows and columns, ...
0
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1answer
214 views

bifurcation diagram MATLAB runs out of memory

I have a 3000 x 2301 matrix 'xfinfin' in MATLAB that I want to plot in the following way: ...
2
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0answers
82 views

How to fix time intervals to store data in a stochastic simulation (continous time markov chain)

I am using FORTRAN to implement Gillespie's stochastic simulation algorithm. I would be running many simulations in parallel (both parallel instances with different seed and parallel functions); if I ...
3
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0answers
958 views

total memory usage of MPI shared memory

I am trying to use the MPI share memory feature. I have several SMP nodes, and each of them has four cores. I need an array of size N for each node that should be accessed by all four cores in each ...
2
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2answers
1k views

How best to use scipy.integrate's ODE solvers when state is not naturally stored as a vector?

I have a large system of ODEs. For various reasons, it is natural to store the values of the dependent variables in a multidimensional array. For example, these values might represent the solution ...
2
votes
1answer
523 views

Not enough memory for GMRES

After realizing that Gauss-Seidel is extremely slow for my simulation, i wanted to try GMRES and luckily found the C++ code here without diving into the theory. The size of the matrix in my case is <...
3
votes
1answer
4k views

How to change the dimensions of an Eigen Matrix in a loop?

I have a while loop, in which I use a Matrix A, vectors B and x with varying dimensions: <...
1
vote
1answer
103 views

How to allocate memory for successive iterative solutions with potentially different non-zero structure?

Background I am solving the unsteady heat equation in 3D using an alternating direction implicit (ADI) method. This means that I am solving three different tridiagonal systems within a single timestep ...
3
votes
2answers
1k views

How Do I solve large systems given UMFPACK memory limitations?

I am trying to solve a system of equations (A x = b) for 3D heat diffusion (i.e. each equation has at most 7 terms not including the constant "b" term) using UMFPACK with boost numeric bindings to C++....
3
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2answers
836 views

Memory management for solving large sparse systems with UMFPACK

I'm using umfpack for solving large systems of equation. However, I'm constantly getting out of memory issues for even modest size problems as pre2, torso3, ohne2 Hamrle3 (all from Tim Devis's ...
3
votes
1answer
317 views

LU Decomposition with memory-mapped matrices

I have a ~4.12 Tb structured relatively-sparse matrix dataset (about 8% of the matrix entries are non-zero) that i want to apply an LU decomposition, however, given the size of it, loading it in ...
2
votes
1answer
238 views

Memory management in time-domain simulation

I develop a parallel time-domain DAE simulation software using OpenMP and Fortran 2003. The main algorithm is: ...
1
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0answers
257 views

Memory allocation error with GSL ODE solver applied to system of 4 ODEs

I am trying to solve a (large) system of ODEs with GSL solvers. When I use driver method I get an error message of could not allocate space for gsl_interp_accel, ...
17
votes
4answers
5k views

Portable multicore/NUMA memory allocation/initialization best practices

When memory bandwidth limited computations are performed in shared memory environments (e.g. threaded via OpenMP, Pthreads, or TBB), there is a dilemma of how to ensure that the memory is correctly ...
8
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4answers
367 views

(How) do you take into account memory fragmentation?

I use an example from finite element theory, but anybody who maintains a large datastructure and successively extends it will find something similar. Suppose I have an unstructured mesh of points and ...