Questions tagged [parallel-computing]
The study of solving computational problems by exploiting the use of multiple processors simultaneously.
279
questions
1
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0answers
29 views
Multigrid Reduction In Time Convergence
I am trying to solve a 2D dynamic linear elasticity model parallel in time using Xbraid. The spatial domain is [0,1]x[0,1] and time domain [0,1]. For time integration I am using a backward Euler ...
2
votes
0answers
146 views
Parallel In Time with Multigrid
I am trying to solve the linear finite element equation $M\ddot{u}+Ku=F(t)$, where $M$ is the mass matrix ,$K$ the stiffness matrix and $F(t)$ the external load vector, parallel in time using XBraid ...
3
votes
1answer
77 views
Dirichlet Boundary Condition finite difference method using sparse-matrix $Ax = b$ system
I am trying to solve the boundary value problem for heat equation:
$$
u_{xx} + u_{yy} = f(x,y)
$$
where the solution $u(x,y) \in [0,1] \times [0,1]$ and the Dirichlet boundary condition $u(x,y) = ...
2
votes
3answers
196 views
On the reordering of sparse matrices
I have been reading on different techniques used to reorder sparse matrices to achieve better performance, the most popular being the Cuthill-McKee or Reverse Cuthill-McKee algorithm. Most of those ...
2
votes
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 ...
1
vote
2answers
106 views
Parallelisation strategies for mixed FE formulations
Mixed FE formulations with LBB-stable elements require two different meshes for the primary and the constraint variables, for example, displacement and pressure. With continuous approximation for the ...
0
votes
1answer
48 views
0
votes
0answers
68 views
Openmp critical section inside if conditional statement
I have a function like this
void foo(x, *y) {
some calculations
if (x > *y) {
*y = x/2;
}
more calculations
}
My parallel section is
<...
2
votes
5answers
283 views
FEM and High Performance Computing
Suppose we want to solve an FEM problem in terms of HPC. What is the most usual way to do it:
Using an open-source software like mfem,deal.ii etc.. or,
Assembly the system by your own(read mesh file,...
1
vote
0answers
84 views
How to debug segmentation faults in large problems?
I am sorry if this question seems like off topic or opinion based, but I was not sure how to go about it.
I am currently working on a 100k x 100k positive definite linear system and trying to solve it ...
2
votes
0answers
58 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
votes
1answer
76 views
How to use 8-cores CPU as a single-core more (8x) powerful CPU?
I use python for my algorithm which uses only one core and I need more processing speed.
I have i7 6700K CPU with 8 cores. How to convert them to one core to have a total performance of 8 cores?
...
22
votes
9answers
9k views
Are there any embarrassingly parallel tasks that require a CPU rather than GPU?
I am looking for tasks that
are unsuitable for GPUs
gain significant speedup as more CPU nodes are added
don't require large data transfer or inter-thread communication between nodes.
Do any ...
0
votes
1answer
49 views
problem in interface operator
https://www.unige.ch/~gander/Preprints/42540.pdf. here I have a problem in section $4,$ of approximating the symbol $\sigma_i(k)$. My understanding is, to get back the operator $S_i$ we have to use ...
2
votes
1answer
74 views
Parallel, matrix-free estimate of the trace
What would be the best way to estimate the trace of a large, distributed matrix, if one only know its action on a vector throug a parallel "matvec" routine?
In the application I am interested in, the ...
2
votes
1answer
66 views
Mesh partition quality
I am working on static FE mesh partitioning and in order to achieve a good quality partitioning I want to know how to drecrease interprocessor communication by increasing the connectivity of elements ...
14
votes
3answers
2k views
Why would you need frameworks like MPI when you can multi-task using threads?
MPI is an interface which enables us to create multiple processes to be run on a single machine or on a cluster of machines, and enables message passing or in short sorts of communication between ...
1
vote
1answer
71 views
Parallel solution of PDEs
Which is the best approach to solve a PDE in parallel:
1.To split the mesh the mesh in N parts and every processor works on its own part or
2.To take the global linear system Ax=b and solve it in ...
0
votes
1answer
59 views
Parallel mesh partitioning
When a mesh partitioning takes place and every process works on a part of the mesh is any way to rename the global numbering of nodes(on each process) into a local numbering?Is there any software that ...
0
votes
3answers
107 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 ...
2
votes
0answers
97 views
What is the state-of-the-art in parallel sparse matrix and dense vector multiplication?
For sure, there has been many highly optimized library on this. But I am working on a matrix-free context since the problem size does not allow explicit storage of sparse matrix elements. I'd love ...
1
vote
1answer
79 views
Full approximation scheme - smoothers - literature recomendation
I would like to use full approximation scheme(FAS) for solving nonlinear PDE. I am looking into practical implementation of FAS in parallel(MPI) settings. I noticed the most common/effective smoother ...
4
votes
1answer
97 views
Parareal for particle simulations
Recently I have stumbled upon this video of M. J. Gander https://www.youtube.com/watch?v=dn5vqN8ezuE
and the coresponding notes that he wrote on Time Parallel Time Integration and I find it a quite ...
0
votes
2answers
181 views
Parallel output in ASCII-format with MPI
After some parallel computations, I need to write the results in a file and for plotting reasons, I want them in ASCII format. Because of performance issues, I want to avoid to ...
1
vote
1answer
35 views
How to compute the mean 2D slice of a 3D set of data in MPI
I have a 3D set of data v(i,j,k), and I want to compute the mean 2D slice vmean(i,j) summing up the ...
4
votes
4answers
392 views
CPU usage when a MPI rank waits during a blocking communication
A typical way of dealing with I/O in MPI parallel programs is to either read all data to a single node and dispatch to the other nodes accordingly, or send all data to a single node and write from ...
3
votes
2answers
183 views
Deep learning using Distributed linear algebra
Is there any deep learning library based on Trillinos or Petsc linear algebra?
3
votes
1answer
199 views
Parallelizing Newton-method in solving non-linear systems
Circuit simulation software based on SPICE (such as ngspice) uses Newton-Raphson method to solve non-linear system of equations ...
3
votes
3answers
144 views
GPGPU computing, software selection
I am using an existing GCC C++ x86 Qt application that filters, displays and stores results computed by some C code. Since the computation by now got too complex for CPUs I intend to port the small C ...
1
vote
2answers
98 views
simulation outputs differ across hardware platforms
We've recently ported our Python/Fortran simulation code to a new supercomputer. Some (not all) of the tests (simulations) that we've run on the new platform yield results that are significantly ...
2
votes
1answer
53 views
How to pass matrices to parallel workers quickly in matlab?
I am trying to solve many different linear systems in parallel in matlab. The problem is, each linear system has entirely different parts and are fairly large, so passing the information to each of ...
0
votes
1answer
85 views
Computer build for scientific or big data computing [closed]
I'm wanting to build a computer for scientific or big data computing (Python, Fortran, Matlab) and I was hoping to get some advice on the type of processor, memory, graphics, etc I would need.
I ...
2
votes
1answer
512 views
Why my parallel code using MPI is much slower than the serial one?
I know that is not the first time someone asks this question but I'm really confused.I'm new to MPI, and I tried to implement the Jacobi solver for a linear system $Ax=b$. I want to compare the time ...
2
votes
2answers
153 views
How to compute 16 different simulations on parallel with pbs script on the same machine
I have a 32 cores machine, and I need to run 16 different dynamics simulations in parallel on it. I want the 16 jobs to run in parallel, not sequentially, on the same machine. The 16 dynamics input ...
0
votes
1answer
87 views
Access PETSc data in totalview?
Is it possible to view the data stored in the various PETSc data types from within totalview?
Ordinarily, PETSc types are integers which act as pointers to the actual data (obviously my understanding ...
3
votes
1answer
77 views
Parallelizing FEM for elliptical PDEs with n >1
For a little personal project, I am picking up my FEM skills again. I learned a lot about the theory back in university and I am able to implement a simple FEM solver for specific problems but I was ...
2
votes
1answer
397 views
How to choose a python parallelization library?
I want to preprocess a relatively large dataset using python. I implemented some Dask parallelization and was stunned by the time reduction. I figure there are other libraries or frameworks I could ...
2
votes
2answers
197 views
C standard for computational science
Which C standard should be used for computational science code ?
Should we keep compatibility with C89/90/ANSI or jump to C99 or C11 ?
Context:
Code will use third-party : BLAS, LAPACK, MKL, ...
3
votes
2answers
135 views
Parallel assembly of matrix
I have a matrix which I want to assembly quickly, which is in block form:
$$
A = \pmatrix{ A_{11} & A_{12} & A_{13} \\ A_{21} & A_{22} & A_{23} \\ A_{31} & A_{32} & A_{33}}
$$
...
-1
votes
1answer
71 views
Writing parallel code for molecular computation [duplicate]
I recently moved towards computational biophysics from an experimental science background. As of now, I am learning the fundamentals and doing some basic monte carlo simulations of LJ fluid on my ...
2
votes
1answer
70 views
GPGPU/FPGA programming for Combinatorial Analysis
Recently, I have taken an interest in performing combinatorial analysis for the game of 21 (blackjack) and attempted to use my AMD APU to try and thread the program via the 4 cores on the chip. ...
1
vote
2answers
78 views
Guaranteed equality between binary results with increasing MPI processes
Testing on an MPI scientific code for compressible flow dynamics I noticed that the results may depend on the number of processors used for the calculation. In fact, comparing the binary files they ...
4
votes
1answer
129 views
Level scheduling of triangular sparse matrices
Assume one has a triangular sparse matrix and want to solve $Lx=b$ where $b$ and $L$ are known. This can be done easily by using forward substitution when $L$ is a lower triangular matrix. Forward ...
1
vote
1answer
214 views
Matlab parpool on Intel Xeon-Phi (KNL)
I am trying to run my matlab script on a Xeon Phi node with 68 physical cores. Using parpool I allocate 16 cores to enable SMD parallelization with a parfor loop. The script looks something like this.
...
7
votes
1answer
203 views
Solving linear system of the form $ABx=b$
I would like to solve a linear system of the form $ABx=b$ in parallel, where $A$ and $B$ are large, sparse matrices. Currently, I am forming the system matrix $AB$ explicitly, but I would like to ...
0
votes
2answers
242 views
How do I interpret the results from MPI_Wtime()?
Say, I have this code
double start = MPI_Wtime();
ParallelMatrixVectorProductRotuine(...);
double end = MPI_Wtime();
How do I interpret the numbers I am getting. ...
1
vote
2answers
150 views
MPI data broadcast or not in C
I have two slightly different but getting the same results MPI code.
The first one is from an open-source package having several data exchange steps in between:
...
8
votes
0answers
112 views
Review of modern homotopy methods and practical techniques
I'm hoping someone can recommend recent literature concerning homotopy methods for solving systems of nonlinear equations. Already by the time of Layne Watson's 1986 paper there were a lot of methods,...
5
votes
1answer
168 views
Parallel decomposition of 2D grid with minimal communication
Consider an $M\times N$ grid with periodicity in both dimensions upon which I want to do some local stencil-like computations using distributed-memory parallelism (MPI). I have two options for ...
0
votes
1answer
135 views
Parallelization of FEM calculations
I need to conduct some FEM calculations and I am wondering whether parallelization would be a good idea.
The trouble is that my model is not especially large so it takes few seconds to solve a single ...
