Questions tagged [parallel-computing]
The study of solving computational problems by exploiting the use of multiple processors simultaneously.
288
questions
1
vote
0answers
39 views
Why does Eigen allocate a temporary to evaluate A.noalias() = B.transpose()*C in parallel?
I wrote a program which iteratively transforms data using matrix multiplications. To minimize the number of large memory allocations, I use two roughly equal-sized ...
0
votes
3answers
88 views
How to apply the boundary condition when global stiffness matrix is stored in csr format? [duplicate]
I am solving the poisson equation and I constructed the global stiffness matrix in compressed row storage format. Then I wrote the preconditioned conjugate gradient solver for solving the system of ...
0
votes
1answer
29 views
MPI_Test not progressing MPI_Isend/MPI_Irecv requests
I am running a CFD simulation with a 200,000-vertex mesh. I've decomposed the mesh into 2 load-balanced sub-domains to test my parallel implementation. In the specific function that I am time-...
0
votes
0answers
29 views
Output solution vector in Petsc
I am using petsc to solve a linear elasticity problem discretized by finite elements.The initial mesh is read by a mesh file and the distribution in each processor is done using METIS.I am using only ...
5
votes
1answer
117 views
Solving PDEs in parallel
I have read different approaches on how to solve pdes in parallel which are discretized using finite element method. For example:
Non-overlapping domain decomposition approach as mentioned in https://...
0
votes
0answers
31 views
Methodology to develop parallel GPU simulations
I'm quite new to GPU or in general parallel programming. I am working on a Lattice-Boltzmann simulation that should be parallelized on GPU's. I wanted to asked more experienced people how to attack ...
2
votes
1answer
121 views
Can one safely use an OpenMP parallel loop with Armadillo?
I have a C++ code performing some Armadillo computations in a loop. I'd like to parallelize this loop with OpenMP. But Armadillo automatically uses OpenMP for some computations. So, would the OpenMP ...
1
vote
1answer
85 views
preconditioner for $u''(x)=\sin(x)$
I am interested in finding preconditioner to solve the problem for one dimensional problem $u''(x)=\sin(x), u(0)=u(1)=0$ using Dirichlet-Neumann method.
The preconditioner $M$ coming from Dirichlet-...
6
votes
1answer
178 views
Parallelize Scipy iterative methods for linear equation systems(bicgstab) in Python
I need to solve linear equations system Ax = b, where A is a sparse CSR matrix with size 500 000 x 500 000. I'am using scipy.bicgstab and it takes almost 10min to solve this system on my PC and I need ...
1
vote
0answers
56 views
performance comparison between PETSc and SLATE
We want to start a new project to solve a large-scale inverse problem (O(10^6) number of parameters) to invert for subsurface wave speeds. We will use FEM to solve forward and adjoint PDEs. In our ...
1
vote
0answers
50 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
151 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
124 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
276 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
57 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
108 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
116 views
0
votes
0answers
170 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
373 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
1answer
106 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
64 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
87 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?
...
24
votes
10answers
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
51 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
75 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
77 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
75 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
65 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
114 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
101 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
92 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
99 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
3answers
314 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
39 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
715 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 ...
4
votes
2answers
203 views
Deep learning using Distributed linear algebra
Is there any deep learning library based on Trillinos or Petsc linear algebra?
3
votes
1answer
313 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
159 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
99 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
62 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
87 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
800 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
166 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
98 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
85 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
694 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
3answers
231 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
138 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
85 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 ...
