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Questions tagged [mpi]

Message Passing Interface - a standard and highly portable parallel programming interface for distributed memory systems.

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57 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 ...
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3answers
183 views

Writing a parallel version of an algorithm. Only which someparts are worth distributing

Say if I wanted to parallelise an algorithm. Only certain parts of this algorithm can be parallelised. The other parts are trivial and not worth distributing. Do I do all of these trivial calculations ...
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2answers
48 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. ...
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1answer
98 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: ...
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0answers
31 views

FFTW on subarray with MPI

With the guru interfaces of FFTW, I can apply transforms only to parts of a multidimensional array by modifying the fftw_iodim ...
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0answers
58 views

Can I MPI_Test for an Ibarrier

In this code, all processes post a barrier, sleep a while for good measure, then first Test and then Wait for the barrier. The <...
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1answer
361 views

General understanding of Intel MKL, threads and MPI

Preface I seem to lack a fundamental understanding of best practise recommendations given by Intels MKL user guides for using MKL in threaded applications. So let's clarify it together. Wording and ...
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40 views

Experience with using HPCX communications stack for MPI codes vs other stacks

I am wondering what is the experience of people with using the HPCX stack to run MPI codes, vs other stacks such as, IntelMPI or MVAPICH2. Do you have any sense of the performance differences between ...
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5answers
388 views

c++ Libraries for large linear system of equations

I am looking for libraries for solving large scale linear system (10e5) of equations using parallelization and shared memory. 1. Sparse, complex symmetric, SPD. 2. Suitable for higher order FEM ,...
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0answers
67 views

MPI_Finalize() only some processors

I want to develop a distributed algorithm with MPI which have load balancing capability. But there is a situation that I'm not very clear about, which is, when the number of tasks is less than the ...
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2answers
150 views

MapReduce with MPI question

I am doing an exercise using MPI to count frequencies of words distributed in several different files following similar steps in this instruction. But I met a problem with step 2. In my ...
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2answers
84 views

Halo Region Communication in Unstructured Mesh Problems

I'm currently using ParMETIS and it is required to determine the halo region of the local elements in a parallel unstructured mesh. Assume that the mesh is large and cannot be stored on a single ...
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1answer
260 views

Distributed (MPI) matrix matrix multiplication

I perform matrix matrix multiplications (between rank-3 and rank-2 arrays) in fortran using following subroutine, ...
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1answer
199 views

setting COMM_WORLD size from petsc4py without mpiexec command line

I would like to create a parallel solver using petsc4py as one component of a larger application. I can easily get PETSc.COMM_WORLD.getSize() to be 4 by calling mpiexec -n 4 python my_prog.py ...
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0answers
139 views

All eigenpairs of large sparse symmetric matrix

In advance I am sorry for my noobish question. I am a physics PHD student and basically I use python for my math/physics problems. But now I have a problem which requires more computing capacity and ...
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1answer
101 views

checksum of a distributed variable

Let say I have N computers and 2 N-by-N matrices distributed across them called A and B. Matrix A is row distributed while B is column distributed. Therefore, processor i knows ...
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2answers
293 views

Direct Solver and domain decomposition

In finite element method, in order to use MPI, we need to decompose the domain into sub-domains first. Then my question is whether we can solve each sub-domain using a direct solver? Of course, unlike ...
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3answers
177 views

MPI in C, all processor run outside of the MPI envir created

I am new to MPI and am trying to figure out the subtleties in it, and for that reason I am just playing around with an easy example. The question I have is that when I run the code below with 2 ...
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0answers
60 views

Compute all eigenvalues of a large sparse matrix [duplicate]

I am a physicist and I am trying to calculate the vibrational spectrum of a very large systems. I need whole spectrum of vibrational modes, that leads to a symmetric system. Basically, I need to solve ...
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0answers
48 views

Under what circumstances does Elemental's distributed SVD not work? [closed]

I am playing around with Elemental's distributed singular value decomposition and am running into two particular issues. Building the test at tests/lapack_like/SVD.cpp, and running with ...
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1answer
69 views

Need help understanding cluster process managers and MPI

I apologize if this is a relative simple question. I am very new to setting up a cluster computer and I am attempting to make heads and tails of the information. I was reading on setting up a cluster ...
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2answers
333 views

How to determine MPI compatibility [closed]

I have recently acquired a server that I will be using for distributed simulations. However, I was wondering how do I determine which MPI version the server is compatible with? The reason that I am ...
3
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3answers
444 views

State of the art in parallel data structures [closed]

I'm currently evaluating how I could implement several algorithms on a parallel computer with a large number of nodes, each also equipped with a powerful GPU. It turns out that for many algorithms, it ...
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2answers
232 views

MPI+OpenMP Scalability

I have a numerical code which is MPI+OpenMP (hybrid) parallelized and an available computational resource of 32 nodes with 16 cores on each node. The code has been tested for MPI scalability up to 16 ...
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4answers
869 views

What is “good” parallel scaling?

I often hear the phrase "good" or "bad" parallel scaling/efficiency. What exactly do people mean when they say that? For example, let $p = 1,\ldots 16$ be the number of processing elements, and A and ...
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2answers
331 views

How does MPI differentiate between two computers?

I am starting to dabble in MPI. I am fairly new to this area and I am currently reading the MPI standard. I would like to write my first MPI program, a simple hello world program, on a cluster that ...
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2answers
159 views

Communication overhead in supercomputing

I am looking for credible references stating how much resources supercomputers spend on coordinating versus doing actual task-related work. Resources could be available processing power but even Watts ...
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2answers
261 views

How does one write MPI-implementation-independent code?

Specifically, how does one go about writing code that works with, say, both MPICH and OpenMPI? I am currently in the process of cleaning up the build scripts and code for a distributed-memory ...
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2answers
430 views

efficient MPI collective non-blocking communication

I am facing a problem with MPI (Fortran). I have a really big matrix at each node and they differ at different nodes. At some point of my calculations, each node needs the matrix from all other nodes, ...
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1answer
207 views

Is there an implementation of MPI_AllReduce which handles sparse data better?

I need to synchronize intermediate solutions of an optimization problem solved distributively over a number of worker processors. The solution vector is known to be sparse. I have noticed that if I ...
4
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1answer
122 views

Balancing number of points in a 2D grid

In a parallel MPI code, I have load balancing issues. My 2D computational domain is distributed on a 2D MPI Cartesian topology, which leads to equal sized 2D sub-domains per MPI process. However, the ...
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1answer
355 views

Comm argument on MPI_Reduce in FORTRAN giving unusual results

I'm putting together a very simple integration program in FORTRAN using MPI. I have done this with C and all was well. However, in my "MAP_REDUCE" call, the comm argument seems problematic. I have ...
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0answers
106 views

What is the best way to stop an asynchronous-heterogeneous MPI program?

I want to stop immediately an MPI program, that has N processors and each processor runs a different algorithm (with different computational complexities). Processors share information to each other ...
12
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1answer
1k views

How to Run MPI-3.0 in shared memory mode like OpenMP

I am parallelizing code to numerically solve a 5 Dimensional population balance model. Currently I have a very good MPICH2 parallelized code in FORTRAN but as we increase parameter values the arrays ...
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1answer
100 views

How do I make sparse solvers to accept custom matvec function insted of matrix?

I have tried it with Lis, Intel mkl and PETSc. Everywhere you need to pass an actual matrix ...
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1answer
91 views

C++ - Starting paraller instances of an executable from a C++ code

Can I start parallel run of LAMMPS from inside a C++ code. Is it possible to compile my code and then do mpirun with my compiled code. I also have one system command inside the code, which starts ...
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1answer
380 views

Why is MPI/PETSc only showing 1 processor even though it works for helloworld?

I am a beginner with Unix and MPI. For the serial program, I run the program by typing make in /directory/buildagain and then <...
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2answers
108 views

Is it possible to configure Linux OpenMPI v1.6.5 to use multiple working directories on a single node?

I am running some quantum chemical calculations on a refurbished PowerEdge rack server, with dual quad-core Xeons, 16GB RAM, and a single 500GB SATA HDD. OS is vanilla Debian Wheezy. For one of the ...
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3answers
122 views

Reference Suggestions for MPI

I'm learning MPI in order to use MPI with a model written in Fortran. What are some good resources (books, websites, etc.)? Introductory/beginner material, and detailed references would both be ...
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1answer
100 views

Is it valid MPI-3 to nest non-blocking collectives?

Is the following a standards-conformant MPI-3 C program? ...
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1answer
376 views

FFT parallel processing in MPI

I am working now in Beowulf Cluster and parallel processing, I want code for Fast Fourier transfer functions written in any language, e.g., C/C++. Without using FFTW library based on message passing ...
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1answer
1k views

Parallel vs Serial Thomas Algorithm

I am currently writing a code that solves a large tridiagonal matrix every iteration and runs for 1,000's of iterations. I am currently using a Thomas algorithm to solve the matrix serially. I found a ...
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1answer
241 views

Debugging in parallel mode using Netbeans

I want to debug a c++ code with Netbeans. I can use the debugger in sequential mode but I dont know how to debug it when I want to run it in parallel. I would be grateful if anyone help me on this ...
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1answer
841 views

Domain Decomposition with PETSc

Does anyone have any experience on Domain Decomposition using PETSc library? I have used PETSc for creating my vectors and matrix within my C++ code. I also used KSP to solve the linear system. I ...
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0answers
843 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 ...
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2answers
4k views

Should I pass command line arguments to MPI_Init or not?

When writing MPI 3.0 code, should I pass argc and argv to the MPI_Init call or not, and why? ...
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1answer
406 views

Python: Computation time Issue with mpi4py

I am using in Python mpi4py to process in parallel 20 minimization functions. Each of the 20 worker processes the same algorithm but with different random initial ...
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0answers
462 views

Issues with Open MPI [closed]

Not sure if this question is more appropriate for StackOverload, but I'm guessing a bunch of people here have experience with MPI2, so thought I would try here first. I have some large dense complex ...
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1answer
2k views

MPI_ERR_TRUNCATE appears for no understandable reason

I am developing some parallel CFD code using Fortran 90 and OpenMPI. The processes are structured into two groups such that half perform a certain type of calculations (let's say Velocity, Pressure ...
7
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3answers
457 views

C - OpenMP, MPI, Serial Program

I'm part of a Computational Science course and come from a non-programming background, so please forgive me my ignorance. I'm working on a set of code in C to numerically solve the Navier Stokes ...