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

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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
166 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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35 views

Virtualization for testing multi-node MPI

I would like to test a library that rests upon another, MPI-ready, library but without deploying it on a computational cluster (for now). My first attempts are involving virtualization techniques ...
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1answer
59 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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116 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
127 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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87 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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37 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 ...
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67 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
66 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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63 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 ...
5
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2answers
327 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
84 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
70 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
147 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
64 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
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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
60 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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100 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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231 views

Iterations of Parallel Jacobi Vs Iterations of Parallel Gauss-Seidal [closed]

Literature says that Gauss-Seidel should converge twice as fast as Jacobi. This translates to saying that "approximately" the number of iterations that Jacobi takes is roughly twice that of ...
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1answer
450 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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90 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
363 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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427 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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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
247 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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250 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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933 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 ...
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238 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 ...
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298 views

C - OpenMP, MPI, Serial Program [duplicate]

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 ...
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97 views

Why would this a pair of E5-2670 cpus be faster than 4 E5-2640 cpus for large matrix diagonalisation problems?

Not really much more to say; Of several computers available for use, these are two of the larger ones; one has 2x E5-2670, and the other has 4x E5-4640. The problems we're looking at essentially boil ...
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1k views

What's the difference between conjugate gradient method and biconjugate gradient method

What's the difference between these two methods? Can a problem be solved by one method will be able to solved by the other? Can both/or one of them be parallelized with OpenMP and/or MPI?
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BLACS context value and multiple MPI communicators

I am reposting here a question previously asked in stackoverflow: as suggested in a reply to my question, scicomp could be a better place to obtain some useful comments/suggestions for my problem. I ...
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1answer
569 views

Parallel 2d heat equation (implicit timestepping) using MPI

I am trying to solve the time dependent heat equation with backward euler timestepping and second order space finite differences. This results in a Poisson system needing to be inverted. In serial ...
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49 views

gather data from processors in FFTW3 MPI

The parallel FFTW3 distributes different portions of a large data to different processors, so that each processor obtains and manipulates only a small fraction of the large size data that wants to be ...
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Which version of FFTW

At the moment, I'm installing the "GADGET-2" application. In its documentation it says "Note that the MPI-capable version 2.x of FFTW is required, the new version 3 lacks MPI capability at this point. ...
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2answers
2k views

Stop process from continuing until others have finished MPI

I am looping an array using MPI. The problem is, i think that some processes are moving onto their next iteration before other precesses have finished theirs. This is causing me problems because data ...
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2answers
280 views

mpi retrieve a variable value from process with known rank to process that made an mpi_something call

I have a need to get a variable value from another process rank of which I know. This happens in context of a parallel solver of a "A x = b" equation, for which process with rank 0 knows matrix A, and ...
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Exploiting parallelism within a single heterogeneous computing node

I'm looking for a library to exploit parallelism within a single heterogeneous computing node (possibly using Accelerators like Xeon Phi or nVidia's GPGPU's) in a C++ FV/DG code using hierarchical ...
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1k views

Any recommendations for unit-testing frameworks compatible with code/libraries that use MPI?

Usually, I write serial code, and when I do, I write unit tests with some xUnit-style testing framework (MATLAB xUnit, PyUnit/nose, or Google's C++ testing framework). Based on a cursory Google ...
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3answers
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When is MPI_Wait necessary for non-blocking calls?

I hope this is not too off-topic here -- I've asked it on SO but I'm hoping I'll get better answers here! I'm a little bit confused about when I should call MPI_Wait (or other variants such as: ...
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1answer
289 views

MPI policy for multiple asynchronous transfers

What is the policy of multiple overlapping asynchronous transfers in MPI? I have a program with several open asynchronous irecv operations. I find that transfers ...
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862 views

What features do users need from an MPI C++ interface?

The 3.0 version of the MPI standard formally deleted the C++ interface (it was previously deprecated). While implementations may still support it, features that are new in MPI-3 do not have a C++ ...
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4answers
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What is an efficient way of notifying MPI processes of receiving messages?

In MPI, is there any built-in mechanism to notify a group of processes that they need to receive messages from other processes? In my application every process ...
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Looking for super computer technology suggestions

I'm writing some image processing software to detect bubbles in oil at work. One of the image filters I need (Perona Malik) seems like it will take a long time to compute. (It involves solving some ...
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695 views

Performance optimization or tuning possible for Scalapack Gemm?

I'm comparing the performance of distributed gemm, using Scalapack over OpenBLAS, with threaded gemm, using OpenBLAS. It seems quite hard for me to get scalapack to give better results than ...
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2answers
379 views

How to make Elemental Gemm run quickly?

How to make Elemental Gemm run quickly? I have the following code: ...
4
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1answer
434 views

Libraries for distributed-memory Cholesky factorization?

What libraries can compute dense Cholesky factorizations in distributed-memory environments (preferably using MPI). I'm using C/C++, and have access to a cluster of between 1 and 40 nodes, where each ...
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85 views

Reshaping a MultiVector in Trilinos

I'm using Trilinos for a problem and I have an Epetra_MultiVector object with 1 vector of length m*n*nFrames. I need to turn it ...
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MPI_Send/Recv not transmitting initial entries

Problem I'm building a simple MPI Send/Recv hello world in Fortran and am running into an odd error. I want to make sure I'm not missing anything trivial before blaming OpenMPI or gfortran. In the ...