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Questions tagged [io]

The process of Inputing and Outputting information, particularly emphasis on user generated input/output at runtime.

2
votes
2answers
107 views

Memory/speed tradeoff for many small matrix inverses

Problem In the case of a finite element code, I have many small (order of 30x30) matrix inverses (or LU factorizations), one per finite element. These matrix inverses never change and must be applied ...
1
vote
1answer
165 views

A fast I/O file format readable by Fortran, Java, PHP?

I am writing a Fortran program that does fairly light weigt computation on fairly large data files. The output must be readable by some Java-script (that i have no insight in) and preferably also by ...
4
votes
2answers
898 views

Many processors reading a single HDF5 file

I'm working on a code that we eventually plan to scale up to 10's or 100's of thousands of processors (using MPI). I have a single HDF5 file (mesh nodes and connectivity, etc) that needs to be read ...
5
votes
2answers
389 views

What are the most common dense matrix storage formats?

I'm looking to write some code to read in a dense matrix from a file, and I was wondering what are the most common storage formats that my code should support?
2
votes
0answers
104 views

Converting matrices L and U output by dgssv() of SuperLU to triples format

How can I convert matrices L and U output by dgssvx() of SuperLU to triples format (to ...
3
votes
3answers
2k views

How do I read a binary file into PETSc as a matrix?

I created a binary matrix using the following loop in c ...
4
votes
1answer
681 views

Outputting a distributed vector in PETSc

I'm working with someone else's code that uses PETSc 3.0.0-p9. They have a vector at the end of the computation that is distributed among a number of different processors, and I want to output that ...
6
votes
2answers
93 views

Performance of Lustre filesystems

The cluster I work on has a filesystem labelled as "fast" with no further explanation. But the filesystem type is "lustre", which strongly hints at a Lustre filesystem. While general information about ...
14
votes
4answers
342 views

How to deal with too much data?

Our plasma dynamics simulations often produce too much information. During the simulations we record various physical properties on a grid (x,y,z,t) that is as large as (8192x1024x1024x1500), for at ...
19
votes
3answers
2k views

Parallel I/O options, in particular parallel HDF5

I have an application that can be trivially parallelized but its performance is to a large extent I/O bound. The application reads a single input array stored in a file that is typically 2-5 GB in ...