All Questions
Tagged with cluster-computing or hpc
149 questions
67
votes
13
answers
52k
views
C++ vs Fortran for HPC
In my computational science PhD program, we are working almost exclusively in C++ and Fortran. It seems like some professors prefer one over the other. I am wondering which one is 'better' or if one ...
- 2,159
57
votes
7
answers
23k
views
Is it a good idea to use vector<vector<double>> to form a matrix class for high performance scientific computing code?
Is it a good idea to use vector<vector<double>> (using std) to form a matrix class for high performance scientific computing code?
If the answer is no. ...
- 703
37
votes
7
answers
2k
views
What programming paradigms should I be investing in if I want my code to run on petascale machines in the future?
It's pretty clear from a survey of the top500 that the industry is trending towards an exponential increase in processing cores. The largest supercomputers all use MPI for communication between nodes,...
- 6,911
35
votes
1
answer
14k
views
CUDA vs OpenCL as of late 2013
How do CUDA and OpenCL compare to each other as of late 2013 from a programmer's perspective? My group is thinking about trying to make use of GPU computing. Would we be limiting ourself ...
- 2,600
25
votes
5
answers
5k
views
When is building a cluster in the cloud cheaper than building one in my lab for MD simulations?
An Amazon EC2 compute cluster costs about \$800-\$1000 (depending on duty cycle) per physical CPU core over the course of 3 years. In our last round of hardware acquisition, my lab picked up 48 cores ...
- 1,370
24
votes
3
answers
21k
views
Intel Fortran Compiler: tips on optimization at compilation
I will start with my personal experience in our lab. Back in the ifort 9 and 10 days, we used to be quite aggressive with the optimizations, compiling with -O3 and processor specific flags (-xW -xSSE4....
- 1,308
23
votes
6
answers
5k
views
Future of OpenCL?
The OpenCL programming paradigm promises to be a royalty free opens standard for heterogenous computing. Should we invest our time in developing software based on OpenCL? Pros/cons?
- 3,226
20
votes
3
answers
3k
views
Log-log parallel scaling/efficiency plots
A lot of my own work revolves around making algorithms scale better, and one of the preferred ways of showing parallel scaling and/or parallel efficiency is to plot the performance of an algorithm/...
- 9,563
19
votes
5
answers
7k
views
State of the Mac OS in Scientific Computing and HPC
Back towards the dawn of OS X, there seemed to be a great deal of hubbub, at least in the Mac world (I was nowhere near scientific computing at the time) about the Mac OS as a platform for scientific ...
- 2,403
19
votes
4
answers
14k
views
Do currently available GPUs support double precision floating point arithmetic?
I have run the molecular dynamics (MD) code GROMACS on a Ubuntu Linux cluster consisting of nodes containing 24 Intel Xeon CPUs. My particular point of interest turns out to be somewhat sensitive to ...
- 711
18
votes
5
answers
3k
views
Parallel Scientific Computation Software Development Language?
I want to develop a parallel scientific computation software from scratch. I want some thoughts on which language to start. The program involves reading/writing data to txt files and doing heavy ...
- 333
17
votes
4
answers
10k
views
Profiling CFD code with Callgrind
I'm using Valgrind + Callgrind to profile a solver I have written. As the Valgrind user manual states, I've compiled my code with the debugging options for the compiler:
"Without debugging info, ...
- 1,916
17
votes
3
answers
357
views
Desktop software with HPC resources for back end number crunching
Our workgroup produces a desktop application that simulates building energy performance. It is a .NET application and when the user is running a lot of simulations, they can be quite time consuming. ...
- 596
16
votes
2
answers
2k
views
Boost::mpi or C MPI for high performance scientific applications?
The thing I dislike most about MPI is dealing with datatypes (i.e. data maps/masks) because they don't fit that nicely with object oriented C++. boost::mpi only ...
- 1,085
16
votes
3
answers
742
views
How should I study creating and programming HPC systems?
I'm in a field that doesn't necessarily do a great deal of HPC work, and when it does encounter it, it's often the result of researchers from other fields exploring new applications to their methods ...
- 2,403
15
votes
4
answers
4k
views
Should I rent computing resources, or buy my own computers
Since this question is related to computation, I decided to post here. Hopefully it will be seen as appropriate.
I've just started running atmospheric and oceanic models, and I realize that I need ...
- 265
14
votes
4
answers
36k
views
Difference between Nodes and CPUs when running software on a cluster?
I'm looking into moving some computations of mine to a data center to get more computation power. In the context of this process, I am getting confused by the differentiation of a computation node and ...
- 994
13
votes
5
answers
612
views
How much should scientific software be optimized?
For applications requiring significant computational resources, high performance can be a critical factor when it comes to delivering scientific results or achieving "break-throughs" in reasonable ...
- 3,226
11
votes
1
answer
261
views
Statistical models for local memory/compute, network latency, and bandwidth jitter in HPC
Parallel computation is frequently modeled using a deterministic local rate of computation, latency overhead, and network bandwidth. In reality, these are spatially variable and non-deterministic. ...
- 25.8k
10
votes
2
answers
260
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 ...
- 201
10
votes
4
answers
2k
views
What is a robust, iterative solver for large 3-d linear-elastic problems?
I'm diving into the fascinating world of finite element analysis and would like to solve a large thermo-mechanical problem (only thermal $\rightarrow$ mechanical, no feedback).
For the mechanical ...
- 317
10
votes
2
answers
466
views
Task-based shared-memory parallel libraries in Scientific Computing
In recent years, several libraries/software projects have appeared that offer some form or another of general-purpose data-driven shared-memory parallelism.
The main idea is that instead of writing ...
- 9,563
9
votes
2
answers
10k
views
What does the priority of a PBS job really mean?
The qsub command which submits PBS jobs has a -p option that allows you to set the priority. From the man page:
Defines the ...
- 3,413
8
votes
4
answers
395
views
(How) do you take into account memory fragmentation?
I use an example from finite element theory, but anybody who maintains a large datastructure and successively extends it will find something similar.
Suppose I have an unstructured mesh of points and ...
- 3,720
8
votes
2
answers
1k
views
Why does sparse linear algebra have a low arithmetic intensity?
I often see the terms "low arithmetic intensity" and "memory-bound" associated with sparse matrix operations. However, my intuition is that a sparse matrix operation should be less memory-bound, if ...
- 108
8
votes
4
answers
230
views
Removing non-determinism from molecular dynamics code
I've been looking through the other answers, and I haven't found a good answer yet. I'll describe the simulation I am running, and then the problems. The program simulates particles undergoing ...
- 297
8
votes
2
answers
1k
views
Intel Knights Landing work loads vs NVIDIA GeForce
There are lot of articles being written about how the newly launched Intel Xeon Phi will steal the HPC\Super Computer market share from the competitors. Intel Knights is equipped with 72 cores and 4 ...
- 183
8
votes
4
answers
1k
views
Prolonging PBS job
It is quite painful to discover that a few-day long job is going to be prematurely killed due to an error in setting walltime limit for it.
Is there a way to change it for a running PBS job?
- 533
8
votes
2
answers
262
views
How to find a computational bottleneck
I am a PhD student and my lab has developed a code to run simulations. It relies on external libraries and code my lab has written. I've run a strong scaling study which shows poor performance, see ...
- 81
8
votes
1
answer
417
views
Red(-Green)-Refinement vs. Newest-Vertex-Bisection
What are the "Pros and Cons" for these two methods of mesh-refinement? Both seem to be the prevalent methods.
I can naturally imagine that global red refinement is comparatively easy to implement and ...
- 3,720
8
votes
2
answers
2k
views
Shape regularity in higher dimensions
In Finite Element theory, and other methods in scientific computing for PDEs, one uses meshes which fulfill several regularity criteria, many of them being equivalent.
It is of interest to have ...
- 3,720
8
votes
1
answer
153
views
Anyone knows references summarizing the history of supercomputing?
Anyone knows references summarizing the history and ideas behind supercomputing including mentioning of developments in parallel programming languages, applications, startup companies (some was ...
- 3,226
7
votes
5
answers
289
views
Computational science contests. Why arent there any?
I was wondering why there are no online or offline computational science contests? At least I couldn't find much by googling. I mean, like a topcoder for computational sciences.
I assume one reason is ...
- 173
7
votes
5
answers
332
views
External hardware resources for running long and computationally intensive simulations
I've written code for an obstructed random walker simulation and I want to run long simulations (6 hours or more on my computer). I don't want to run this simulation on my computer because I will want ...
- 241
7
votes
4
answers
3k
views
Best hardware solution for microsecond Molecular Dynamics
We would like to reach Molecular Dynamics simulation of proteins with around 20000 atoms in explicit water with trajectories of around 1 microsecond each. We are looking at different options for ...
- 711
7
votes
1
answer
237
views
Online resources for reviewing graphics cards for GPGPU
Can anyone recommend a site that maintains up-to-date reviews of graphics cards for GPGPU use? Most benchmarks focus on gaming performance, whereas I am interested in the performance of scientific ...
- 348
6
votes
2
answers
2k
views
Borrow computational power from machines around me
I'm a computational chemist working with little computational power and dealing with increasingly demanding chemical systems. My work machines are part of a big network (mixed with windows and linux) ...
- 163
6
votes
3
answers
6k
views
What is the best high performance computing platform for engineering simulations?
What is the best platform for high performance computing (HPC)?
Windows is long gone, I think. So only Unix and Linux stand the chance. What platform will strongly back my interest on computational ...
- 203
6
votes
1
answer
296
views
Working with large mesh files
I am working on some medium to large scale finite element codes. By using established and available tools I am able to have an algorithm that scales well up to about 10,000 cores. Investigating ...
- 3,293
6
votes
1
answer
679
views
Benchmarking performance in CFD: how to compare machines and codes?
Informally in our lab, we have developed 2 metrics to compare CFD solvers over
the range of machines we have access to. One is called COMP, which stands
for COde Machine Performance. This single ...
- 1,308
5
votes
5
answers
360
views
Will MPI continue to be a popular basis writing scalable massively parallel solvers on future many-core CPUs? [duplicate]
Possible Duplicate:
What programming paradigms should I be investing in if I want my code to run on petascale machines in the future?
Having entered the multi-core era (som already refers to as ...
- 3,226
5
votes
2
answers
6k
views
Where can I get access to GPU cluster for educational purpose?
I want to work on NVIDIA GPU cluster for my thesis. But the cost of clusters are too high for me to bear. Although I can buy a couple of latest GPU cards, but buying cluster is impossible for me at ...
- 181
5
votes
3
answers
288
views
How to efficiently structure simulation data in memory for cells with varying degrees of freedom?
For a discontinuous Galerkin-based simulation I need to store cell-based simulation data in memory. Since the order of the polynomial approximation $N_p$ may vary between cells, I wonder what the most ...
5
votes
1
answer
128
views
Additional cost associated with quad (or higher) precision
In going from double precision to quad (or higher) precision,
roughly how much of a performance hit is taken on various architectures and frameworks. Do floating point operations take twice as much ...
- 3,225
5
votes
1
answer
117
views
Is there a way to ensure that PBS array jobs will be run in order?
I run many PBS scripts that take advantage of the job array structure for similar jobs (e.g. 12345[0] through 12345[9]). With the way that the code is written, job [0] needs to run first, and then any ...
- 51
4
votes
3
answers
3k
views
A good, simple book/resource on Parallel Programming in C++ for scientific computing
I am a Mechanical Engineering grad student, currently working on a project which will be scaled up in the new future to require quite some processing power. I am using C++ for the code that I have, ...
- 149
4
votes
2
answers
347
views
Direct Numerical Simulation of reacting flows
I need to write a DNS code for simulating reacting flows in turbulent conditions. The code has to be highly scalable, because the computational cost of simulations is expected very large.
My idea is ...
- 41
4
votes
2
answers
599
views
Leveraging scipy for matrix free finite elements
This will be a very general question.
I have a 3D finite element code in Python which I would like to extend to handle "large" problems (~10^8 unknowns in the global system). Right now I am using the ...
- 672
4
votes
5
answers
2k
views
Finding the correct Molecular Dynamics library
I just started working on some Biophysics research, and I was looking around for a good MD library to use. There is one right now at the university set up in C, with openMC parallelization, but the ...
- 297
4
votes
2
answers
3k
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 ...
- 542