Survey: need for large-scale computational support

Anything that doesn't fit elsewhere.
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ted
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Posts: 5935
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
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Survey: need for large-scale computational support

Post by ted »

Note: the easiest way to reply to this poll will be to click on the quote button
(just to the right of the Post subject line above), and just type your answers
right into my questions.

To help us meet the ever-changing needs of NEURON users, please let us know if
your modeling work is presenting either (or both) of these kinds of problems:
1. Running a very large number of simulations, e.g. for optimization or exploration
of parameter space.
2 Simulating large scale models, i.e. the model itself is so complex that it's hard to fit
onto a single computer, and even a single run takes a long time.

If you are facing either or both of these problems, please indicate which it is,
and provide the following information:

Time per run is _________ sec/min/hr
Total number of simulations is _________
Total simulation time _________ (i.e. time per run X number of simulations)

Hardware:
Individual computer / Workstation cluster / Beowulf / Other (what?)
CPU type Intel / AMD / PPC / Other (which?)
CPU speed < 1GHz / 1-2GHz / 2-3GHz / > 3GHz
How many CPUs 1 / 2 / ___
Memory < 512 MB / 512 MB-1 GB / > 1 GB (how much more?)

Operating system
Win98, Me, or earlier
WinNT, 2K, or XP
UNIX / Linux / OS X
Other (what?)
Last edited by ted on Sun Oct 23, 2005 7:02 pm, edited 1 time in total.
ram
Posts: 3
Joined: Thu Jul 28, 2005 10:23 pm

Re: Survey: need for large-scale computational support

Post by ram »

YES
1. Running a very large number of simulations, e.g. for optimization or exploration
of parameter space.


Time per run is ____variable, maybe average 0/3/0_____ sec/min/hr
Total number of simulations is ____1000_____
Total simulation time _____48 hours____ (i.e. time per run X number of simulations)

( I am also saving very large data files between runs, so not all is "pure" simulation time).

Hardware:
Individual computer
CPU type Intel / AMD athlon 64
CPU speed > 3GHz
How many CPUs 1
Memory 4 GB

XP 64
fhamzei

Re: Survey: need for large-scale computational support

Post by fhamzei »

Time per run is ___30min______ sec/min/hr
Total number of simulations is __50000_______


Hardware:
Individual computer / Workstation
CPU type AMD
CPU speed 2-3GHz
How many CPUs 2
Memory < 16 GB
Operating system
WinX
jtmoyer
Posts: 14
Joined: Fri Jun 17, 2005 10:01 am
Location: Philadelphia, PA, USA
Contact:

Re: Survey: need for large-scale computational support

Post by jtmoyer »

2 Simulating large scale models, i.e. the model itself is so complex that it's hard to fit
onto a single computer, and even a single run takes a long time.

Time per run is ___5 min______
Total number of simulations is ____480_____
Total simulation time ___40 hrs______ (i.e. time per run X number of simulations)

Hardware:
Workstation cluster
CPU type PPC
CPU speed 2-3GHz
How many CPUs _24_
Memory > 1 GB (2 GB per 2 CPUs)

Operating system
UNIX / Linux / OS X

Really our biggest hindrance is that the single cell simulations take 5 minutes to run on a single processor - often we tweak parameters by hand and it wastes a lot of time to sit and wait for each simulation to finish.
moritz

Re: Survey: need for large-scale computational support

Post by moritz »

ted wrote:Note: the easiest way to reply to this poll will be to click on the quote button
(just to the right of the Post subject line above), and just type your answers
right into my questions.

To help us meet the ever-changing needs of NEURON users, please let us know if
your modeling work is presenting either (or both) of these kinds of problems:
1. Running a very large number of simulations, e.g. for optimization or exploration
of parameter space.
2 Simulating large scale models, i.e. the model itself is so complex that it's hard to fit
onto a single computer, and even a single run takes a long time.

If you are facing either or both of these problems, please indicate which it is,
and provide the following information:

* Usage: we are using NEURON with a genetic algorithm written in Python
Time per run is ____~2-6 min_____ sec/min/hr
Total number of simulations is ___~5000______
Total simulation time __a week or more___ (i.e. time per run X number of simulations)

Hardware:
Individual computer / Workstation cluster / Beowulf / Other (what?)
CPU type Intel / AMD / PPC / Other (which?)
CPU speed < 1GHz / 1-2GHz / 2-3GHz / > 3GHz
How many CPUs 1 / 2 / _1__
Memory < 512 MB / 512 MB-1 GB / > 1 GB (how much more?)

Operating system
Win98, Me, or earlier
WinNT, 2K, or XP
UNIX / Linux / OS X
Other (what?)
ted
Site Admin
Posts: 5935
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Interim survey results

Post by ted »

So far a total of 25 users have responded to this survey (including those who replied to
the msg I posted to the NEURON Users' Group mailing list). The survey is still "active"
so any stragglers who want to add their two bits are encouraged to do so.

Most are doing optimization/parameter search simulations, at least two are gathering
data for information theoretical analysis of cell/network function, and 8 are simulating
large models (note that there is considerable overlap among these three sets).

Execution times range widely, from a few seconds to as long as 2 weeks, as do the
number of runs ("tens" for the person with 2 week runtimes, 10^5 - 10^6 for the person
with 5-30 second runtimes (who also happens to have a Beowulf cluster)).

Most respondents are using individual PCs, some with multiple CPUs. Five use a
Beowulf cluster, and three use other kinds of parallel hardware.

Ten are running WinXP, and 17 use UNIX/Linux/OS X (these counts include a few
who use both XP and UNIX/Linux/OS X). Nobody owned up to Win98/Me/NT/2k.

Thanks to those who have already responded, and once more I encourage anyone
who has not already replied to do so. Don't be bashful--this is a chance to have some
influence on the future development of resources for large-scale computational
support.
xyang

Re: Survey: need for large-scale computational support

Post by xyang »

Time per run is __40 sec_______ sec/min/hr
Total number of simulations is ___30______
Total simulation time ____1200sec_____ (i.e. time per run X number of simulations)

[b]Hardware:[/b]
Individual computer
CPU type Intel4
CPU speed 1.80GHz
How many CPUs 1
Memory 512 MB

[b]Operating system[/b]
WinXP
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