[Gate-users] writing output files

[David Sarrut]

Hi,

yes, Bryan is right, hits increase comp time and disk size, be sure you
need it. There is now a "summary" output to print the number of hits, but
that do not store the hits themselves.
https://opengate.readthedocs.io/en/latest/data_output_management.html?highlight=summary#additional-output-summary

Some times ago, we tried to investigate the setOutFileSizeLimit, but it did
not change anything. Nowadays, disks cache is really powerful, not fully
sure that a ram disk will help (but I might be wrong). See here:
https://github.com/OpenGATE/Gate/pull/339

David


On Wed, Jan 6, 2021 at 2:31 PM Josh Knowland <jknowland at lucernodynamics.com>
wrote:

> Hi Bryan – thanks a bunch, very good ideas.
>
> I’m typically simulating gamma cameras, so singles are what I’m most
> interested in. I’ll try a ramdisk, though. That seems like it should speed
> up the sim.
>
>
>
> -josh
>
>
>
>
>
>
>
> *From:* Gate-users <gate-users-bounces at lists.opengatecollaboration.org> *On
> Behalf Of *Bryan McIntosh
> *Sent:* Wednesday, January 6, 2021 8:26 AM
> *To:* gate-users at lists.opengatecollaboration.org
> *Subject:* Re: [Gate-users] writing output files
>
>
>
> Hi Josh,
>
>
>
> I did some benchmarking work in 2018 looking at the impact of the
> Spectre/Meltdown exploits on GATE simulation time; since those impacted I/O
> operations, I ran them on a RAM disk to remove my hard drive speed as a
> limiting factor. I've found that the following helps:
>
>
>
> 1) Remove hits or singles from the ROOT file output if you are simulating
> a PET system. In most simulations Hits aren't necessary, and if you are
> only using coincidences for creating projection data then you don't
> necessarily need the singles either. This also dramatically saves on disk
> space!
>
>
>
> 2) Since you have plenty of RAM, you can use a RAM disk as your output
> device. I used the guide at
> https://www.techrepublic.com/article/how-to-use-a-ramdisk-on-linux/,
> substituting 2 GB for whatever size of output data you needed. Once I
> created the RAM disk, I set my output path to it in the macro and
> everything worked seamlessly. This is a bit more dangerous since if the
> system crashes (unlikely) or if you lose power (depends on where you're
> located) you can lose some data, but it does offer a dramatic speed
> increase if you're running into storage speed limits.
>
>
>
> I hope that this helps!
>
>
>
> -Bryan McIntosh
>
>
>
> On Wed, Jan 6, 2021 at 1:13 AM <
> gate-users-request at lists.opengatecollaboration.org> wrote:
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>    1. writing output files (Josh Knowland)
>    2. Re: output unit (David Sarrut)
>    3. Re: Gate settings for Linac photon beam simulation (David Sarrut)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 5 Jan 2021 22:05:11 +0000
> From: Josh Knowland <jknowland at lucernodynamics.com>
> To: "gate-users at lists.opengatecollaboration.org"
>         <gate-users at lists.opengatecollaboration.org>
> Subject: [Gate-users] writing output files
> Message-ID:
>         <
> BN8PR15MB3283B4A09BD77A39BFE2ACABAFD10 at BN8PR15MB3283.namprd15.prod.outlook.com
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>
> All -
> I have noticed that running simulations is non-linear in terms of
> real-world time vs simulated time. For instance, simulating 100 seconds
> takes longer than 100x a 1-second simulation.
>
> My guess is that this could be due to file IO and the significantly larger
> file sizes resulting from longer simulations. I searched through the
> mailing list and the source code, but I couldn't find anything about the
> timing of file IO. I'd prefer not to use the "setOutFileSizeLimit" flag if
> I don't have to.
>
> Since the computer I run GATE on has plenty of RAM, is it possible to
> increase the time between file IO writes in order to speed up the overall
> simulation?
>
> -Josh
>
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-- 
David Sarrut, Phd
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