use mallocMC for species storage #640

psychocoderHPC · 2015-01-21T14:48:02Z

This pull request use mallocMC to manage the shared species memory.

add mallocMC to CMakeLists.txt
add PointerWrapper class Pointer<>
delete old Heap- and RingBuffer/Boxes
remove the possibility that species device memory can directly copied to host memory

Tests:

KHI heating comparison to current dev
add more documentation

~~Do not merge before~~ #717

ax3l · 2015-01-21T14:53:45Z

src/picongpu/CMakeLists.txt

for now: +EXACT due to upcoming interface changes in mallocMC 2.1.0

ax3l · 2015-02-16T09:26:29Z

src/picongpu/CMakeLists.txt

ok for now, but as talked offline: we will simply add a include in the final version to reduce install dependencies.

opened #717

ax3l · 2015-02-16T09:28:08Z

looks good 👍

psychocoderHPC · 2015-02-16T09:32:19Z

This version needs a small refactoring against the current mallocMC release.
I am back tomorrow and will do this.

ax3l · 2015-02-16T09:36:07Z

fantastico! ✨

psychocoderHPC · 2015-02-17T10:03:24Z

After our compile suite is updated it is ready to merge.

psychocoderHPC · 2015-02-17T10:04:45Z

electron/positron heating on 16gpus

ax3l · 2015-02-17T12:10:45Z

After our compile suite is updated it is ready to merge.

I will update it asap - nevertheless, I think we should

import mallocMC via subtree
before we can merge :)

psychocoderHPC · 2015-02-20T09:13:25Z

rebased against #717

- add `mallocMC` to CMake - add previues and next pointer to the `Frame` class - add PointerWrapper class `Pointer<>`

delete not maintained classes

- add documentation - CMakeLists.txt: search for exact `mallocMC` version - ParticlesFunctors.hpp: fix hard coded `FrameType`

add threadfence_block() after one thread cleared all `multi masks`.

- change github annotations - change pagesize to 2MiB - set reset free pages to `true`

ax3l · 2015-02-20T14:15:52Z

src/picongpu/CMakeLists.txt

pls revert the changes in this file

- ParticleBox: - remove host modifier for all methods - use mallocMC::malloc and mallocMC::free

ax3l · 2015-02-20T14:52:49Z

It would be cool if we could add a plain benchmark "before" - "after" mallocMC (without plugins) to just document the performance stayed the same.
(last time we did that check we found some bugs that were then fixed in mallocMC)

psychocoderHPC · 2015-02-20T15:44:26Z

Runtime KHI 3d Esirkepov [in seconds] on 16 K80 GPUs 10k simulation steps:

	init	simulation
dev	26	1575
branch	10	1569

ax3l · 2015-02-20T17:33:27Z

well done, good work! 👍

use mallocMC for species storage

PrometheusPi · 2015-02-24T12:18:21Z

👍 cool

psychocoderHPC assigned ax3l Jan 21, 2015

psychocoderHPC added this to the Open Beta milestone Jan 21, 2015

psychocoderHPC added component: core in PIConGPU (core application) component: PMacc in PMacc feature refactoring code change to improve performance or to unify a concept but does not change public API labels Jan 21, 2015

ax3l removed the refactoring code change to improve performance or to unify a concept but does not change public API label Jan 21, 2015

ax3l reviewed Jan 21, 2015
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for now: +EXACT due to upcoming interface changes in mallocMC 2.1.0

n01r mentioned this pull request Jan 28, 2015

Start simulation with neutral atoms n01r/picongpu#5

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ax3l reviewed Feb 16, 2015
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psychocoderHPC force-pushed the topic-useMallocMC-rb2 branch from 40957b1 to 00f1c1a Compare February 17, 2015 09:43

psychocoderHPC removed the need-info/blocked label Feb 17, 2015

ax3l closed this Feb 17, 2015

ax3l reopened this Feb 17, 2015

n01r mentioned this pull request Feb 17, 2015

Remove attribute chargeState, add boundElectrons #706

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psychocoderHPC force-pushed the topic-useMallocMC-rb2 branch from 00f1c1a to 2ce8d0a Compare February 17, 2015 14:51

ax3l mentioned this pull request Feb 18, 2015

Restructure Third Party Software #717

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psychocoderHPC force-pushed the topic-useMallocMC-rb2 branch from 2ce8d0a to efb68eb Compare February 20, 2015 09:12

psychocoderHPC closed this Feb 20, 2015

psychocoderHPC reopened this Feb 20, 2015

psychocoderHPC added 5 commits February 20, 2015 14:17

use mallocMC for particle memory

702133c

- add `mallocMC` to CMake - add previues and next pointer to the `Frame` class - add PointerWrapper class `Pointer<>`

delete old Heap and RingBuffer/Boxes

1aac874

delete not maintained classes

add documentation, minor changes

1d9ca4c

- add documentation - CMakeLists.txt: search for exact `mallocMC` version - ParticlesFunctors.hpp: fix hard coded `FrameType`

add threadfence_block

e4f8aa3

add threadfence_block() after one thread cleared all `multi masks`.

fix documentation, change mallocMC config

5e68185

- change github annotations - change pagesize to 2MiB - set reset free pages to `true`

psychocoderHPC force-pushed the topic-useMallocMC-rb2 branch from efb68eb to dad4184 Compare February 20, 2015 13:23

ax3l reviewed Feb 20, 2015
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pls revert the changes in this file

psychocoderHPC force-pushed the topic-useMallocMC-rb2 branch 2 times, most recently from 90ef4d1 to 8e088ea Compare February 20, 2015 14:35

rebase and refactor ParticleBox

8275f29

- ParticleBox: - remove host modifier for all methods - use mallocMC::malloc and mallocMC::free

psychocoderHPC force-pushed the topic-useMallocMC-rb2 branch from 8e088ea to 8275f29 Compare February 20, 2015 14:39

ax3l added a commit that referenced this pull request Feb 20, 2015

Merge pull request #640 from psychocoderHPC/topic-useMallocMC-rb2

699c983

use mallocMC for species storage

ax3l merged commit 699c983 into ComputationalRadiationPhysics:dev Feb 20, 2015

use mallocMC for species storage #640

use mallocMC for species storage #640

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