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

+# Find mallocMC
+###############################################################################
+
+find_package(mallocMC 2.0.1 REQUIRED)


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

ax3l · 2015-02-16T09:26:29Z

src/picongpu/CMakeLists.txt

@@ -253,6 +252,12 @@ if( (Boost_VERSION EQUAL 105500) AND
      "${CUDA_NVCC_FLAGS} \"-DBOOST_NOINLINE=__attribute__((noinline))\" ")
 endif()

+################################################################################


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

@@ -39,7 +39,6 @@ set(CMAKE_PREFIX_PATH "/usr/lib/x86_64-linux-gnu/" "$ENV{MPI_ROOT}"
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH}
    ${CMAKE_CURRENT_SOURCE_DIR}/../../thirdParty/cmake-modules/)

-


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
View reviewed changes

n01r mentioned this pull request Jan 28, 2015

Start simulation with neutral atoms n01r/picongpu#5

Closed

ax3l reviewed Feb 16, 2015
View reviewed changes

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

Merged

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

Merged

6 tasks

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
View reviewed changes

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

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use mallocMC for species storage #640

use mallocMC for species storage #640

psychocoderHPC commented Jan 21, 2015

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PrometheusPi commented Feb 24, 2015

		@@ -39,7 +39,6 @@ set(CMAKE_PREFIX_PATH "/usr/lib/x86_64-linux-gnu/" "$ENV{MPI_ROOT}"
		set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH}
		${CMAKE_CURRENT_SOURCE_DIR}/../../thirdParty/cmake-modules/)

use mallocMC for species storage #640

use mallocMC for species storage #640

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