Profile: Draco (MPCDF) by ax3l · Pull Request #2308 · ComputationalRadiationPhysics/picongpu

ax3l · 2017-10-12T10:41:58Z

Adds a picongpu.profile.example for the Draco cluster at MPCDF.

To Do

add in manual (.rst)
add .tpl for submission via tbg @psychocoderHPC

Adds a picongpu.profile.example for the Draco cluster at MPCDF.

- add alias `getNode` to allocate an interactive job - add architecture to the back-end environment variable

add slurm template

ax3l · 2017-10-13T12:26:43Z

+# Other Software ##############################################################
+#
+# needs to be compiled by the user
+export PNG_ROOT=$HOME/lib/libpng-1.6.32


is this the correct hint? system zlib and system libpng might be taken currently

ax3l · 2017-10-13T12:26:51Z

+export LD_LIBRARY_PATH=$PNGWRITER_ROOT/lib:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=$SPLASH_ROOT/lib:$LD_LIBRARY_PATH
+
+# export MPI_ROOT=$MPICH_DIR


ax3l · 2017-10-13T12:27:25Z

+module purge
+
+module load git/2.14
+module load gcc/6.3


to do: add

export CXX=$(which g++) export CC=$(which gcc)

otherwise the system g++ (4.X) was taken by cmake

ax3l · 2017-10-13T12:28:01Z

+cd !TBG_dstPath
+
+export MODULES_NO_OUTPUT=1
+source !TBG_profile


does not need to be loaded on this cluster?

psychocoderHPC · 2017-10-13T12:34:19Z

export CXX and CC must be defined to find the correct c++ and c compiler

Currently, we do not add RPATHs during build.

ax3l · 2017-10-16T14:54:50Z

+export PNGWRITER_ROOT=$HOME/lib/pngwriter-0.6.0
+export SPLASH_ROOT=$HOME/lib/splash-1.6.0
+
+export LD_LIBRARY_PATH=$PNG_ROOT/lib:$LD_LIBRARY_PATH


can be removed if zlib and libpng are taken from system

This can be removed. I got feedback from Katharina that it is not needed.

ax3l · 2017-10-16T14:55:02Z

+# PIConGPU Helper Variables ###################################################
+#
+export PICSRC=$HOME/src/picongpu
+export PIC_BACKEND="omp2b"


add architecture again? :haswell did not work in our first tests, but this could have been due to an too old gcc in the beginning.

Yes please add it.

did it work now (with the right version of gcc after setting $CXX?)

Adds the profile of the Max Plack "Draco" Cluster to the manual. http://www.mpcdf.mpg.de

PrometheusPi

From a review without testing this on the cluster, this looks good to me. @ax3l Did this setup work for you?

ax3l · 2017-10-18T07:25:20Z

this setup worked for our colleague at IPP.
I have some inline comments that I would improve but since I can not test it personally we can also keep it as it is currently.

psychocoderHPC · 2017-10-19T15:15:01Z

We need to load numctl, I will check how the module is named on the cluster

ax3l · 2017-10-19T15:16:42Z

since @psychocoderHPC and I tested on the cluster we will make the final merge when it is ready, but a general review from a third person such as you @PrometheusPi is very welcome here! :)

psychocoderHPC · 2017-10-20T12:07:21Z

numactl is fixed installed on all compute nodes.

psychocoderHPC · 2017-10-23T08:43:22Z

@ax3l I added an PR ax3l#7 to your PR to change the last points (remove own compiled PNG and add architecture)

ax3l · 2017-10-23T10:15:30Z

@psychocoderHPC just push the new commit directly on my branch please :) that's a new feature, you have push rights

ax3l · 2017-10-23T10:16:08Z

we still need to test this please, the reason I did not add those comments yet was the lack of testing on the system

psychocoderHPC · 2017-10-23T11:37:51Z

I know know that I can push directly but I love to create PR for a PR^^. Could you please press merge, than there is no need for me to switch the current branch :-)

- remove `PNG_ROOT` (use system installed PNG library) - add architecture `haswell` for the backend

Profile: Draco (MPCDF)

f049f3a

Adds a picongpu.profile.example for the Draco cluster at MPCDF.

ax3l added the documentation regarding documentation or wiki discussions label Oct 12, 2017

ax3l added this to the 0.4.0 / 1.0.0: Next Stable milestone Oct 12, 2017

psychocoderHPC added 2 commits October 12, 2017 13:38

add alias getNode

edb5149

- add alias `getNode` to allocate an interactive job - add architecture to the back-end environment variable

add tbg template for draco-mpcdf

09611c0

add slurm template

psychocoderHPC force-pushed the doc-mpcdf branch from ffcdf8b to 09611c0 Compare October 12, 2017 11:46

ax3l commented Oct 13, 2017

View reviewed changes

Add more LD_LIBRARY_PATH Hints

83c67f3

Currently, we do not add RPATHs during build.

ax3l commented Oct 16, 2017

View reviewed changes

ax3l changed the title ~~[WIP] Profile: Draco (MPCDF)~~ Profile: Draco (MPCDF) Oct 16, 2017

ax3l force-pushed the doc-mpcdf branch from e2287ef to a9707a2 Compare October 16, 2017 14:58

Draco (MPCDF): Add to Manual

79e6b56

Adds the profile of the Max Plack "Draco" Cluster to the manual. http://www.mpcdf.mpg.de

ax3l force-pushed the doc-mpcdf branch from a9707a2 to 79e6b56 Compare October 16, 2017 15:00

PrometheusPi self-assigned this Oct 17, 2017

PrometheusPi previously approved these changes Oct 17, 2017

View reviewed changes

ax3l requested a review from psychocoderHPC October 19, 2017 08:52

ax3l assigned psychocoderHPC and ax3l and unassigned PrometheusPi Oct 19, 2017

update picongpu.profile.examples

50b78c4

- remove `PNG_ROOT` (use system installed PNG library) - add architecture `haswell` for the backend

ax3l dismissed PrometheusPi’s stale review via 50b78c4 October 24, 2017 14:51

psychocoderHPC approved these changes Oct 25, 2017

View reviewed changes

psychocoderHPC merged commit 88dd19d into ComputationalRadiationPhysics:dev Oct 25, 2017

ax3l deleted the doc-mpcdf branch October 25, 2017 08:28

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