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Gcc bgq docu [skip ci] #447

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merged 9 commits into from Aug 17, 2016
Merged

Gcc bgq docu [skip ci] #447

merged 9 commits into from Aug 17, 2016

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@apeyser
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apeyser commented Aug 3, 2016

Replacement for pull request #385 and issue #412

@heplesser please take a look at it

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apeyser commented Aug 5, 2016

Add @gtrensch to look at this

INSTALL Outdated
PyNEST on BlueGene/Q, you have to compile dynamically, i.e. `-Dstatic-libraries=OFF`
and you have to cythonize the `pynest/pynestkernel.pyx/.pxd`
on a machine with Cython installed:
If you compile dynamically, be aware that the BlueGene/Q system might not provide a `ltdl`

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jougs Aug 8, 2016

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"an ltdl library" instead of "a ltdl library" ?
If yes, the same applies below.

INSTALL Outdated
compile and install a `ltdl` yourself and add `-Dwith-ltdl=<ltdl-install-dir>`
to the `cmake` line. Otherwise add `-Dwith-ltdl=OFF`.

Additionally, the design of cmake's mpi handling has a broken design, which is

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jougs Aug 8, 2016

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make "mpi" uppercase

INSTALL Outdated
to the `cmake` line. Otherwise add `-Dwith-ltdl=OFF`.

Additionally, the design of cmake's mpi handling has a broken design, which is
brittle in the case of BGQ and certain libraries (flags to use sionlib, for example).

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jougs Aug 8, 2016

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"sionlib" -> "SIONlib"

INSTALL Outdated
Additionally, the design of cmake's mpi handling has a broken design, which is
brittle in the case of BGQ and certain libraries (flags to use sionlib, for example).

If you run into that, you must force cmake to use the wrappers rather than

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jougs Aug 8, 2016

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put "cmake" in backticks

INSTALL Outdated
-DPYTHON_INCLUDE_DIR=/bgsys/local/python3/3.4.2/include/python3.4m

A complete `cmake` line for PyNEST could look like this:

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@jougs

jougs Aug 8, 2016

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add ``` and remove indentation

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apeyser Aug 11, 2016

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@jougs So, use github markup? And do this piecewise as we go?

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jougs Aug 11, 2016

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I assumed so as single backticks were already used in other places of the file. I'd say that the triple ones at least don't hurt readability in a non-markdown enabled environment and help if rendered correctly.

INSTALL Outdated
-DPYTHON_LIBRARY=/bgsys/local/python3/3.4.2/lib/libpython3.4m.a \
-DPYTHON_INCLUDE_DIR=/bgsys/local/python3/3.4.2/include/python3.4m \
-Dwith-ltdl=OFF \
<nest-src>

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INSTALL Outdated
-DPYTHON_LIBRARY=/bgsys/local/python3/3.4.2/lib/libpython3.4m.a \
-DPYTHON_INCLUDE_DIR=/bgsys/local/python3/3.4.2/include/python3.4m \
-Dwith-ltdl=OFF \
<nest-src>

Further, for running PyNEST, make sure all python dependencies are installed and
environment variables are set properly:

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jougs Aug 8, 2016

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add ``` and remove indentation

INSTALL Outdated
--exp-env PYTHONPATH \
... \
: /bgsys/local/python3/3.4.2/bin/python3.4 script.py

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jougs Aug 8, 2016

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INSTALL Outdated

Compiling NEST with GCC (`-DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ_GCC`)
might require you to use a GSL library compiled using GCC, otherwise undefined
symbols break your build. After the GSL is build with GCC and installed in

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jougs Aug 8, 2016

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second "build" -> "built"

INSTALL Outdated
Compiling NEST with GCC (`-DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ_GCC`)
might require you to use a GSL library compiled using GCC, otherwise undefined
symbols break your build. After the GSL is build with GCC and installed in
<gsl-install-dir>, add `-Dwith-gsl=<gsl-install-dir>` to the `cmake` line.

Compiling for Fujitsu Sparc64

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jougs Aug 8, 2016

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Please also put the code blocks in this section in triple backticks and remove their indentation

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jougs commented Aug 8, 2016

Nice work. Please see my minor comments on language and layout.

INSTALL Outdated

Building PyNEST on BlueGene/Q requires you to compile dynamically, i.e.
`-Dstatic-libraries=OFF`. Further, you have to cythonize the
`pynest/pynestkernel.pyx/.pxd` on a machine with Cython installed:

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@heplesser

heplesser Aug 10, 2016

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What is the .pxd ending?

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apeyser Aug 11, 2016

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@heplesser .pxd is the equivalent of a cython header, and goes with the .pyx. Will change that to pyx, for simplicities sake.

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heplesser commented Aug 10, 2016

@apeyser I tested the instructions for NEST with XLC and Python 3.4 on Juqueen and they work like a charm!

👍

@apeyser apeyser changed the title Gcc bgq docu Gcc bgq docu [skip ci] Aug 11, 2016
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apeyser commented Aug 15, 2016

@jougs Can you check the current state?

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apeyser commented Aug 17, 2016

@jougs : any problem merging and closing?

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jougs commented Aug 17, 2016

@apeyser: nope. Just skipped my attention. Happy and merging!

@apeyser apeyser merged commit f3c22d2 into nest:master Aug 17, 2016
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@apeyser apeyser deleted the apeyser:gcc_bgq_docu branch Aug 17, 2016
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