Gcc bgq docu [skip ci] #447

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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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Add @gtrensch to look at this

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apeyser commented Aug 5, 2016

Add @gtrensch to look at this

INSTALL
-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.

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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
+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

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jougs Aug 8, 2016

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make "mpi" uppercase

INSTALL
+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"

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jougs Aug 8, 2016

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"sionlib" -> "SIONlib"

INSTALL
+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

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jougs Aug 8, 2016

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put "cmake" in backticks

INSTALL
+ -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 Aug 8, 2016

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add ``` and remove indentation

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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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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.

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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
+ -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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jougs Aug 8, 2016

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INSTALL
+ -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

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jougs Aug 8, 2016

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add ``` and remove indentation

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

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INSTALL
+
+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"

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jougs Aug 8, 2016

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second "build" -> "built"

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

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

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jougs commented Aug 8, 2016

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

INSTALL
+
+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 Aug 10, 2016

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What is the .pxd ending?

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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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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 Aug 10, 2016

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

👍

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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 from Gcc bgq docu to Gcc bgq docu [skip ci] Aug 11, 2016

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@jougs Can you check the current state?

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apeyser commented Aug 15, 2016

@jougs Can you check the current state?

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apeyser Aug 17, 2016

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@jougs : any problem merging and closing?

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apeyser commented Aug 17, 2016

@jougs : any problem merging and closing?

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

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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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