Dear Hans,

Thank you for your answer and your various pieces of advice! I understand these problems are quite basic, but I still have a problem when doing all the steps you suggested earlier. Everything went correctly until I ran ake and make install (see the whole terminal script attached) where I got the following error message:

(nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien NEST % sudo make install

Password:

[ 2%] Built target nestutil

[ 25%] Built target sli_lib

[ 53%] Built target nestkernel

[ 94%] Built target models

[ 95%] Built target sli_readline

[ 95%] Built target sli

[ 96%] Built target nest_lib

[ 97%] Built target nest

[ 98%] Built target run_all_cpptests

[100%] Built target pynestkernel

Install the project...

-- Install configuration: ""

Extracting help information. This may take a little while.

-- Installing: /share/doc/nest/help

CMake Error at doc/cmake_install.cmake:56 (file):

file INSTALL cannot make directory "/share/doc/nest/help": No such file or

directory.

Call Stack (most recent call first):

cmake_install.cmake:42 (include)

make: *** [install] Error 1

----------

Can you help me with this issue please? I have been looking for this file but I couldn't find it either. Am I supposed to create it myself?

Thank you for all the help you can give me,

Best feelings,

Julien BALLBÉ

Le mar. 16 nov. 2021 à 08:10, Hans Ekkehard Plesser < hans.ekkehard.plesser@nmbu.no> a écrit :

Dear Julien,

As a starting doctoral student in the field of computational neurosciences, I am particularly interested in using NEST in my research works. However, I am a bit confused about the procedure to install NEST on a M1 macbook pro, therefore, I prefer to ask you before doing anything. From what I understood from your website here are the steps that, I suppose, I should do to install NEST properly:

• as I use a M1MAX Mac (MacOS 12.0) , I can't just install nest, I have to

build it. To do so:

• Download Miniforge for arm64 (from which I will be able to use Conda

right?)

Yes.

• NOT NECESSARY: Install Python 3.9.4 for arm Mac macOS 64-bit universal2

installer https://www.python.org/ftp/python/3.9.8/python-3.9.8-macos11.pkg

• Download the nest source code directly from github (

https://github.com/nest/nest-simulator)

Yes. Use the most recent released tarball/zip archive of NEST.

• Create a conda environment using the following command conda env create

-f extras/conda-nest-simulator-dev.yml

Yes. IMPORTANT: Since you are using Apple Silicon, you must open the conda-nest-simulator-dev.yml file and remove the following lines:

# Running NEST Server ----

• flask

• flask_cors

• requests

• uwsgi

• werkzeug

This is because some packages (uwsgi) is not available for M1 yet (last checked two weeks ago).

• Activate this environment ( conda activate...)

• Create a build directory outside the NEST source and go into it

• Install cmake package using conda ( conda install -c anaconda cmake)

• Configure NEST by running: cmake -DCMAKE_INSTALL_PREFIX:PATH=<nest_install_dir>

<nest_source_dir>

• Once done I can run make. make install. make installcheck

Yes to the five above.

Here are my questions:

• Is this installation procedure correct?

• Once installed, how can I launch NEST from a python interpreter such as

Spyder? Or is it only possible to launch it within a terminal window?

You need to make sure that the path to the NEST installation is in your PYTHONPATH. In the Terminal, that is handled by sourcing `nest_vars.sh`. I am off-hand not entirely certain how to make it work in Spyder.

• I am quite new to managing packages, so correct me if I am wrong, but

have I to install everything using exclusively Conda ?

Installing all via Conda makes things a lot easier.

• What is the purpose of creating a new environment to build NEST

Very briefly, to have all in place you need without cluttering your overall Python setup. There are many more answers to that out on the net, see eg

https://www.freecodecamp.org/news/why-you-need-python-environments-and-how-t...

I realize how many questions I ask you, and I am very grateful for every advice you could give me.

If it is more convenient for you, we can have a phone call when you want.

We can help with NEST-specific issues, but for basic issues of how to install, build and run software it might be more productive to see if you can get help locally?

Best,

Hans Ekkehard

--

*Julien BALLBÉ Y SABATÉ*

*Étudiant en thèse - PhD student*

*Neurophysiology of Visual Computation*

Centre Giovanni Borelli - CNRS UMR 9010

Université de Paris

45 rue des Saint-Pères, 75006 Paris, France

Tel: +33 6 79 03 40 35 _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

Hi Robin,

Thank you for your response, I tried as you suggested, I removed the build folder and repeated the CMake, make and make install commands, and I obtained similar results. Here are the full outputs, I highlighted my line commands in yellow to be more readable:

(nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien ~ % cmake -DCMAKE_INSTALL_PREFIX:PATH= /Users/julienballbe /Users/julienballbe/Downloads/nest-simulator-master

-- The CXX compiler identification is AppleClang 13.0.0.13000029

-- The C compiler identification is AppleClang 13.0.0.13000029

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped

-- Detecting C compile features

-- Detecting C compile features - done

-- Found Doxygen: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/doxygen (found version "1.9.1") found components: doxygen dot

-- Looking for include file inttypes.h

-- Looking for include file inttypes.h - found

-- Looking for include file mach-o/dyld.h

-- Looking for include file mach-o/dyld.h - found

-- Looking for include file mach/mach.h

-- Looking for include file mach/mach.h - found

-- Looking for include file memory.h

-- Looking for include file memory.h - found

-- Looking for include file stdint.h

-- Looking for include file stdint.h - found

-- Looking for include file sys/types.h

-- Looking for include file sys/types.h - found

-- Looking for C++ include istream

-- Looking for C++ include istream - found

-- Looking for C++ include ostream

-- Looking for C++ include ostream - found

-- Looking for C++ include sstream

-- Looking for C++ include sstream - found

-- Looking for stddef.h

-- Looking for stddef.h - found

-- Check size of long long

-- Check size of long long - done

-- Check size of u_int16_t

-- Check size of u_int16_t - done

-- Check size of uint16_t

-- Check size of uint16_t - done

-- Check size of u_int64_t

-- Check size of u_int64_t - done

-- Check size of uint64_t

-- Check size of uint64_t - done

-- Looking for NAN

-- Looking for NAN - found

-- Looking for isnan

-- Looking for isnan - found

-- Looking for M_E

-- Looking for M_E - found

-- Looking for M_PI

-- Looking for M_PI - found

-- Looking for expm1

-- Looking for expm1 - found

-- Host triple: arm64-apple-darwin

-- Target triple: arm64-apple-darwin

-- Found Python: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/python3.9 (found suitable version "3.9.7", minimum required is "3.8") found components: Interpreter Development.Module

-- Found Cython: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/cython (found suitable version "0.29.24", minimum required is "0.28.3")

-- Found LTDL: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libltdl.dylib (found version "2.4.6")

-- Found Readline: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libreadline.dylib (found version "4.2")

-- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE)

-- Found GSL: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/include (found version "2.7")

-- Found OpenMP_C: -Xclang -fopenmp (found version "5.0")

-- Found OpenMP_CXX: -Xclang -fopenmp (found version "5.0")

-- Found OpenMP: TRUE (found version "5.0")

-- Found Boost: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/cmake/Boost-1.76.0/BoostConfig.cmake (found suitable version "1.76.0", minimum required is "1.69.0")

-- Check the abort exitcode.

-- Check the abort exitcode. 134

-- Check the segmentation fault exitcode.

-- Check the segmentation fault exitcode. 139

-- Check whether the compiler ignores cmath makros.

-- Check whether the compiler ignores cmath makros. OFF

-- Check whether the compiler does NOT include <*.h> headers ISO conformant.

-- Check whether the compiler does NOT include <*.h> headers ISO conformant. OFF

-- Check whether the compiler respects symbolic signal names in signal.h.

-- Check whether the compiler respects symbolic signal names in signal.h. OFF

-- Check static template member declaration.

-- Check static template member declaration. OFF

-- Check for STL vector capacity base unity.

-- Check for STL vector capacity base unity. ON

-- Check for STL vector capacity doubling strategy.

-- Check for STL vector capacity doubling strategy. ON

-- Check whether the compiler fails with ICE.

-- Check whether the compiler fails with ICE. OFF

-- Check if ::nan is available from cmath.

-- Check if ::nan is available from cmath. ON

-- Check if ::isnan is available from cmath.

-- Check if ::isnan is available from cmath. ON

-- Check if Random123 generators work.

-- Check if Random123 generators work. ON

-- NEST version: UNKNOWN

-- Found PythonInterp: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/python (found version "3.9.7")

--------------------------------------------------------------------------------

NEST Configuration Summary

--------------------------------------------------------------------------------

Build type :

Target System : Darwin

Cross Compiling : FALSE

C compiler : AppleClang 13.0.0.13000029 (/Library/Developer/CommandLineTools/usr/bin/cc)

C compiler flags : -O2 -Wall -Xclang -fopenmp

C++ compiler : AppleClang 13.0.0.13000029 (/Library/Developer/CommandLineTools/usr/bin/c++)

C++ compiler flags : -std=c++11 -O2 -Wall -Xclang -fopenmp

Build dynamic : ON

Built-in modules : models

User modules : None

Python bindings : Yes (Python 3.9.7: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/python3.9)

Includes : /Users/julienballbe/miniforge3/envs/nest-simulator-dev/include/python3.9

Libraries :

Cython bindings : Yes (Cython 0.29.24: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/cython)

MPI4PY header : NO

Use threading : Yes (OpenMP: -Xclang -fopenmp)

Use GSL : Yes (GSL 2.7)

Includes : /Users/julienballbe/miniforge3/envs/nest-simulator-dev/include

Libraries : /Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libgsl.dylib;/Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libgslcblas.dylib

Use Readline : Yes (GNU Readline 4.2)

Includes : /Library/Developer/CommandLineTools/SDKs/MacOSX12.0.sdk/usr/include

Libraries : /Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libreadline.dylib;/Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libncurses.dylib

Use libltdl : Yes (LTDL 2.4.6)

Includes : /Users/julienballbe/miniforge3/envs/nest-simulator-dev/include

Libraries : /Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libltdl.dylib

Use doxygen : Yes (/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/doxygen)

: target `doc` available

`dot` available : Yes (/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/dot)

: target `fulldoc` available

Use MPI : No

Detailed timers : No

Use MUSIC : No

Use libneurosim : No

Use Boost : Yes (Boost 1.76.0)

Includes : /Users/julienballbe/miniforge3/envs/nest-simulator-dev/include

Libraries :

Use SIONlib : No

--------------------------------------------------------------------------------

The NEST executable will be installed to:

/bin/

NEST dynamic libraries and user modules will be installed to:

/lib/nest/

Documentation and examples will be installed to:

/share/doc/nest/

PyNEST will be installed to:

/lib/python3.9/site-packages

To set necessary environment variables, add the following line

to your ~/.bashrc :

source /bin/nest_vars.sh

--------------------------------------------------------------------------------

You can now build and install NEST with

make

make install

make installcheck

If you experience problems with the installation or the use of NEST,

please see https://www.nest-simulator.org/frequently_asked_questions

or go to https://www.nest-simulator.org/community to find out how to

join the user mailing list.

-- Configuring done

-- Generating done

-- Build files have been written to: /Users/julienballbe

(nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien ~ % make

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[ 94%] *Linking CXX shared library libmodels.dylib*

[ 94%] Built target models

[ 94%] Building CXX object sli/CMakeFiles/sli_readline.dir/gnureadline.cc.o

[ 95%] *Linking CXX shared library libsli_readline.dylib*

[ 95%] Built target sli_readline

[ 95%] Building CXX object sli/CMakeFiles/sli.dir/puresli.cc.o

[ 95%] *Linking CXX executable sli*

[ 95%] Built target sli

[ 96%] Building CXX object nest/CMakeFiles/nest_lib.dir/neststartup.cpp.o

[ 96%] *Linking CXX shared library libnest.dylib*

[ 96%] Built target nest_lib

[ 96%] Building CXX object nest/CMakeFiles/nest.dir/main.cpp.o

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[ 97%] *Linking CXX executable nest*

[ 97%] Built target nest

[ 97%] Building CXX object testsuite/cpptests/CMakeFiles/run_all_cpptests.dir/run_all.cpp.o

[ 98%] *Linking CXX executable run_all_cpptests*

[ 98%] Built target run_all_cpptests

[ 99%] *Compiling Cython CXX source for pynestkernel...*

warning: /Users/julienballbe/Downloads/nest-simulator-master/pynest/pynestkernel.pyx:624:4: Unreachable code

warning: /Users/julienballbe/Downloads/nest-simulator-master/pynest/pynestkernel.pyx:624:4: Unreachable code

*Scanning dependencies of target pynestkernel*

[ 99%] Building CXX object pynest/CMakeFiles/pynestkernel.dir/pynestkernel.cxx.o

[100%] *Linking CXX shared module pynestkernel.so*

[100%] Built target pynestkernel

(nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien ~ % make install

*Consolidate compiler generated dependencies of target nestutil*

[ 2%] Built target nestutil

*Consolidate compiler generated dependencies of target sli_lib*

[ 25%] Built target sli_lib

*Consolidate compiler generated dependencies of target nestkernel*

[ 53%] Built target nestkernel

*Consolidate compiler generated dependencies of target models*

[ 94%] Built target models

*Consolidate compiler generated dependencies of target sli_readline*

[ 95%] Built target sli_readline

*Consolidate compiler generated dependencies of target sli*

[ 95%] Built target sli

*Consolidate compiler generated dependencies of target nest_lib*

[ 96%] Built target nest_lib

*Consolidate compiler generated dependencies of target nest*

[ 97%] Built target nest

*Consolidate compiler generated dependencies of target run_all_cpptests*

[ 98%] Built target run_all_cpptests

*Consolidate compiler generated dependencies of target pynestkernel*

[100%] Built target pynestkernel

Install the project...

-- Install configuration: ""

Extracting help information. This may take a little while.

-- Installing: /share/doc/nest/help

CMake Error at doc/cmake_install.cmake:56 (file):

file INSTALL cannot make directory "/share/doc/nest/help": No such file or

directory.

Call Stack (most recent call first):

cmake_install.cmake:42 (include)

make: *** [install] Error 1

Do you have any ideas?

Best feelings, Julien BALLBÉ

Le mar. 16 nov. 2021 à 17:23, Robin Gilbert De Schepper < robingilbert.deschepper@unipv.it> a écrit :

Hi,

It's best not to use sudo for the CMake and make commands! Remove the build folder and try the CMake and make commands again. Please attach the full outputs of both commands to give us a clearer picture of what is going on :)

On Tue, 16 Nov 2021, 17:03 Julien Ballbé, julien.ballbe@gmail.com wrote:

...

Dear Hans,

Thank you for your answer and your various pieces of advice! I understand these problems are quite basic, but I still have a problem when doing all the steps you suggested earlier. Everything went correctly until I ran ake and make install (see the whole terminal script attached) where I got the following error message:

(nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien NEST % sudo make install

Password:

[ 2%] Built target nestutil

[ 25%] Built target sli_lib

[ 53%] Built target nestkernel

[ 94%] Built target models

[ 95%] Built target sli_readline

[ 95%] Built target sli

[ 96%] Built target nest_lib

[ 97%] Built target nest

[ 98%] Built target run_all_cpptests

[100%] Built target pynestkernel

Install the project...

-- Install configuration: ""

Extracting help information. This may take a little while.

-- Installing: /share/doc/nest/help

CMake Error at doc/cmake_install.cmake:56 (file):

file INSTALL cannot make directory "/share/doc/nest/help": No such file or

directory.

Call Stack (most recent call first):

cmake_install.cmake:42 (include)

make: *** [install] Error 1

---

Can you help me with this issue please? I have been looking for this file but I couldn't find it either. Am I supposed to create it myself?

Thank you for all the help you can give me,

Best feelings,

Julien BALLBÉ

Le mar. 16 nov. 2021 à 08:10, Hans Ekkehard Plesser < hans.ekkehard.plesser@nmbu.no> a écrit :

...

Dear Julien,

As a starting doctoral student in the field of computational neurosciences, I am particularly interested in using NEST in my research works. However, I am a bit confused about the procedure to install NEST on a M1 macbook pro, therefore, I prefer to ask you before doing anything. From what I understood from your website here are the steps that, I suppose, I should do to install NEST properly:

• as I use a M1MAX Mac (MacOS 12.0) , I can't just install nest, I have

to build it. To do so:

• Download Miniforge for arm64 (from which I will be able to use Conda

right?)

Yes.

• NOT NECESSARY: Install Python 3.9.4 for arm Mac macOS 64-bit

universal2 installer https://www.python.org/ftp/python/3.9.8/python-3.9.8-macos11.pkg

• Download the nest source code directly from github (

https://github.com/nest/nest-simulator)

Yes. Use the most recent released tarball/zip archive of NEST.

• Create a conda environment using the following command conda env

create -f extras/conda-nest-simulator-dev.yml

Yes. IMPORTANT: Since you are using Apple Silicon, you must open the conda-nest-simulator-dev.yml file and remove the following lines:

# Running NEST Server ----

• flask

• flask_cors

• requests

• uwsgi

• werkzeug

This is because some packages (uwsgi) is not available for M1 yet (last checked two weeks ago).

• Activate this environment ( conda activate...)

• Create a build directory outside the NEST source and go into it

• Install cmake package using conda ( conda install -c anaconda cmake)

• Configure NEST by running: cmake -DCMAKE_INSTALL_PREFIX:PATH=<nest_install_dir>

<nest_source_dir>

• Once done I can run make. make install. make installcheck

Yes to the five above.

Here are my questions:

• Is this installation procedure correct?

• Once installed, how can I launch NEST from a python interpreter such

as Spyder? Or is it only possible to launch it within a terminal window?

You need to make sure that the path to the NEST installation is in your PYTHONPATH. In the Terminal, that is handled by sourcing `nest_vars.sh`. I am off-hand not entirely certain how to make it work in Spyder.

• I am quite new to managing packages, so correct me if I am wrong, but

have I to install everything using exclusively Conda ?

Installing all via Conda makes things a lot easier.

• What is the purpose of creating a new environment to build NEST

Very briefly, to have all in place you need without cluttering your overall Python setup. There are many more answers to that out on the net, see eg

https://www.freecodecamp.org/news/why-you-need-python-environments-and-how-t...

I realize how many questions I ask you, and I am very grateful for every advice you could give me.

If it is more convenient for you, we can have a phone call when you want.

We can help with NEST-specific issues, but for basic issues of how to install, build and run software it might be more productive to see if you can get help locally?

Best,

Hans Ekkehard

--

*Julien BALLBÉ Y SABATÉ*

*Étudiant en thèse - PhD student*

*Neurophysiology of Visual Computation*

Centre Giovanni Borelli - CNRS UMR 9010

Université de Paris

45 rue des Saint-Pères, 75006 Paris, France

Tel: +33 6 79 03 40 35 _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

--

*Julien BALLBÉ Y SABATÉ*

*Étudiant en thèse - PhD student*

*Neurophysiology of Visual Computation*

Centre Giovanni Borelli - CNRS UMR 9010

Université de Paris

45 rue des Saint-Pères, 75006 Paris, France

Tel: +33 6 79 03 40 35 _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

---

NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

Using just `cmake path/to/src` should give you the default installation to the active Python env

On Wed, 17 Nov 2021, 09:56 Hans Ekkehard Plesser, < hans.ekkehard.plesser@nmbu.no> wrote:

Hi Julien,

The problem is the empty install path. Make tries to install to

"/share/doc/nest/help": No such file or

directory.

at the root of the file hierarchy, which cannot (and should not) work. This is also shown in the configuration report provided by cmake:

The NEST executable will be installed to:

/bin/

NEST dynamic libraries and user modules will be installed to:

/lib/nest/

Documentation and examples will be installed to:

/share/doc/nest/

PyNEST will be installed to:

/lib/python3.9/site-packages

To set necessary environment variables, add the following line

to your ~/.bashrc :

source /bin/nest_vars.sh

You need to specify a directory for installation behind the ...:PATH= in the following line

(nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien ~ % cmake -DCMAKE_INSTALL_PREFIX:PATH= /Users/julienballbe /Users/julienballbe/Downloads/nest-simulator-master

I seems that you intended to install to your home directory, but that a stray space after ...PATH= misled cmake. It should be ...PATH=/Users/julienballbe.

Best,

Hans Ekkehard

--

Prof. Dr. Hans Ekkehard Plesser

Head, Department of Data Science

Faculty of Science and Technology

Norwegian University of Life Sciences

PO Box 5003, 1432 Aas, Norway

Phone +47 6723 1560

Email hans.ekkehard.plesser@nmbu.no

Home http://arken.nmbu.no/~plesser

On 17/11/2021, 09:41, "Julien Ballbé" julien.ballbe@gmail.com wrote:

Hi Robin,

Thank you for your response, I tried as you suggested, I removed the build folder and repeated the CMake, make and make install commands, and I obtained similar results. Here are the full outputs, I highlighted my line commands in yellow to be more readable:

(nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien ~ % cmake -DCMAKE_INSTALL_PREFIX:PATH= /Users/julienballbe /Users/julienballbe/Downloads/nest-simulator-master

-- The CXX compiler identification is AppleClang 13.0.0.13000029

-- The C compiler identification is AppleClang 13.0.0.13000029

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped

-- Detecting C compile features

-- Detecting C compile features - done

-- Found Doxygen: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/doxygen (found version "1.9.1") found components: doxygen dot

-- Looking for include file inttypes.h

-- Looking for include file inttypes.h - found

-- Looking for include file mach-o/dyld.h

-- Looking for include file mach-o/dyld.h - found

-- Looking for include file mach/mach.h

-- Looking for include file mach/mach.h - found

-- Looking for include file memory.h

-- Looking for include file memory.h - found

-- Looking for include file stdint.h

-- Looking for include file stdint.h - found

-- Looking for include file sys/types.h

-- Looking for include file sys/types.h - found

-- Looking for C++ include istream

-- Looking for C++ include istream - found

-- Looking for C++ include ostream

-- Looking for C++ include ostream - found

-- Looking for C++ include sstream

-- Looking for C++ include sstream - found

-- Looking for stddef.h

-- Looking for stddef.h - found

-- Check size of long long

-- Check size of long long - done

-- Check size of u_int16_t

-- Check size of u_int16_t - done

-- Check size of uint16_t

-- Check size of uint16_t - done

-- Check size of u_int64_t

-- Check size of u_int64_t - done

-- Check size of uint64_t

-- Check size of uint64_t - done

-- Looking for NAN

-- Looking for NAN - found

-- Looking for isnan

-- Looking for isnan - found

-- Looking for M_E

-- Looking for M_E - found

-- Looking for M_PI

-- Looking for M_PI - found

-- Looking for expm1

-- Looking for expm1 - found

-- Host triple: arm64-apple-darwin

-- Target triple: arm64-apple-darwin

-- Found Python: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/python3.9 (found suitable version "3.9.7", minimum required is "3.8") found components: Interpreter Development.Module

-- Found Cython: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/cython (found suitable version "0.29.24", minimum required is "0.28.3")

-- Found LTDL: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libltdl.dylib (found version "2.4.6")

-- Found Readline: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libreadline.dylib (found version "4.2")

-- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE)

-- Found GSL: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/include (found version "2.7")

-- Found OpenMP_C: -Xclang -fopenmp (found version "5.0")

-- Found OpenMP_CXX: -Xclang -fopenmp (found version "5.0")

-- Found OpenMP: TRUE (found version "5.0")

-- Found Boost: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/cmake/Boost-1.76.0/BoostConfig.cmake (found suitable version "1.76.0", minimum required is "1.69.0")

-- Check the abort exitcode.

-- Check the abort exitcode. 134

-- Check the segmentation fault exitcode.

-- Check the segmentation fault exitcode. 139

-- Check whether the compiler ignores cmath makros.

-- Check whether the compiler ignores cmath makros. OFF

-- Check whether the compiler does NOT include <*.h> headers ISO conformant.

-- Check whether the compiler does NOT include <*.h> headers ISO conformant. OFF

-- Check whether the compiler respects symbolic signal names in signal.h.

-- Check whether the compiler respects symbolic signal names in signal.h. OFF

-- Check static template member declaration.

-- Check static template member declaration. OFF

-- Check for STL vector capacity base unity.

-- Check for STL vector capacity base unity. ON

-- Check for STL vector capacity doubling strategy.

-- Check for STL vector capacity doubling strategy. ON

-- Check whether the compiler fails with ICE.

-- Check whether the compiler fails with ICE. OFF

-- Check if ::nan is available from cmath.

-- Check if ::nan is available from cmath. ON

-- Check if ::isnan is available from cmath.

-- Check if ::isnan is available from cmath. ON

-- Check if Random123 generators work.

-- Check if Random123 generators work. ON

-- NEST version: UNKNOWN

-- Found PythonInterp: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/python (found version "3.9.7")

---

NEST Configuration Summary

---

Build type :

Target System : Darwin

Cross Compiling : FALSE

C compiler : AppleClang 13.0.0.13000029 (/Library/Developer/CommandLineTools/usr/bin/cc)

C compiler flags : -O2 -Wall -Xclang -fopenmp

C++ compiler : AppleClang 13.0.0.13000029 (/Library/Developer/CommandLineTools/usr/bin/c++)

C++ compiler flags : -std=c++11 -O2 -Wall -Xclang -fopenmp

Build dynamic : ON

Built-in modules : models

User modules : None

Python bindings : Yes (Python 3.9.7: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/python3.9)

   Includes     :

/Users/julienballbe/miniforge3/envs/nest-simulator-dev/include/python3.9

   Libraries    :

Cython bindings : Yes (Cython 0.29.24: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/cython)

MPI4PY header : NO

Use threading : Yes (OpenMP: -Xclang -fopenmp)

Use GSL : Yes (GSL 2.7)

Includes        :

/Users/julienballbe/miniforge3/envs/nest-simulator-dev/include

Libraries       :

/Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libgsl.dylib;/Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libgslcblas.dylib

Use Readline : Yes (GNU Readline 4.2)

Includes        :

/Library/Developer/CommandLineTools/SDKs/MacOSX12.0.sdk/usr/include

Libraries       :

/Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libreadline.dylib;/Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libncurses.dylib

Use libltdl : Yes (LTDL 2.4.6)

Includes        :

/Users/julienballbe/miniforge3/envs/nest-simulator-dev/include

Libraries       :

/Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libltdl.dylib

Use doxygen : Yes (/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/doxygen)

                : target `doc` available

`dot` available : Yes

(/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/dot)

                : target `fulldoc` available

Use MPI : No

Detailed timers : No

Use MUSIC : No

Use libneurosim : No

Use Boost : Yes (Boost 1.76.0)

Includes        :

/Users/julienballbe/miniforge3/envs/nest-simulator-dev/include

Libraries       :

Use SIONlib : No

---

The NEST executable will be installed to:

/bin/

NEST dynamic libraries and user modules will be installed to:

/lib/nest/

Documentation and examples will be installed to:

/share/doc/nest/

PyNEST will be installed to:

/lib/python3.9/site-packages

To set necessary environment variables, add the following line

to your ~/.bashrc :

source /bin/nest_vars.sh

---

You can now build and install NEST with

make

make install

make installcheck

If you experience problems with the installation or the use of NEST,

please see https://www.nest-simulator.org/frequently_asked_questions

or go to https://www.nest-simulator.org/community to find out how to

join the user mailing list.

-- Configuring done

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Hi,

It depends on where you want NEST installed. Personally, I prefer to place NEST in a directory of its own, but that is mainly because as a developer I usually have a number of NEST builds around. Thus, I would use something like

cmake -DCMAKE_INSTALL_PREFIX:PATH=/Users/julienballbe/NEST /Users/julienballbe/Downloads/nest-simulator-master

On the other hand, you can also choose to install NEST right with your other Python packages using just

cmake /Users/julienballbe/Downloads/nest-simulator-master

Then, NEST will be installed in the site-packages part of your nest-simulator-dev conda environment. This makes it even easier for Python to find the nest Python module.

Best, Hans Ekkehard

--

Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science

Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway

Phone +47 6723 1560 Email hans.ekkehard.plesser@nmbu.nomailto:hans.ekkehard.plesser@nmbu.no Home http://arken.nmbu.no/~plesser

On 17/11/2021, 11:09, "Julien Ballbé" <julien.ballbe@gmail.commailto:julien.ballbe@gmail.com> wrote:

Hi,

Thank you for all your responses. I attached the full log file. I found the CMAKE_INSTALL_PREFIX instruction on the nest installation guidelines (https://nest-simulator.readthedocs.io/en/v3.1/installation/mac_install.html) in the building NEST section. Indeed, I did not see the space in the command line. That should fix it, but before I do anything, would you recommend that : 1) I create a build directory NEST and run (nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien ~ % cmake -DCMAKE_INSTALL_PREFIX:PATH=/Users/julienballbe/NEST /Users/julienballbe/Downloads/nest-simulator-master

or

2) use as Robin suggested 'cmake path/to/src', in which case the command line will be, I supposed, cmake path/to/src /Users/julienballbe/Downloads/nest-simulator-master ?

Thank you for your help! Best,

Julien

Le mer. 17 nov. 2021 à 10:04, Robin Gilbert De Schepper <robingilbert.deschepper@unipv.itmailto:robingilbert.deschepper@unipv.it> a écrit :

Here, something goes wrong with library paths, so that NEST apparently looks for the wrong versions of GSL and readline. I won't have time to attend more to this today. The only remaining suggestion is to try the "other" way, i.e., explicitly specifying a installation directory. Also, it looks like you might be building and running from your home directory. I'd suggest to build in a separate directory. Delete everything in that build directory before making new attempts to be sure no old information is left in CMake caches.

Best, Hans Ekkehard

--

Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science

Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway

Phone +47 6723 1560 Email hans.ekkehard.plesser@nmbu.nomailto:hans.ekkehard.plesser@nmbu.no Home http://arken.nmbu.no/~plesser

On 17/11/2021, 12:12, "Julien Ballbé" <julien.ballbe@gmail.commailto:julien.ballbe@gmail.com> wrote:

Hi,

I did as you suggested and ran cmake /Users/julienballbe/Downloads/nest-simulator-master

It went well for the cmake, make and make install commands but when I ran the make installcheck I got the following message (I attach the full log output):

(nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien ~ % make installcheck

Executing NEST's testsuite...

dyld[12978]: Library not loaded: @rpath/libgsl.25.dylib

Referenced from: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/sli

Reason: tried: '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../lib/nest/libgsl.25.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../lib/nest/libgsl.25.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../../nest/libgsl.25.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../lib/nest/libgsl.25.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../lib/nest/libgsl.25.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../../nest/libgsl.25.dylib' (no such file), '/usr/local/lib/libgsl.25.dylib' (no such file), '/usr/lib/libgsl.25.dylib' (no such file)

2021-11-17 11:34:30.712 defaults[12980:953560]

The domain/default pair of (com.apple.CrashReporter, DialogType) does not exist

================================================================================

NEST testsuite

Date: Mer 17 nov 2021 10:34:30 UTC

Sysinfo: Darwin 21.0.1 arm64

dyld[12984]: Library not loaded: @rpath/libgsl.25.dylib

Referenced from: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/sli

Reason: tried: '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../lib/nest/libgsl.25.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../lib/nest/libgsl.25.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../../nest/libgsl.25.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../lib/nest/libgsl.25.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../lib/nest/libgsl.25.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../../nest/libgsl.25.dylib' (no such file), '/usr/local/lib/libgsl.25.dylib' (no such file), '/usr/lib/libgsl.25.dylib' (no such file)

NEST executable .... nest_serial (version )

PREFIX ............. /Users/julienballbe/miniforge3/envs/nest-simulator-dev

Python executable .. /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/python3.9 (version 3.9.7)

PYTHONPATH ......... /Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/python3.9/site-packages

Pytest version ..... 6.2.5

timeout ..... 120 s

Running MPI tests .. no (compiled without MPI support)

TEST_BASEDIR ....... /Users/julienballbe/miniforge3/envs/nest-simulator-dev/share/nest/testsuite

REPORTDIR .......... /Users/julienballbe/reports

PATH ............... /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin

/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin

/Users/julienballbe/miniforge3/condabin

/usr/local/bin

/usr/bin

/bin

/usr/sbin

/sbin

================================================================================

dyld[12998]: Library not loaded: @rpath/libreadline.8.dylib

Referenced from: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/nest

Reason: tried: '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../lib/nest/libreadline.8.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../lib/nest/libreadline.8.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../../nest/libreadline.8.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../lib/nest/libreadline.8.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../lib/nest/libreadline.8.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../../nest/libreadline.8.dylib' (no such file), '/usr/local/lib/libreadline.8.dylib' (no such file), '/usr/lib/libreadline.8.dylib' (no such file)

Phase 1: Testing if SLI can execute scripts and report errors

-------------------------------------------------------------

Running test 'selftests/test_pass.sli'... Failed: unexpected exit code 134

==================================================

Following is the full output of the test:

==================================================

dyld[13021]: Library not loaded: @rpath/libgsl.25.dylib

Referenced from: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/sli

Reason: tried: '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../lib/nest/libgsl.25.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../lib/nest/libgsl.25.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../../nest/libgsl.25.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../lib/nest/libgsl.25.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../lib/nest/libgsl.25.dylib' (no such file), '/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../../nest/libgsl.25.dylib' (no such file), '/usr/local/lib/libgsl.25.dylib' (no such file), '/usr/lib/libgsl.25.dylib' (no such file)

==================================================

***

*** An unexpected exit code usually hints at a bug in the test suite!

/Users/julienballbe/miniforge3/envs/nest-simulator-dev/share/nest/testsuite/run_test.sh: line 169: ask_results: command not found

make[3]: *** [CMakeFiles/installcheck] Error 2

make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2

make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2

Is that normal? Thank you for your help,

Best,

Julien

Le mer. 17 nov. 2021 à 11:16, Hans Ekkehard Plesser <hans.ekkehard.plesser@nmbu.nomailto:hans.ekkehard.plesser@nmbu.no> a écrit :

Hi,

It depends on where you want NEST installed. Personally, I prefer to place NEST in a directory of its own, but that is mainly because as a developer I usually have a number of NEST builds around. Thus, I would use something like

cmake -DCMAKE_INSTALL_PREFIX:PATH=/Users/julienballbe/NEST /Users/julienballbe/Downloads/nest-simulator-master

On the other hand, you can also choose to install NEST right with your other Python packages using just

cmake /Users/julienballbe/Downloads/nest-simulator-master

Then, NEST will be installed in the site-packages part of your nest-simulator-dev conda environment. This makes it even easier for Python to find the nest Python module.

Best, Hans Ekkehard

--

Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science

Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway

Phone +47 6723 1560 Email hans.ekkehard.plesser@nmbu.nomailto:hans.ekkehard.plesser@nmbu.no Home http://arken.nmbu.no/~plesser

On 17/11/2021, 11:09, "Julien Ballbé" <julien.ballbe@gmail.commailto:julien.ballbe@gmail.com> wrote:

Hi,

Thank you for all your responses. I attached the full log file. I found the CMAKE_INSTALL_PREFIX instruction on the nest installation guidelines (https://nest-simulator.readthedocs.io/en/v3.1/installation/mac_install.html) in the building NEST section. Indeed, I did not see the space in the command line. That should fix it, but before I do anything, would you recommend that : 1) I create a build directory NEST and run (nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien ~ % cmake -DCMAKE_INSTALL_PREFIX:PATH=/Users/julienballbe/NEST /Users/julienballbe/Downloads/nest-simulator-master

or

2) use as Robin suggested 'cmake path/to/src', in which case the command line will be, I supposed, cmake path/to/src /Users/julienballbe/Downloads/nest-simulator-master ?

Thank you for your help! Best,

Julien

Le mer. 17 nov. 2021 à 10:04, Robin Gilbert De Schepper <robingilbert.deschepper@unipv.itmailto:robingilbert.deschepper@unipv.it> a écrit :

_______________________________________________ NEST Users mailing list -- users@nest-simulator.orgmailto:users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.orgmailto:users-leave@nest-simulator.org

Hi!

Just as a quick add-on information:

The problem of being able to specify an empty installation prefix is addressed by #2166https://github.com/nest/nest-simulator/pull/2166.

Cheers, Jochen!

On 17.11.21 09:53, Hans Ekkehard Plesser wrote:

Hi Julien,

The problem is the empty install path. Make tries to install to

"/share/doc/nest/help": No such file or directory.

at the root of the file hierarchy, which cannot (and should not) work. This is also shown in the configuration report provided by cmake:

The NEST executable will be installed to: /bin/

NEST dynamic libraries and user modules will be installed to: /lib/nest/

Documentation and examples will be installed to: /share/doc/nest/

PyNEST will be installed to: /lib/python3.9/site-packages

To set necessary environment variables, add the following line to your ~/.bashrc : source /bin/nest_vars.sh

You need to specify a directory for installation behind the ...:PATH= in the following line

(nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien ~ % cmake -DCMAKE_INSTALL_PREFIX:PATH= /Users/julienballbe /Users/julienballbe/Downloads/nest-simulator-master

I seems that you intended to install to your home directory, but that a stray space after ...PATH= misled cmake. It should be ...PATH=/Users/julienballbe.

Best, Hans Ekkehard

--

Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science

Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway

Phone +47 6723 1560 Email hans.ekkehard.plesser@nmbu.nomailto:hans.ekkehard.plesser@nmbu.no Home http://arken.nmbu.no/~plesser

On 17/11/2021, 09:41, "Julien Ballbé" <julien.ballbe@gmail.commailto:julien.ballbe@gmail.com> wrote:

Hi Robin,

Thank you for your response, I tried as you suggested, I removed the build folder and repeated the CMake, make and make install commands, and I obtained similar results. Here are the full outputs, I highlighted my line commands in yellow to be more readable:

(nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien ~ % cmake -DCMAKE_INSTALL_PREFIX:PATH= /Users/julienballbe /Users/julienballbe/Downloads/nest-simulator-master

-- The CXX compiler identification is AppleClang 13.0.0.13000029

-- The C compiler identification is AppleClang 13.0.0.13000029

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped

-- Detecting C compile features

-- Detecting C compile features - done

-- Found Doxygen: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/doxygen (found version "1.9.1") found components: doxygen dot

-- Looking for include file inttypes.h

-- Looking for include file inttypes.h - found

-- Looking for include file mach-o/dyld.h

-- Looking for include file mach-o/dyld.h - found

-- Looking for include file mach/mach.h

-- Looking for include file mach/mach.h - found

-- Looking for include file memory.h

-- Looking for include file memory.h - found

-- Looking for include file stdint.h

-- Looking for include file stdint.h - found

-- Looking for include file sys/types.h

-- Looking for include file sys/types.h - found

-- Looking for C++ include istream

-- Looking for C++ include istream - found

-- Looking for C++ include ostream

-- Looking for C++ include ostream - found

-- Looking for C++ include sstream

-- Looking for C++ include sstream - found

-- Looking for stddef.h

-- Looking for stddef.h - found

-- Check size of long long

-- Check size of long long - done

-- Check size of u_int16_t

-- Check size of u_int16_t - done

-- Check size of uint16_t

-- Check size of uint16_t - done

-- Check size of u_int64_t

-- Check size of u_int64_t - done

-- Check size of uint64_t

-- Check size of uint64_t - done

-- Looking for NAN

-- Looking for NAN - found

-- Looking for isnan

-- Looking for isnan - found

-- Looking for M_E

-- Looking for M_E - found

-- Looking for M_PI

-- Looking for M_PI - found

-- Looking for expm1

-- Looking for expm1 - found

-- Host triple: arm64-apple-darwin

-- Target triple: arm64-apple-darwin

-- Found Python: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/python3.9 (found suitable version "3.9.7", minimum required is "3.8") found components: Interpreter Development.Module

-- Found Cython: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/cython (found suitable version "0.29.24", minimum required is "0.28.3")

-- Found LTDL: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libltdl.dylib (found version "2.4.6")

-- Found Readline: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libreadline.dylib (found version "4.2")

-- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE)

-- Found GSL: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/include (found version "2.7")

-- Found OpenMP_C: -Xclang -fopenmp (found version "5.0")

-- Found OpenMP_CXX: -Xclang -fopenmp (found version "5.0")

-- Found OpenMP: TRUE (found version "5.0")

-- Found Boost: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/cmake/Boost-1.76.0/BoostConfig.cmake (found suitable version "1.76.0", minimum required is "1.69.0")

-- Check the abort exitcode.

-- Check the abort exitcode. 134

-- Check the segmentation fault exitcode.

-- Check the segmentation fault exitcode. 139

-- Check whether the compiler ignores cmath makros.

-- Check whether the compiler ignores cmath makros. OFF

-- Check whether the compiler does NOT include <*.h> headers ISO conformant.

-- Check whether the compiler does NOT include <*.h> headers ISO conformant. OFF

-- Check whether the compiler respects symbolic signal names in signal.h.

-- Check whether the compiler respects symbolic signal names in signal.h. OFF

-- Check static template member declaration.

-- Check static template member declaration. OFF

-- Check for STL vector capacity base unity.

-- Check for STL vector capacity base unity. ON

-- Check for STL vector capacity doubling strategy.

-- Check for STL vector capacity doubling strategy. ON

-- Check whether the compiler fails with ICE.

-- Check whether the compiler fails with ICE. OFF

-- Check if ::nan is available from cmath.

-- Check if ::nan is available from cmath. ON

-- Check if ::isnan is available from cmath.

-- Check if ::isnan is available from cmath. ON

-- Check if Random123 generators work.

-- Check if Random123 generators work. ON

-- NEST version: UNKNOWN

-- Found PythonInterp: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/python (found version "3.9.7")

--------------------------------------------------------------------------------

NEST Configuration Summary

--------------------------------------------------------------------------------

Build type :

Target System : Darwin

Cross Compiling : FALSE

C compiler : AppleClang 13.0.0.13000029 (/Library/Developer/CommandLineTools/usr/bin/cc)

C compiler flags : -O2 -Wall -Xclang -fopenmp

C++ compiler : AppleClang 13.0.0.13000029 (/Library/Developer/CommandLineTools/usr/bin/c++)

C++ compiler flags : -std=c++11 -O2 -Wall -Xclang -fopenmp

Build dynamic : ON

Built-in modules : models

User modules : None

Python bindings : Yes (Python 3.9.7: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/python3.9)

Includes : /Users/julienballbe/miniforge3/envs/nest-simulator-dev/include/python3.9

Libraries :

Cython bindings : Yes (Cython 0.29.24: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/cython)

MPI4PY header : NO

Use threading : Yes (OpenMP: -Xclang -fopenmp)

Use GSL : Yes (GSL 2.7)

Includes : /Users/julienballbe/miniforge3/envs/nest-simulator-dev/include

Libraries : /Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libgsl.dylib;/Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libgslcblas.dylib

Use Readline : Yes (GNU Readline 4.2)

Includes : /Library/Developer/CommandLineTools/SDKs/MacOSX12.0.sdk/usr/include

Libraries : /Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libreadline.dylib;/Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libncurses.dylib

Use libltdl : Yes (LTDL 2.4.6)

Includes : /Users/julienballbe/miniforge3/envs/nest-simulator-dev/include

Libraries : /Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/libltdl.dylib

Use doxygen : Yes (/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/doxygen)

: target `doc` available

`dot` available : Yes (/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/dot)

: target `fulldoc` available

Use MPI : No

Detailed timers : No

Use MUSIC : No

Use libneurosim : No

Use Boost : Yes (Boost 1.76.0)

Includes : /Users/julienballbe/miniforge3/envs/nest-simulator-dev/include

Libraries :

Use SIONlib : No

--------------------------------------------------------------------------------

The NEST executable will be installed to:

/bin/

NEST dynamic libraries and user modules will be installed to:

/lib/nest/

Documentation and examples will be installed to:

/share/doc/nest/

PyNEST will be installed to:

/lib/python3.9/site-packages

To set necessary environment variables, add the following line

to your ~/.bashrc :

source /bin/nest_vars.sh

--------------------------------------------------------------------------------

You can now build and install NEST with

make

make install

make installcheck

If you experience problems with the installation or the use of NEST,

please see https://www.nest-simulator.org/frequently_asked_questions

or go to https://www.nest-simulator.org/community to find out how to

join the user mailing list.

-- Configuring done

-- Generating done

-- Build files have been written to: /Users/julienballbe

(nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien ~ % make

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[ 99%] Compiling Cython CXX source for pynestkernel...

warning: /Users/julienballbe/Downloads/nest-simulator-master/pynest/pynestkernel.pyx:624:4: Unreachable code

warning: /Users/julienballbe/Downloads/nest-simulator-master/pynest/pynestkernel.pyx:624:4: Unreachable code

Scanning dependencies of target pynestkernel

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(nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien ~ % make install

Consolidate compiler generated dependencies of target nestutil

[ 2%] Built target nestutil

Consolidate compiler generated dependencies of target sli_lib

[ 25%] Built target sli_lib

Consolidate compiler generated dependencies of target nestkernel

[ 53%] Built target nestkernel

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Consolidate compiler generated dependencies of target nest

[ 97%] Built target nest

Consolidate compiler generated dependencies of target run_all_cpptests

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Consolidate compiler generated dependencies of target pynestkernel

[100%] Built target pynestkernel

Install the project...

-- Install configuration: ""

Extracting help information. This may take a little while.

-- Installing: /share/doc/nest/help

CMake Error at doc/cmake_install.cmake:56 (file):

file INSTALL cannot make directory "/share/doc/nest/help": No such file or

directory.

Call Stack (most recent call first):

cmake_install.cmake:42 (include)

make: *** [install] Error 1

Do you have any ideas?

Best feelings, Julien BALLBÉ

Le mar. 16 nov. 2021 à 17:23, Robin Gilbert De Schepper <robingilbert.deschepper@unipv.itmailto:robingilbert.deschepper@unipv.it> a écrit : Hi,

It's best not to use sudo for the CMake and make commands! Remove the build folder and try the CMake and make commands again. Please attach the full outputs of both commands to give us a clearer picture of what is going on :)

On Tue, 16 Nov 2021, 17:03 Julien Ballbé, <julien.ballbe@gmail.commailto:julien.ballbe@gmail.com> wrote: Dear Hans,

Thank you for your answer and your various pieces of advice! I understand these problems are quite basic, but I still have a problem when doing all the steps you suggested earlier. Everything went correctly until I ran ake and make install (see the whole terminal script attached) where I got the following error message:

(nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien NEST % sudo make install

Password:

[ 2%] Built target nestutil

[ 25%] Built target sli_lib

[ 53%] Built target nestkernel

[ 94%] Built target models

[ 95%] Built target sli_readline

[ 95%] Built target sli

[ 96%] Built target nest_lib

[ 97%] Built target nest

[ 98%] Built target run_all_cpptests

[100%] Built target pynestkernel

Install the project...

-- Install configuration: ""

Extracting help information. This may take a little while.

-- Installing: /share/doc/nest/help

CMake Error at doc/cmake_install.cmake:56 (file):

file INSTALL cannot make directory "/share/doc/nest/help": No such file or

directory.

Call Stack (most recent call first):

cmake_install.cmake:42 (include)

make: *** [install] Error 1

----------

Can you help me with this issue please? I have been looking for this file but I couldn't find it either. Am I supposed to create it myself?

Thank you for all the help you can give me,

Best feelings,

Julien BALLBÉ

Le mar. 16 nov. 2021 à 08:10, Hans Ekkehard Plesser <hans.ekkehard.plesser@nmbu.nomailto:hans.ekkehard.plesser@nmbu.no> a écrit :

Dear Julien,

As a starting doctoral student in the field of computational neurosciences, I am particularly interested in using NEST in my research works. However, I am a bit confused about the procedure to install NEST on a M1 macbook pro, therefore, I prefer to ask you before doing anything. From what I understood from your website here are the steps that, I suppose, I should do to install NEST properly: - as I use a M1MAX Mac (MacOS 12.0) , I can't just install nest, I have to build it. To do so:

- Download Miniforge for arm64 (from which I will be able to use Conda right?)

Yes.

- NOT NECESSARY: Install Python 3.9.4 for arm Mac macOS 64-bit universal2 installerhttps://www.python.org/ftp/python/3.9.8/python-3.9.8-macos11.pkg

- Download the nest source code directly from github (https://github.com/nest/nest-simulator)

Yes. Use the most recent released tarball/zip archive of NEST.

- Create a conda environment using the following command conda env create -f extras/conda-nest-simulator-dev.yml

Yes. IMPORTANT: Since you are using Apple Silicon, you must open the conda-nest-simulator-dev.yml file and remove the following lines:

# Running NEST Server ---- - flask - flask_cors - requests - uwsgi - werkzeug

This is because some packages (uwsgi) is not available for M1 yet (last checked two weeks ago).

- Activate this environment ( conda activate...) - Create a build directory outside the NEST source and go into it - Install cmake package using conda ( conda install -c anaconda cmake) - Configure NEST by running: cmake -DCMAKE_INSTALL_PREFIX:PATH=<nest_install_dir> <nest_source_dir> - Once done I can run make. make install. make installcheck

Yes to the five above.

Here are my questions: - Is this installation procedure correct? - Once installed, how can I launch NEST from a python interpreter such as Spyder? Or is it only possible to launch it within a terminal window?

You need to make sure that the path to the NEST installation is in your PYTHONPATH. In the Terminal, that is handled by sourcing `nest_vars.sh`. I am off-hand not entirely certain how to make it work in Spyder.

- I am quite new to managing packages, so correct me if I am wrong, but have I to install everything using exclusively Conda ?

Installing all via Conda makes things a lot easier.

- What is the purpose of creating a new environment to build NEST

Very briefly, to have all in place you need without cluttering your overall Python setup. There are many more answers to that out on the net, see eg

https://www.freecodecamp.org/news/why-you-need-python-environments-and-how-t...

I realize how many questions I ask you, and I am very grateful for every advice you could give me. If it is more convenient for you, we can have a phone call when you want.

We can help with NEST-specific issues, but for basic issues of how to install, build and run software it might be more productive to see if you can get help locally?

Best, Hans Ekkehard

-- Julien BALLBÉ Y SABATÉ Étudiant en thèse - PhD student Neurophysiology of Visual Computation Centre Giovanni Borelli - CNRS UMR 9010 Université de Paris 45 rue des Saint-Pères, 75006 Paris, France Tel: +33 6 79 03 40 35 _______________________________________________ NEST Users mailing list -- users@nest-simulator.orgmailto:users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.orgmailto:users-leave@nest-simulator.org

-- Julien BALLBÉ Y SABATÉ Étudiant en thèse - PhD student Neurophysiology of Visual Computation Centre Giovanni Borelli - CNRS UMR 9010 Université de Paris 45 rue des Saint-Pères, 75006 Paris, France Tel: +33 6 79 03 40 35 _______________________________________________ NEST Users mailing list -- users@nest-simulator.orgmailto:users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.orgmailto:users-leave@nest-simulator.org _______________________________________________ NEST Users mailing list -- users@nest-simulator.orgmailto:users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.orgmailto:users-leave@nest-simulator.org

_______________________________________________ NEST Users mailing list -- users@nest-simulator.orgmailto:users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.orgmailto:users-leave@nest-simulator.org

​

-- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653 ---------------------------------- Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation

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