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

-- 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 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

- 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-to-manage-them-with-conda-85f155f4353c/

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