Hi,
I've been trying to compile the latest version on github (c1cebdc) without success.
The system is a HPC running RHEL7. Pre-installed software includes gsl-2.7, cmake 3.17.5 and openMPI-1.10.3-gnu, although I have tried variations with similar results.
I've created a fresh conda environment with packages necessary for nest and nestml: conda create --name pythonfornestml -c conda-forge boost readline ipython pyqt wxpython cython pip install mpi4py
cmake -DCMAKE_INSTALL_PREFIX:PATH=/headnode1/dnao/nest-installs/nest3-23.07.2022 \ -Dwith-mpi=ON \ /headnode1/dnao/gitnest/nest-simulator
make
make fails at 47%. I have uploaded the make output here: https://drive.google.com/file/d/1FXVsidFLXYvnHk4Tob2zDi4wQJJNW-yw/view?usp=s...
As well as the output of cmake to show the build configuration: https://drive.google.com/file/d/1HWH_KqILEyQYujzd4B1ma4ZrzUXbG231/view?usp=s...
Thank you in advance for any assistance.
The drive links don't work for me. Are .txt attachments a possibility?
On Thu, 28 Jul 2022, 17:08 Daniel Naoumenko, dnao9498@uni.sydney.edu.au wrote:
Hi,
I've been trying to compile the latest version on github (c1cebdc) without success.
The system is a HPC running RHEL7. Pre-installed software includes gsl-2.7, cmake 3.17.5 and openMPI-1.10.3-gnu, although I have tried variations with similar results.
I've created a fresh conda environment with packages necessary for nest and nestml: conda create --name pythonfornestml -c conda-forge boost readline ipython pyqt wxpython cython pip install mpi4py
cmake -DCMAKE_INSTALL_PREFIX:PATH=/headnode1/dnao/nest-installs/nest3-23.07.2022 \ -Dwith-mpi=ON \ /headnode1/dnao/gitnest/nest-simulator
make
make fails at 47%. I have uploaded the make output here:
https://drive.google.com/file/d/1FXVsidFLXYvnHk4Tob2zDi4wQJJNW-yw/view?usp=s...
As well as the output of cmake to show the build configuration:
https://drive.google.com/file/d/1HWH_KqILEyQYujzd4B1ma4ZrzUXbG231/view?usp=s...
Thank you in advance for any assistance. _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
Sure, I will try.
From: Robin Gilbert De Schepper robingilbert.deschepper@unipv.it Sent: Friday, 29 July 2022 3:23 AM To: NEST User Mailing List users@nest-simulator.org Subject: [NEST Users] Re: Compiling nest-simulator from source
The drive links don't work for me. Are .txt attachments a possibility?
On Thu, 28 Jul 2022, 17:08 Daniel Naoumenko, <dnao9498@uni.sydney.edu.aumailto:dnao9498@uni.sydney.edu.au> wrote: Hi,
I've been trying to compile the latest version on github (c1cebdc) without success.
The system is a HPC running RHEL7. Pre-installed software includes gsl-2.7, cmake 3.17.5 and openMPI-1.10.3-gnu, although I have tried variations with similar results.
I've created a fresh conda environment with packages necessary for nest and nestml: conda create --name pythonfornestml -c conda-forge boost readline ipython pyqt wxpython cython pip install mpi4py
cmake -DCMAKE_INSTALL_PREFIX:PATH=/headnode1/dnao/nest-installs/nest3-23.07.2022 \ -Dwith-mpi=ON \ /headnode1/dnao/gitnest/nest-simulator
make
make fails at 47%. I have uploaded the make output here: https://drive.google.com/file/d/1FXVsidFLXYvnHk4Tob2zDi4wQJJNW-yw/view?usp=s...https://protect-au.mimecast.com/s/MGyQCD1vlpTBgKZW4tWHTe3?domain=drive.google.com
As well as the output of cmake to show the build configuration: https://drive.google.com/file/d/1HWH_KqILEyQYujzd4B1ma4ZrzUXbG231/view?usp=s...https://protect-au.mimecast.com/s/fOB5CE8wmrtWRJjzEUwFqby?domain=drive.google.com
Thank you in advance for any assistance. _______________________________________________ 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
I have also uploaded them to github: https://github.com/nest/nest-simulator/files/9260227/make_output.txt https://github.com/nest/nest-simulator/files/9260220/cmake_output.txt
This is the first error that appears: In file included from /usr/include/c++/4.8.2/bits/stl_algobase.h:64:0, from /usr/include/c++/4.8.2/bits/char_traits.h:39, from /usr/include/c++/4.8.2/ios:40, from /usr/include/c++/4.8.2/istream:38, from /usr/include/c++/4.8.2/sstream:38, from /headnode1/dnao/gitnest/nest-simulator/thirdparty/compose.hpp:36, from /headnode1/dnao/gitnest/nest-simulator/nestkernel/recording_backend_ascii.cpp:24: /usr/include/c++/4.8.2/bits/stl_pair.h: In instantiation of ‘constexpr std::pair<_T1, _T2>::pair(const _T1&, const _T2&) [with _T1 = long unsigned int; _T2 = nest::RecordingBackendASCII::DeviceData]’: /usr/include/c++/4.8.2/bits/stl_pair.h:281:72: required from ‘constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = const long unsigned int&; _T2 = nest::RecordingBackendASCII::DeviceData; typename std::__decay_and_strip<_T2>::__type = nest::RecordingBackendASCII::DeviceData; typename std::__decay_and_strip<_Tp>::__type = long unsigned int]’ /headnode1/dnao/gitnest/nest-simulator/nestkernel/recording_backend_ascii.cpp:69:108: required from here /usr/include/c++/4.8.2/bits/stl_pair.h:113:31: error: use of deleted function ‘nest::RecordingBackendASCII::DeviceData::DeviceData(const nest::RecordingBackendASCII::DeviceData&)’ : first(__a), second(__b) { }
Hi Daniel,
It looks like you are using GCC 4.8, which is ancient and probably struggles with C++11 features NEST uses. Please upgrade to a newer compiler. Current versions are GCC 11 and Clang 13, if I am not mistaken.
Best regards, Hans Ekkehard
Dear Hans Ekkehard,
Thank you very much. After much wrangling with compiling its dependencies I managed to install gcc 13 and successfully compile the latest version of NEST. The joy of working with shared clusters running legacy software!
Best, Daniel
-
Daniel Naoumenko -
Hans Ekkehard Plesser -
Robin Gilbert De Schepper