dbbs-lab / bsb-daint Goto Github PK
View Code? Open in Web Editor NEWLicense: MIT License
License: MIT License
To compile I had to slightly modify the install-nest.sh:
module load daint-mc
module unload PrgEnv-gnu/6.0.8
module load PrgEnv-cray/6.0.8
module load PyExtensions/python3-CrayGNU-20.08
module load GSL/2.5-CrayCCE-20.08
module list
export CRAYPE_LINK_TYPE=dynamic
CDIR=$PWD
#cd
rm -rf nest-simulator
git clone https://github.com/dbbs-lab/nest-simulator.git --depth 1
mkdir build
cd build
rm -rf $HOME/nest-2.18.0-install/
cmake \
-Dwith-mpi=ON \
-Dwith-python=3 \
-DPYTHON_EXECUTABLE=/opt/python/3.8.2.1/bin/python \
-DPYTHON_LIBRARY=/opt/python/3.8.2.1/lib/libpython3.8.so \
-DPYTHON_INCLUDE_DIR=/opt/python/3.8.2.1/include/python3.8 \
-DCMAKE_CXX_COMPILER=CC \
-DCMAKE_C_COMPILER=cc \
-Dstatic-libraries=OFF \
-DCMAKE_INSTALL_PREFIX:PATH=$HOME/nest-2.18.0-install \
../nest-simulator
make -j
make install
cd $CDIR
Here is the full log file obtained by running bash install-nest.sh | tee install-nest.log 2>&1
:
install-nest.log
After complete install I had to run the load.sh script but this fails to load the modules.
So I have run:
. helpers/modules.sh
Resulting in this module list:
Currently Loaded Modulefiles:
1) modules/3.2.11.4(default) 17) gni-headers/5.0.12.0-7.0.2.1_2.5__g3b1768f.ari
2) cge/3.2.1463_r03f4dfb_fe3.3.0_2019062614 18) xpmem/2.2.20-7.0.2.1_2.21__g87eb960.ari
3) cray-mpich/7.7.15(default) 19) job/2.2.4-7.0.2.1_2.24__g36b56f4.ari
4) slurm/20.02.6-1 20) dvs/2.12_2.2.165-7.0.2.1_4.4__g22f4fff6
5) xalt/2.8.10 21) alps/6.6.59-7.0.2.1_3.14__g872a8d62.ari
6) daint-mc 22) rca/2.2.20-7.0.2.1_2.27__g8e3fb5b.ari
7) cray-python/3.8.2.1(default) 23) atp/3.7.4(default)
8) gcc/8.3.0(default) 24) perftools-base/20.08.0(default)
9) craype-broadwell 25) PrgEnv-gnu/6.0.8
10) craype-network-aries 26) cdt/20.08
11) craype/2.7.0(default) 27) CrayGNU/.20.08
12) cray-libsci/20.06.1(default) 28) PyExtensions/python3-CrayGNU-20.08
13) udreg/2.3.2-7.0.2.1_2.21__g8175d3d.ari 29) HDF5/1.10.6-CrayGNU-20.08-parallel
14) ugni/6.0.14.0-7.0.2.1_3.21__ge78e5b0.ari 30) h5py/2.10.0-CrayGNU-20.08-python3-parallel
15) pmi/5.0.16(default) 31) GSL/2.5-CrayGNU-20.08
16) dmapp/7.1.1-7.0.2.1_2.26__g38cf134.ari
Then I have rune the . helpers/activate-console-scripts.sh:
bp000432@daint104:~/src/NEST/dbbs/bsb-daint> echo $PATH
/users/bp000432/nest-2.18.0-install/bin:/users/bp000432/.local/bin:/apps/daint/UES/jenkins/7.0.UP02/mc/easybuild/software/GSL/2.5-CrayGNU-20.08/bin:/apps/daint/UES/jenkins/7.0.UP02/mc/easybuild/software/h5py/2.10.0-CrayGNU-20.08-python3-parallel/bin:/apps/daint/UES/jenkins/7.0.UP02/mc/easybuild/software/HDF5/1.10.6-CrayGNU-20.08-parallel/bin:/apps/daint/UES/jenkins/7.0.UP02/mc/easybuild/software/PyExtensions/python3-CrayGNU-20.08/bin:/opt/cray/pe/perftools/20.08.0/bin:/opt/cray/pe/papi/6.0.0.2/bin:/opt/cray/rca/2.2.20-7.0.2.1_2.27__g8e3fb5b.ari/bin:/opt/cray/alps/6.6.59-7.0.2.1_3.14__g872a8d62.ari/sbin:/opt/cray/alps/default/bin:/opt/cray/job/2.2.4-7.0.2.1_2.24__g36b56f4.ari/bin:/opt/cray/pe/craype/2.7.0/bin:/opt/gcc/8.3.0/bin:/opt/python/3.8.2.1/bin:/apps/daint/UES/xalt/xalt2/software/xalt/2.8.10/sbin:/apps/daint/UES/xalt/xalt2/software/xalt/2.8.10/bin:/opt/cray/pe/mpt/7.7.15/gni/bin:/apps/cscs/daint/bin:/apps/daint/system/bin:/apps/common/system/bin:/opt/cray/cge/3.2.1463_r03f4dfb_fe3.3.0_2019062614/bin:/opt/cray/pe/modules/3.2.11.4/bin:/usr/local/bin:/usr/bin:/bin:/usr/lib/mit/bin:/usr/lib/mit/sbin:/opt/cray/pe/bin
. /users/bp000432/nest-2.18.0-install/bin/nest_vars.sh
pip list > pip_list.log
Then I run your command to test the versions:
bp000432@daint104:~/src/NEST/dbbs/bsb-daint> srun -p debug -C mc -A ich002 python -c "import mpi4py.MPI; import nest; print(nest.__path__); print(nest.__version__)"
[INFO] [2021.2.17 12:13:15 /users/bp000432/src/NEST/dbbs/bsb-daint/nest-simulator/nestkernel/rng_manager.cpp:217 @ Network::create_rngs_] : Creating default RNGs
[INFO] [2021.2.17 12:13:15 /users/bp000432/src/NEST/dbbs/bsb-daint/nest-simulator/nestkernel/rng_manager.cpp:260 @ Network::create_grng_] : Creating new default global RNG
Nothing else happens and I have to stop it with CTRL-C.
I'm trying to install NEST after the last PizDaint update but I get a weird error during the cmake command. I followed the the instruction in the README, I cloned the repo, added the required lines in the .bashrc and run the command source install-nest.sh
.
This is the output:
ModuleCmd_Switch.c(179):ERROR:152: Module 'PrgEnv-cray/6.0.9' is currently not loaded
GSL(3):ERROR:105: Unable to locate a modulefile for 'GSL/2.5-CrayGNU-20.11'
Cloning into 'nest-simulator'...
remote: Enumerating objects: 1919, done.
remote: Counting objects: 100% (1919/1919), done.
remote: Compressing objects: 100% (1589/1589), done.
remote: Total 1919 (delta 566), reused 741 (delta 313), pack-reused 0
Receiving objects: 100% (1919/1919), 11.63 MiB | 12.85 MiB/s, done.
Resolving deltas: 100% (566/566), done.
Updating files: 100% (1854/1854), done.
-- The CXX compiler identification is Clang 12.0.0
-- The C compiler identification is Clang 12.0.0
-- Cray Programming Environment 2.7.10 CXX
-- Check for working CXX compiler: /opt/cray/pe/craype/2.7.10/bin/CC
-- Check for working CXX compiler: /opt/cray/pe/craype/2.7.10/bin/CC -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Cray Programming Environment 2.7.10 C
-- Check for working C compiler: /opt/cray/pe/craype/2.7.10/bin/cc
-- Check for working C compiler: /opt/cray/pe/craype/2.7.10/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.14") found components: doxygen missing components: 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 - not found
-- Looking for include file mach/mach.h
-- Looking for include file mach/mach.h - not 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: x86_64-pc-linux
-- Target triple: x86_64-pc-linux
CMake Error at cmake/ProcessOptions.cmake:436 (message):
Invalid option: -Dwith-python=3
Call Stack (most recent call first):
CMakeLists.txt:130 (nest_process_with_python)
-- Configuring incomplete, errors occurred!
See also "/users/bgambosi/nest-simulator/build/CMakeFiles/CMakeOutput.log".
See also "/users/bgambosi/nest-simulator/build/CMakeFiles/CMakeError.log".
make: *** No targets specified and no makefile found. Stop.
make: *** No rule to make target 'install'. Stop.
@Helveg, did I skip any step? any idea about what is failing?
Also, these are the cmake log files
CMakeError.log
CMakeOutput.log
-- Found Python: /opt/python/3.9.4.1/bin/python3.9 (found suitable version "3.9.4", minimum required is "3.8") found components: Interpreter Development
CMake Warning at cmake/ProcessOptions.cmake:391 (message):
Could not locate Python ABI, using shared libraries and header file
instead. Please clear your CMake cache and build folder and verify that
CMake is up-to-date (3.18+).
Call Stack (most recent call first):
CMakeLists.txt:130 (nest_process_with_python)
CMake Error at cmake/ProcessOptions.cmake:403 (message):
No virtual Python environment found and no installation prefix specified.
Please either build and install NEST in a virtual Python environment or
specify CMake option -DCMAKE_INSTALL_PREFIX=<nest_install_dir>.
Call Stack (most recent call first):
CMakeLists.txt:130 (nest_process_with_python)
-- Configuring incomplete, errors occurred!
See also "/users/mcalice/nest-simulator/build/CMakeFiles/CMakeOutput.log".
See also "/users/mcalice/nest-simulator/build/CMakeFiles/CMakeError.log".
make: *** No targets specified and no makefile found. Stop.
make: *** No rule to make target 'install'. Stop.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.