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BlueBrain / CoreNeuron

Simulator optimized for large scale neural network simulations.
BSD 3-Clause "New" or "Revised" License
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Compilation issues (NEURON with coreNEURON) #580

Closed jhielson closed 3 years ago

jhielson commented 3 years ago

**Hi all,

I have been trying to simulate a network with a few thousand of neurons on the NEURON simulator (Ubuntu). I was told that using the coreNEURON module it would be possible to execute my model using the GPU (Nvidia) from my laptop. Based on that, I followed the steps provided on the documentation (https://neuronsimulator.github.io/nrn/coreneuron/how-to/coreneuron.html) but the compilation did not work. I got several errors and I am not sure how to fix them.**

My setup: cmake version 3.10.2 Python 3 NVIDIA HPC SDK CUDA 11.3

When I execute the command:

$ cmake .. -DNRN_ENABLE_CORENEURON=ON -DCORENRN_ENABLE_GPU=ON -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_RX3D=OFF -DCMAKE_INSTALL_PREFIX=$HOME/install -DCMAKE_C_COMPILER=nvc -DCMAKE_CXX_COMPILER=nvc++ -DCMAKE_LIBRARY_ARCHITECTURE="x86_64-linux-gnu"             -DCMAKE_CXX_FLAGS="-O3 -g"  -DCMAKE_C_FLAGS="-O3 -g"

It generates the following output:

-- Found PythonInterp: /usr/bin/python3 (found suitable version "3.6.9", minimum required is "3") 
-- Building CoreNEURON from submodule
-- Sub-project : using coreneuron from from /home/jhielson/neuron/nrn/external/coreneuron
-- CORENRN_FORMATTING: OFF
-- CORENRN_FORMATTING_ON: all
-- CORENRN_FORMATTING_CPP_CHANGES_ONLY: OFF
-- CORENRN_TEST_FORMATTING: OFF
-- CORENRN_FORMATTING_NO_SUBMODULES: ON
-- CORENRN_CLANG_FORMAT: OFF
-- CORENRN_CMAKE_FORMAT: OFF
-- CORENRN_GIT_HOOKS: OFF
-- CORENRN_GIT_COMMIT_HOOKS: 
-- CORENRN_GIT_PUSH_HOOKS: courtesy-msg
-- CORENRN_STATIC_ANALYSIS: OFF
-- CORENRN_TEST_STATIC_ANALYSIS: OFF
-- Found PythonInterp: /usr/bin/python3 (found version "3.6.9") 
-- Using mod2c submodule from /home/jhielson/neuron/nrn/external/coreneuron/external/mod2c
-- mod2c is used as APPLICATION_NAME
-- 
-- Configured CoreNEURON 0.21.0
-- 
-- Some things you can do now:
-- --------------------+--------------------------------------------------------
-- Command             |   Description
-- --------------------+--------------------------------------------------------
-- make install        | Will install CoreNEURON to: /home/jhielson/install
-- make docs           | Build full docs. Calls targets: doxygen, sphinx
-- --------------------+--------------------------------------------------------
--  Build option       | Status
-- --------------------+--------------------------------------------------------
-- C COMPILER          | /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc
-- CXX COMPILER        | /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc++
-- COMPILE FLAGS       | -O3 -g -acc -gpu=cuda11.3,cc60,cc70 --diag_suppress 161,177,550 -mp   -g  -O2  --c++14
-- Build Type          | STATIC
-- MPI                 | ON
--   INC               | /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/include
-- OpenMP              | ON
-- Use legacy units    | OFF
-- NMODL               | OFF
-- MOD2CPP PATH        | /home/jhielson/neuron/nrn/build/bin/mod2c_core
-- GPU Support         | ON
--   CUDA              | /usr/local/cuda-11.3
--   Unified Memory    | OFF
--   HOST COMPILER     | /usr/bin/gcc
-- Auto Timeout        | ON
-- Wrap exp()          | OFF
-- SplayTree Queue     | ON
-- NetReceive Buffer   | ON
-- Caliper             | OFF
-- Likwid              | OFF
-- Unit Tests          | OFF
-- Reporting           | OFF
-- --------------+--------------------------------------------------------------
--  See documentation : https://github.com/BlueBrain/CoreNeuron/
-- --------------+--------------------------------------------------------------
-- 
NOTICEUsing Target in compiling and linking, you should take care of it if
                    it fail miserabily (CODE: 1234567890)
-- 
-- Configured NEURON 8.0
-- 
-- You can now build NEURON using:
--   cmake --build . [--target TARGET] -- -j 8
-- You might want to adjust the number of parallel build jobs for your system.
-- Some non-default targets you might want to build:
-- --------------+--------------------------------------------------------------
--  Target       |   Description
-- --------------+--------------------------------------------------------------
-- install       | Will install NEURON to: /home/jhielson/install
--               | Change the install location of NEURON using:
--               |   cmake <src_path> -DCMAKE_INSTALL_PREFIX=<install_path>
-- docs          | Build full docs. Calls targets: doxygen, notebooks, sphinx
-- uninstall     | Removes files installed by make install (todo)
-- --------------+--------------------------------------------------------------
--  Build option | Status
-- --------------+--------------------------------------------------------------
-- C COMPILER    | /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc
-- CXX COMPILER  | /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc++
-- BUILD_TYPE    | RelWithDebInfo (allowed: Custom;Debug;Release;RelWithDebInfo;Fast)
-- COMPILE FLAGS | -g  -O2 
-- Shared        | ON
-- Default units | modern units (2019 nist constants)
-- MPI           | ON
--   INC         | /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/include
--   LIB         | /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/lib/libmpi_cxx.so
--   DYNAMIC     | OFF
-- Python        | ON
--   EXE         | /usr/bin/python3
--   INC         | /usr/include/python3.6m
--   LIB         | /usr/lib/x86_64-linux-gnu/libpython3.6m.so
--   MODULE      | ON
--   DYNAMIC     | OFF
-- Readline      | /usr/lib/x86_64-linux-gnu/libreadline.so
-- Curses        | /usr/lib/x86_64-linux-gnu/libcurses.so;/usr/lib/x86_64-linux-gnu/libform.so
-- RX3D          | OFF
-- Interviews    | OFF
-- CoreNEURON    | ON
--   PATH        | /home/jhielson/neuron/nrn/external/coreneuron
--   LINK FLAGS  | -acc -gpu=cuda11.3,cc60,cc70 -rdynamic -lrt -Wl,--whole-archive -Lx86_64 -lcorenrnmech -L/home/jhielson/install/lib -lcoreneuron -lcudacoreneuron -Wl,--no-whole-archive /usr/local/cuda-11.3/lib64/libcudart_static.a
--   Legacy Units| OFF
-- --------------+--------------------------------------------------------------
--  See documentation : https://www.neuron.yale.edu/neuron/
-- --------------+--------------------------------------------------------------
-- 
-- Configuring done
-- Generating done
-- Build files have been written to: /home/jhielson/neuron/nrn/build  

**It seems to be everything fine until this point. But, when I compile the package (make -j), I get the following errors:**

[  0%] Built target nrnivmodl-core
[  1%] Generating help_data.dat
[  1%] Built target rxdmath
[  3%] Built target coreneuron-copy-nrnivmodl-core-dependencies
[  3%] Built target kin_deriv_header
[  3%] Update hh.mod for CoreNEURON compatibility
[  4%] Built target scopmath

... Removed a few lines to make it shorter

[ 14%] Building CXX object src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/solve.cpp.o
nvc++-Info-Switch -Mvect forces -O2nvc++-Info-Switch -Mvect forces -O2

nvc++-Info-Switch -Mvect forces -O2
nvc++-Info-Switch -Mvect forces -O2
nvc++-Info-Switch -Mvect forces -O2
nvc++-Info-"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: duplicate specifier in declaration
    typedef __SIZE_TYPE__   size_t;
                            ^

"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: invalid combination of type specifiers
    typedef __SIZE_TYPE__   size_t;
                            ^

nvc++-Info-Switch -Mvect forces -O2
Switch -Mvect forces -O2
nvc++-Info-nvc++-Info-Switch -Mvect forces -O2
nvc++-Info-Switch -Mvect forces -O2
Switch -Mvect forces -O2
nvc++-Info-Switch -Mvect forces -O2
nvc++-Info-Switch -Mvect forces -O2
"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: duplicate specifier in declaration
    typedef __SIZE_TYPE__   size_t;
                            ^

"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: invalid combination of type specifiers
    typedef __SIZE_TYPE__   size_t;
                            ^

"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: duplicate specifier in declaration
    typedef __SIZE_TYPE__   size_t;
                            ^

nvc++-Info-Switch -Mvect forces -O2
nvc++-Info-Switch -Mvect forces -O2
"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: invalid combination of type specifiers
    typedef __SIZE_TYPE__   size_t;
                            ^

nvc++-Info-Switch -Mvect forces -O2
"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: duplicate specifier in declaration
    typedef __SIZE_TYPE__   size_t;
                            ^

"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: invalid combination of type specifiers
    typedef __SIZE_TYPE__   size_t;
                            ^

nvc++-Info-Switch -Mvect forces -O2
"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: duplicate specifier in declaration
    typedef __SIZE_TYPE__   size_t;
                            ^

"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: invalid combination of type specifiers
    typedef __SIZE_TYPE__   size_t;
                            ^

"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: duplicate specifier in declaration
    typedef __SIZE_TYPE__   size_t;
                            ^

"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: invalid combination of type specifiers
    typedef __SIZE_TYPE__   size_t;
                            ^

nvc++-Info-Switch -Mvect forces -O2
nvc++-Info-Switch -Mvect forces -O2
"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: duplicate specifier in declaration
    typedef __SIZE_TYPE__   size_t;
                            ^

"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: duplicate specifier in declaration
    typedef __SIZE_TYPE__   size_t;
                            ^

"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: invalid combination of type specifiers
    typedef __SIZE_TYPE__   size_t;
                            ^

"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: duplicate specifier in declaration
    typedef __SIZE_TYPE__   size_t;
                            ^

"/usr/include/x86_64-linux-gnu/c++/7/bits/c++config.h", line 231: error: invalid combination of type specifiers
    typedef __SIZE_TYPE__   size_t;
                            ^

"/usr/include/c++/7/new", line 120: error: expected an identifier
  void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc)
                          ^

"/usr/include/c++/7/new", line 120: error: invalid combination of type specifiers
  void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc)
                          ^

"/usr/include/c++/7/new", line 122: error: expected an identifier
  void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
                            ^

"/usr/include/c++/7/new", line 122: error: invalid combination of type specifiers
  void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
                            ^

"/usr/include/c++/7/new", line 134: error: expected an identifier
  void* operator new(std::size_t, const std::nothrow_t&) _GLIBCXX_USE_NOEXCEPT
                          ^

"/usr/include/c++/7/new", line 134: error: invalid combination of type specifiers
  void* operator new(std::size_t, const std::nothrow_t&) _GLIBCXX_USE_NOEXCEPT
                          ^

"/usr/include/c++/7/new", line 136: error: expected an identifier
  void* operator new[](std::size_t, const std::nothrow_t&) _GLIBCXX_USE_NOEXCEPT
                            ^

"/usr/include/c++/7/new", line 136: error: invalid combination of type specifiers
  void* operator new[](std::size_t, const std::nothrow_t&) _GLIBCXX_USE_NOEXCEPT
                            ^

"/usr/include/c++/7/new", line 168: error: expected an identifier
  inline void* operator new(std::size_t, void* __p) _GLIBCXX_USE_NOEXCEPT
                                 ^

"/usr/include/c++/7/new", line 168: error: invalid combination of type specifiers
  inline void* operator new(std::size_t, void* __p) _GLIBCXX_USE_NOEXCEPT
                                 ^

"/usr/include/c++/7/new", line 170: error: expected an identifier
  inline void* operator new[](std::size_t, void* __p) _GLIBCXX_USE_NOEXCEPT
                                   ^

"/usr/include/c++/7/new", line 170: error: invalid combination of type specifiers
  inline void* operator new[](std::size_t, void* __p) _GLIBCXX_USE_NOEXCEPT
                                   ^

nvc++-Info-Switch -Mvect forces -O2
nvc++-Info-Switch -Mvect forces -O2
"/usr/include/c++/7/type_traits", line 362: error: expected an identifier
    template<typename _Tp, std::size_t _Size>
                                ^

"/usr/include/c++/7/type_traits", line 362: error: invalid combination of type specifiers
    template<typename _Tp, std::size_t _Size>
                                ^

...
... ... Removed several lines to make it shorter
...

"/home/jhielson/neuron/nrn/src/nmodl/lex.lpp", line 221: warning: conversion from a string literal to "char *" is deprecated
    diag("equation addition can't occur in this type of block", (char *)0);
         ^

"/home/jhielson/neuron/nrn/src/nmodl/lex.lpp", line 231: warning: conversion from a string literal to "char *" is deprecated
    diag("equations can't occur in this type of block", (char *)0);
         ^

"/home/jhielson/neuron/nrn/src/nmodl/lex.lpp", line 244: warning: conversion from a string literal to "char *" is deprecated
  { yylval.qp = putintoken("{", 0); return yytext[0]; }
                           ^

"/home/jhielson/neuron/nrn/src/nmodl/lex.lpp", line 245: warning: statement is unreachable
    YY_BREAK
    ^

"/home/jhielson/neuron/nrn/src/nmodl/lex.lpp", line 245: warning: conversion from a string literal to "char *" is deprecated
  { yylval.qp = putintoken("}", 0); return yytext[0]; }
                           ^

"/home/jhielson/neuron/nrn/src/nmodl/lex.lpp", line 246: warning: statement is unreachable
    YY_BREAK
    ^

"/home/jhielson/neuron/nrn/src/nmodl/lex.lpp", line 247: warning: statement is unreachable
    YY_BREAK
    ^

98 errors detected in the compilation of "/home/jhielson/neuron/nrn/src/modlunit/lex.cpp".
src/nrniv/CMakeFiles/modlunit.dir/build.make:97: recipe for target 'src/nrniv/CMakeFiles/modlunit.dir/__/modlunit/lex.cpp.o' failed
make[2]: *** [src/nrniv/CMakeFiles/modlunit.dir/__/modlunit/lex.cpp.o] Error 2
CMakeFiles/Makefile2:1750: recipe for target 'src/nrniv/CMakeFiles/modlunit.dir/all' failed
make[1]: *** [src/nrniv/CMakeFiles/modlunit.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
"/usr/include/c++/7/ext/new_allocator.h", line 130: error: type name is not allowed
        { return size_t(-1) / sizeof(_Tp); }
                 ^
          detected during:
            instantiation of "std::allocator_traits<std::allocator<_Tp>>::size_type std::allocator_traits<std::allocator<_Tp>>::max_size(const std::allocator_traits<std::allocator<_Tp>>::allocator_type &) [with _Tp=char]" at line 932 of "/usr/include/c++/7/bits/basic_string.h"
            instantiation of "std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::max_size() const [with _CharT=char, _Traits=std::char_traits<char>, _Alloc=std::allocator<char>]" at line 311 of "/usr/include/c++/7/bits/basic_string.h"
            instantiation of "void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_check_length(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type, std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type, const char *) const [with _CharT=char, _Traits=std::char_traits<char>, _Alloc=std::allocator<char>]" at line 1257 of "/usr/include/c++/7/bits/basic_string.h"
            instantiation of "std::__cxx11::basic_string<_CharT, _Traits, _Alloc> &std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::append(const _CharT *) [with _CharT=char, _Traits=std::char_traits<char>, _Alloc=std::allocator<char>]" at line 5929 of "/usr/include/c++/7/bits/basic_string.h"
            instantiation of "std::__cxx11::basic_string<_CharT, _Traits, _Alloc> std::operator+(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc> &, const _CharT *) [with _CharT=char, _Traits=std::char_traits<char>, _Alloc=std::allocator<char>]" at line 351 of "/usr/include/c++/7/system_error"

"/usr/include/c++/7/ext/new_allocator.h", line 130: error: expected a ";"
        { return size_t(-1) / sizeof(_Tp); }
                 ^
          detected during:
            instantiation of "std::allocator_traits<std::allocator<_Tp>>::size_type std::allocator_traits<std::allocator<_Tp>>::max_size(const std::allocator_traits<std::allocator<_Tp>>::allocator_type &) [with _Tp=char]" at line 932 of "/usr/include/c++/7/bits/basic_string.h"
            instantiation of "std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::max_size() const [with _CharT=char, _Traits=std::char_traits<char>, _Alloc=std::allocator<char>]" at line 311 of "/usr/include/c++/7/bits/basic_string.h"
            instantiation of "void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_check_length(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type, std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type, const char *) const [with _CharT=char, _Traits=std::char_traits<char>, _Alloc=std::allocator<char>]" at line 1257 of "/usr/include/c++/7/bits/basic_string.h"
            instantiation of "std::__cxx11::basic_string<_CharT, _Traits, _Alloc> &std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::append(const _CharT *) [with _CharT=char, _Traits=std::char_traits<char>, _Alloc=std::allocator<char>]" at line 5929 of "/usr/include/c++/7/bits/basic_string.h"
            instantiation of "std::__cxx11::basic_string<_CharT, _Traits, _Alloc> std::operator+(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc> &, const _CharT *) [with _CharT=char, _Traits=std::char_traits<char>, _Alloc=std::allocator<char>]" at line 351 of "/usr/include/c++/7/system_error"

"/home/jhielson/neuron/nrn/src/nmodl/lex.cpp", line 1494: warning: function "yyunput" was declared but never referenced
      static void yyunput (int c, char * yy_bp )
                  ^

98 errors detected in the compilation of "/home/jhielson/neuron/nrn/src/nmodl/lex.cpp".
src/nrniv/CMakeFiles/nocmodl.dir/build.make:128: recipe for target 'src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/lex.cpp.o' failed
make[2]: *** [src/nrniv/CMakeFiles/nocmodl.dir/__/nmodl/lex.cpp.o] Error 2
CMakeFiles/Makefile2:1681: recipe for target 'src/nrniv/CMakeFiles/nocmodl.dir/all' failed
make[1]: *** [src/nrniv/CMakeFiles/nocmodl.dir/all] Error 2
Makefile:151: recipe for target 'all' failed
make: *** [all] Error 2
olupton commented 3 years ago

Can you please verify that your installation's nvc/nvc++ is able to build and link some trivial C/C++ "hello world" examples?

It looks like something may have gone wrong in the makelocalrc part of the NVHPC toolkit installation (i.e. there is something wrong in the localrc file being read by the compiler).

You do have slightly newer versions of NVHPC and CUDA than I have tested recently, but I would guess that is not the problem.

jhielson commented 3 years ago

Thanks! I will check it out and keep you posted.

jhielson commented 3 years ago

Hi,

I have created and compiled hello world applications (.c and .cpp) using nvc and nvc++ respectively and it worked fine.

I am not sure if I understood the second part about the makelocalrc.

olupton commented 3 years ago

I will try and find time to test with the newer CUDA and NVHPC versions that you have.

In the meantime, could you paste the output of nvc++ -dryrun -c foo.cpp ? (foo.cpp does not need to exist) That might give some clues.

In the output of that command you will (I assume) see some line like

Reading rcfile {...}/localrc.{hostname}

that localrc file should be generated as part of installation by the makelocalrc script bundled with the compilers. This will steer which version of the GCC headers is picked up. I don't know quite what the problem is here, but I wonder from the errors if two different sets of system headers are being mixed together.

jhielson commented 3 years ago

Thanks! I execute the command you suggested. It seems there is something wrong. You can find the output below:

Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/.nvc++rc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/nativerc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/fnativerc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/ccrc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/ccirc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/cpprc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/cppcurc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/paralgorc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/x86rc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/x8664rc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/lin86rc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/lin8664rc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/llvmcomprc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/llvmrc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/llvmx86rc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/llvmx8664rc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/omprc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/iparc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/acc1rc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/acclin8664rc
Skipping rcfiles/accxrc (not found)
Skipping rcfiles/acctoolsrc (not found)
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/targetrc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/c++llvmrc
Skipping rcfiles/llvmxrc (not found)
Skipping rcfiles/gccxrc (not found)
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/rcfiles/persnvirc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/localrc
Reading rcfile /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/localrc.jhielson-Robotics
Skipping siterc (not found)
Skipping siterc.jhielson-Robotics (not found)
Skipping .mynvrc (not found)
Skipping .mynvc++rc (not found)
Skipping .mynvcpprc (not found)
Skipping .mynvx86rc (not found)
Skipping $MYLOCALRC (not found)
Skipping cudarc (not found)

/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/tools/cpp1 --llalign -Dunix -D__unix -D__unix__ -Dlinux -D__linux -D__linux__ -D__NO_MATH_INLINES -D__LP64__ -D__x86_64 -D__x86_64__ -D__LONG_MAX__=9223372036854775807L '-D__SIZE_TYPE__=unsigned long int' '-D__PTRDIFF_TYPE__=long int' -D__amd64 -D__amd64__ -D__k8 -D__k8__ -D__MMX__ -D__SSE__ -D__SSE2__ -D__SSE3__ -D__SSSE3__ -D__SSE4_1__ -D__SSE4_2__ -D__AVX__ -D__AVX2__ -D__FMA__ -D__XSAVE__ -D__POPCNT__ -D__FXSR__ -D__PGI -D__NVCOMPILER -D_GNU_SOURCE -D_PGCG_SOURCE -I- -I/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/include-gcc70 -I/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/include -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include -I/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/include-gcc70 -I/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include -D__PGLLVM__ -D__NVCOMPILER_LLVM__ -D__extension__= --preinclude _cplus_preinclude.h --preinclude_macros _cplus_macros.h --gnu_version=70500 -D__pgnu_vsn=70500 -q -o foo.il foo.cpp

/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/tools/cpp2 foo.cpp -opt 1 -terse 1 -inform warn -x 119 0xa10000 -x 122 0x40 -x 123 0x1000 -x 127 4 -x 127 17 -x 19 0x400000 -x 28 0x40000 -x 120 0x10000000 -x 70 0x8000 -x 122 1 -x 125 0x20000 -quad -x 59 4 -tp haswell -x 120 0x1000 -astype 0 -x 121 1 -fn foo.cpp -il foo.il -x 117 0x200 -x 123 0x80000000 -x 123 4 -x 119 0x20 -def __pgnu_vsn=70500 -x 70 0x40000000 -x 183 4 -x 121 0x800 -x 6 0x20000 -x 249 110 -x 120 0x200000 -x 70 0x40000000 -x 8 0x40000000 -x 164 0x800000 -x 85 0x2000 -x 85 0x4000 -x 34 0x40000000 -x 53 0x800000 -x 68 0x1 -x 39 4 -x 56 0x10 -x 26 0x10 -x 26 1 -x 56 0x4000 -y 163 0xc0000000 -x 189 0x10 -y 189 0x4000000 -gnuvsn 70500 -x 69 0x200 -x 123 0x400 -asm foo.ll

/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/share/llvm/bin/llc foo.ll -march=x86-64 -mcpu=native -O1 -fast-isel=0 -non-global-value-max-name-size=4294967295 -x86-cmov-converter=0 --frame-pointer=none -o foo.s

/usr/bin/as foo.s -o foo.o
jhielson commented 3 years ago

Hi,

Which versions of neuron and CUDA and NVHPC you have? I could install them on my computer to see if it works for me.

olupton commented 3 years ago

I don't see any red flags there.

NEURON master has worked for me with NVHPC 21.2 (with the standard library/headers from GCC 9.3.0; you seem to have GCC 7.5.0) and CUDA 11.0.2. I am more inclined to suspect the problem is related to GCC7 vs. GCC9 rather than the minor differences in CUDA/NVHPC versions, but I am not sure.

olupton commented 3 years ago

I have finally reproduced your issue: with NVHPC 21.5 + GCC 7.5.0 and CUDA 11.3.1 then changing from CMake 3.20.3 to CMake 3.10.2 triggers your errors. I'll look into it.

jhielson commented 3 years ago

Thanks! CMake 3.10.2 is considered to be the latest version on Ubuntu 18.04. Please, let me know if there is a way to solve the compilation problem using Ubuntu 18.04 and CMake 3.10.2.

olupton commented 3 years ago

Can you please test the following patch?

diff --git a/cmake/MacroHelper.cmake b/cmake/MacroHelper.cmake
index a8289e017..c450955c2 100644
--- a/cmake/MacroHelper.cmake
+++ b/cmake/MacroHelper.cmake
@@ -56,13 +56,15 @@ macro(nrn_check_type_exists HEADER TYPE DEFAULT_TYPE VARIABLE)
       if (sizeof (@type@))
         return 0\;
       return 0\;
-    }")
+    }
+")
   string(REPLACE "@header@" ${HEADER} CONFTEST_TYPE "${CONFTEST_TYPE_TPL}")
   string(REPLACE "@type@" ${TYPE} CONFTEST_TYPE "${CONFTEST_TYPE}")

(i.e. just add a new line after the } and ensure the " is the first character on the line)

jhielson commented 3 years ago

Hi,

Thanks! That was really interesting. It solved that issue. But, I got a new one when was close to end the compilation:

[ 97%] Running nrnivmodl-core with halfgap.mod
[INFO] Running: make -j1 -f /home/jhielson/neuron/nrn/build/share/coreneuron/nrnivmodl_core_makefile ROOT=/home/jhielson/neuron/nrn/build MOD2CPP_BINARY=/home/jhielson/neuron/nrn/build/bin/mod2c_core MODS_PATH=x86_64/corenrn/mod2c BUILD_TYPE=STATIC
Default NMODL flags: 
diff: x86_64/corenrn/mod2c/_mod_func.cpp: No such file or directory
Translating x86_64/corenrn/mod2c/exp2syn.mod into x86_64/corenrn/mod2c//exp2syn.cpp
cvode_emit=0 cvode_not_allowed=0
Thread Safe
Translating x86_64/corenrn/mod2c/expsyn.mod into x86_64/corenrn/mod2c//expsyn.cpp
cvode_emit=0 cvode_not_allowed=0
Thread Safe
Translating x86_64/corenrn/mod2c/halfgap.mod into x86_64/corenrn/mod2c//halfgap.cpp
cvode_emit=0 cvode_not_allowed=0
Thread Safe
Translating x86_64/corenrn/mod2c/hh.mod into x86_64/corenrn/mod2c//hh.cpp
cvode_emit=0 cvode_not_allowed=0
Thread Safe
Translating x86_64/corenrn/mod2c/netstim.mod into x86_64/corenrn/mod2c//netstim.cpp
cvode_emit=0 cvode_not_allowed=0
Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it
only affects and is affected by discrete events. As such it is not
located in a section and is not associated with an integrator
Thread Safe
Translating x86_64/corenrn/mod2c/passive.mod into x86_64/corenrn/mod2c//passive.cpp
cvode_emit=0 cvode_not_allowed=0
Thread Safe
Translating x86_64/corenrn/mod2c/pattern.mod into x86_64/corenrn/mod2c//pattern.cpp
cvode_emit=0 cvode_not_allowed=0
Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it
only affects and is affected by discrete events. As such it is not
located in a section and is not associated with an integrator
Thread Safe
Translating x86_64/corenrn/mod2c/stim.mod into x86_64/corenrn/mod2c//stim.cpp
cvode_emit=0 cvode_not_allowed=0
Thread Safe
Translating x86_64/corenrn/mod2c/svclmp.mod into x86_64/corenrn/mod2c//svclmp.cpp
cvode_emit=0 cvode_not_allowed=0
Thread Safe
NVC++-W-1053-External and Static variables are not supported in acc routine - _ZN10coreneuron11nrn_threadsE (x86_64/corenrn/mod2c/exp2syn.cpp: 396)
NVC++/x86-64 Linux 21.5-0: compilation completed with warnings
NVC++-W-1053-External and Static variables are not supported in acc routine - _ZN10coreneuron11nrn_threadsE (x86_64/corenrn/mod2c/expsyn.cpp: 378)
NVC++/x86-64 Linux 21.5-0: compilation completed with warnings
/home/jhielson/neuron/nrn/build/bin
 => Binary creating x86_64/special-core
/home/jhielson/neuron/nrn/build/share/coreneuron/coreneuron.cpp:
/home/jhielson/anaconda3/envs/p27/x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/librt.so: undefined reference to `__vdso_clock_gettime@GLIBC_PRIVATE'
pgacclnk: child process exit status 1: /usr/bin/ld
/home/jhielson/neuron/nrn/build/share/coreneuron/nrnivmodl_core_makefile:183: recipe for target 'x86_64/special-core' failed
make[3]: *** [x86_64/special-core] Error 2
external/coreneuron/coreneuron/CMakeFiles/nrniv-core.dir/build.make:75: recipe for target 'bin/x86_64/special-core' failed
make[2]: *** [bin/x86_64/special-core] Error 2
CMakeFiles/Makefile2:1564: recipe for target 'external/coreneuron/coreneuron/CMakeFiles/nrniv-core.dir/all' failed
make[1]: *** [external/coreneuron/coreneuron/CMakeFiles/nrniv-core.dir/all] Error 2
Makefile:151: recipe for target 'all' failed
make: *** [all] Error 2

Can you help me with this one?

olupton commented 3 years ago

OK, great that it fixed it. We can merge a similar fix into NEURON.

Your new error seems to be related to a conda environment (/home/jhielson/anaconda3/...), can you try in a cleaner shell?

A brief explanation, if you're curious: CMake versions from v3.9.0 to v3.19.0 were passing the -A option to the compiler when detecting the presence of certain symbols (nrn_check_type_exists), which makes PGI/NVHPC compilers very pedantic. Specifically they were aborting because the code generated by NEURON to detect the presence of size_t did not end with a new line character...then NEURON defines size_t itself and you get the errors you reported.

One reason this does not seem to be such a widespread problem is that the Spack version of CMake patches out the -A flag for v3.15+.

jhielson commented 3 years ago

Thanks a lot. It was indeed because of the conda environment. Sorry to bring another error. I downloaded the package again and tried to rebuild it and now I get the following error:

$cmake .. -DNRN_ENABLE_CORENEURON=ON -DCORENRN_ENABLE_GPU=ON -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_RX3D=OFF -DCMAKE_INSTALL_PREFIX=$HOME/nvidia/nvhpc_2021_215_Linux_x86_64_cuda_11.3/install -DCMAKE_C_COMPILER=nvc -DCMAKE_CXX_COMPILER=nvc++ -DCMAKE_LIBRARY_ARCHITECTURE="x86_64-linux-gnu"             -DCMAKE_CXX_FLAGS="-O3 -g"  -DCMAKE_C_FLAGS="-O3 -g"   

CMake Error at cmake/ExternalProjectHelper.cmake:50 (add_subdirectory):
  The source directory

    /home/jhielson/neuron/nrn/external/coreneuron

  does not contain a CMakeLists.txt file.
Call Stack (most recent call first):
  CMakeLists.txt:377 (add_external_project)

NOTICEUsing Target in compiling and linking, you should take care of it if
                    it fail miserabily (CODE: 1234567890)
olupton commented 3 years ago

CoreNEURON is a git submodule of NEURON. The cmake step should automatically fetch it if needed...I would hope there was an error message from git a little above the one about add_subdirectory? Can you post the full output?

You can also update the submodule manually, with

git submodule init
git submodule update

from the top-level NEURON directory, but this shouldn't be needed.

jhielson commented 3 years ago

After executing the git commands I got new errors:

-- The C compiler identification is PGI 21.5.0
-- The CXX compiler identification is PGI 21.5.0
-- Check for working C compiler: /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc
-- Check for working C compiler: /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc++
-- Check for working CXX compiler: /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
heads/master
-- Setting build type to 'RelWithDebInfo' as none was specified.
-- Found BISON: /usr/bin/bison (found version "3.0.4") 
-- Found FLEX: /usr/bin/flex (found version "2.6.4") 
-- Found Readline: /usr/include  
-- Found MPI_C: /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/lib/libmpi.so (found version "3.1") 
-- Found MPI_CXX: /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/lib/libmpi_cxx.so (found version "3.1") 
-- Found MPI: TRUE (found version "3.1")  
-- Found PythonInterp: /usr/bin/python3.6 (found suitable version "3.6.9", minimum required is "3.6") 
-- Found PythonInterp: /usr/bin/python3.6 (found suitable version "3.6.9", minimum required is "3") 
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.6m.so
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE  
-- Building CoreNEURON from submodule
-- Sub-project : using coreneuron from from /home/jhielson/neuron/nrn/external/coreneuron
-- Could NOT find HpcCodingConv (missing: HpcCodingConv_PROJ) 
-- Sub-module CMake/hpc-coding-conventions missing: running git submodule update --init
Submodule 'CMake/hpc-coding-conventions' (https://github.com/BlueBrain/hpc-coding-conventions.git) registered for path 'CMake/hpc-coding-conventions'
Cloning into '/home/jhielson/neuron/nrn/external/coreneuron/CMake/hpc-coding-conventions'...
Submodule path 'CMake/hpc-coding-conventions': checked out 'c57f78f505acb17c39c8406b3d2101d8dfecd48b'
-- CORENRN_FORMATTING: OFF
-- CORENRN_FORMATTING_ON: all
-- CORENRN_FORMATTING_CPP_CHANGES_ONLY: OFF
-- CORENRN_TEST_FORMATTING: OFF
-- CORENRN_FORMATTING_NO_SUBMODULES: ON
-- CORENRN_CLANG_FORMAT: OFF
-- CORENRN_CMAKE_FORMAT: OFF
-- CORENRN_GIT_HOOKS: OFF
-- CORENRN_GIT_COMMIT_HOOKS: 
-- CORENRN_GIT_PUSH_HOOKS: courtesy-msg
-- CORENRN_STATIC_ANALYSIS: OFF
-- CORENRN_TEST_STATIC_ANALYSIS: OFF
-- Could NOT find Random123 (missing: Random123_PROJ) 
-- Sub-module Random123 missing: running git submodule update --init --recursive
Submodule 'external/Random123' (https://github.com/BlueBrain/Random123.git) registered for path 'external/Random123'
Cloning into '/home/jhielson/neuron/nrn/external/coreneuron/external/Random123'...
Submodule path 'external/Random123': checked out 'b5cb15614e8f3eb0ff316bdc50c300ddd32fa3c1'
-- Found CLI11: /home/jhielson/neuron/nrn/bin  
-- Found Git: /usr/bin/git (found version "2.17.1") 
CMake Error at external/coreneuron/CMakeLists.txt:68 (add_subdirectory):
  The source directory

    /home/jhielson/neuron/nrn/external/coreneuron/external/CLI11

  does not contain a CMakeLists.txt file.

-- Found CUDA: /usr/local/cuda-11.3 (found suitable version "11.3", minimum required is "9.0") 
-- Found PythonInterp: /usr/bin/python3.6 (found version "3.6.9") 
-- Found Perl: /usr/bin/perl (found version "5.26.1") 
-- Found MOD2C: /home/jhielson/neuron/nrn/bin  
-- Using mod2c submodule from /home/jhielson/neuron/nrn/bin
CMake Error at external/coreneuron/CMake/AddMod2cSubmodule.cmake:30 (add_subdirectory):
  The source directory

    /home/jhielson/neuron/nrn/external/coreneuron/external/mod2c

  does not contain a CMakeLists.txt file.
Call Stack (most recent call first):
  external/coreneuron/CMakeLists.txt:278 (include)

-- 
-- Configured CoreNEURON 0.21.0
-- 
-- Some things you can do now:
-- --------------------+--------------------------------------------------------
-- Command             |   Description
-- --------------------+--------------------------------------------------------
-- make install        | Will install CoreNEURON to: /home/jhielson/nvidia/nvhpc_2021_215_Linux_x86_64_cuda_11.3/install
-- make docs           | Build full docs. Calls targets: doxygen, sphinx
-- --------------------+--------------------------------------------------------
--  Build option       | Status
-- --------------------+--------------------------------------------------------
-- C COMPILER          | /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc
-- CXX COMPILER        | /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc++
-- COMPILE FLAGS       | -O3 -g -acc -gpu=cuda11.3,cc60,cc70 --diag_suppress 161,177,550 -mp   -g  -O2  --c++14
-- Build Type          | STATIC
-- MPI                 | ON
--   INC               | /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/include
-- OpenMP              | ON
-- Use legacy units    | OFF
-- NMODL               | OFF
-- MOD2CPP PATH        | /home/jhielson/neuron/nrn/build/bin/mod2c_core
-- GPU Support         | ON
--   CUDA              | /usr/local/cuda-11.3
--   Unified Memory    | OFF
--   HOST COMPILER     | /usr/bin/gcc
-- Auto Timeout        | ON
-- Wrap exp()          | OFF
-- SplayTree Queue     | ON
-- NetReceive Buffer   | ON
-- Caliper             | OFF
-- Likwid              | OFF
-- Unit Tests          | OFF
-- Reporting           | OFF
-- --------------+--------------------------------------------------------------
--  See documentation : https://github.com/BlueBrain/CoreNeuron/
-- --------------+--------------------------------------------------------------
-- 
NOTICEUsing Target in compiling and linking, you should take care of it if
                    it fail miserabily (CODE: 1234567890)
-- 
-- Configured NEURON 8.0
-- 
-- You can now build NEURON using:
--   cmake --build . [--target TARGET] -- -j 8
-- You might want to adjust the number of parallel build jobs for your system.
-- Some non-default targets you might want to build:
-- --------------+--------------------------------------------------------------
--  Target       |   Description
-- --------------+--------------------------------------------------------------
-- install       | Will install NEURON to: /home/jhielson/nvidia/nvhpc_2021_215_Linux_x86_64_cuda_11.3/install
--               | Change the install location of NEURON using:
--               |   cmake <src_path> -DCMAKE_INSTALL_PREFIX=<install_path>
-- docs          | Build full docs. Calls targets: doxygen, notebooks, sphinx
-- uninstall     | Removes files installed by make install (todo)
-- --------------+--------------------------------------------------------------
--  Build option | Status
-- --------------+--------------------------------------------------------------
-- C COMPILER    | /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc
-- CXX COMPILER  | /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc++
-- BUILD_TYPE    | RelWithDebInfo (allowed: Custom;Debug;Release;RelWithDebInfo;Fast)
-- COMPILE FLAGS | -g  -O2 
-- Shared        | ON
-- Default units | modern units (2019 nist constants)
-- MPI           | ON
--   INC         | /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/include
--   LIB         | /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/lib/libmpi_cxx.so
--   DYNAMIC     | OFF
-- Python        | ON
--   EXE         | /usr/bin/python3.6
--   INC         | /usr/include/python3.6m
--   LIB         | /usr/lib/x86_64-linux-gnu/libpython3.6m.so
--   MODULE      | ON
--   DYNAMIC     | OFF
-- Readline      | /usr/lib/x86_64-linux-gnu/libreadline.so
-- Curses        | /usr/lib/x86_64-linux-gnu/libcurses.so;/usr/lib/x86_64-linux-gnu/libform.so
-- RX3D          | OFF
-- Interviews    | OFF
-- CoreNEURON    | ON
--   PATH        | /home/jhielson/neuron/nrn/external/coreneuron
--   LINK FLAGS  | -acc -gpu=cuda11.3,cc60,cc70 -rdynamic -lrt -Wl,--whole-archive -Lx86_64 -lcorenrnmech -L/home/jhielson/nvidia/nvhpc_2021_215_Linux_x86_64_cuda_11.3/install/lib -lcoreneuron -lcudacoreneuron -Wl,--no-whole-archive /usr/local/cuda-11.3/lib64/libcudart_static.a
--   Legacy Units| OFF
-- --------------+--------------------------------------------------------------
--  See documentation : https://www.neuron.yale.edu/neuron/
-- --------------+--------------------------------------------------------------
-- 
-- Configuring incomplete, errors occurred!
See also "/home/jhielson/neuron/nrn/build/CMakeFiles/CMakeOutput.log".
See also "/home/jhielson/neuron/nrn/build/CMakeFiles/CMakeError.log".
olupton commented 3 years ago

Sorry, I forgot an option for updating manually: git submodule update --init --recursive from the top level should do it.

jhielson commented 3 years ago

Thanks. It works. When I run make install I get the following error:

Install the project...
-- Install configuration: "RelWithDebInfo"
-- Installing: /home/jhielson/nvidia/nvhpc_2021_215_Linux_x86_64_cuda_11.3/install/share/nrn/lib
CMake Error at cmake_install.cmake:49 (file):
  file INSTALL cannot make directory
  "/home/jhielson/nvidia/nvhpc_2021_215_Linux_x86_64_cuda_11.3/install/share/nrn/lib":
  Not a directory

Makefile:139: recipe for target 'install' failed
make: *** [install] Error 1

The directory "share/nrn/lib/" can be found at /usr/share/nrn/lib/hoc/...

Should I change my cmake flag from

 -DCMAKE_INSTALL_PREFIX=$HOME/nvidia/nvhpc_2021_215_Linux_x86_64_cuda_11.3/install

to

 -DCMAKE_INSTALL_PREFIX=$/usr
jhielson commented 3 years ago

Hi,

After changing my cmake command to

cmake .. -DNRN_ENABLE_CORENEURON=ON -DCORENRN_ENABLE_GPU=ON -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_RX3D=OFF -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_C_COMPILER=nvc -DCMAKE_CXX_COMPILER=nvc++ -DCMAKE_LIBRARY_ARCHITECTURE="x86_64-linux-gnu" -DCMAKE_CXX_FLAGS="-O3 -g"  -DCMAKE_C_FLAGS="-O3 -g"

I could install the package (output bellow). But python does not recognize neuron (ModuleNotFoundError: No module named 'neuron' ).

[  4%] Built target mod2c_core
[  5%] Built target cudacoreneuron
[  7%] Built target coreneuron-copy-nrnivmodl-core-dependencies
[  7%] Built target nrnivmodl-core
[  7%] Built target kin_deriv_header
[ 17%] Built target coreneuron
[ 18%] Built target scopmath
[ 20%] Built target nrniv-core
[ 24%] Built target nocmodl
[ 27%] Built target modlunit
[ 27%] Built target nrnversion_h
[ 28%] Generating help_data.dat
[ 28%] Built target help_data_dat
[ 28%] Update hh.mod for CoreNEURON compatibility
[ 28%] Built target hh_update
[ 98%] Built target nrniv_lib
[100%] Built target nrniv
Building python module with: /usr/bin/python3.6
[100%] Built target hoc_module
[100%] Built target rxdmath
Install the project...
-- Install configuration: "RelWithDebInfo"
-- Up-to-date: /usr/share/nrn/lib
-- Installing: /usr/share/nrn/lib/helpdict
-- Installing: /usr/share/nrn/lib/hocload.sh
-- Installing: /usr/share/nrn/lib/shape.cm1
-- Up-to-date: /usr/share/nrn/lib/hoc
-- Installing: /usr/share/nrn/lib/hoc/electrod.hoc
-- Installing: /usr/share/nrn/lib/hoc/varmeth1.hoc
-- Installing: /usr/share/nrn/lib/hoc/impedanc.hoc
-- Installing: /usr/share/nrn/lib/hoc/single1.hoc
-- Installing: /usr/share/nrn/lib/hoc/showmech.hoc
-- Installing: /usr/share/nrn/lib/hoc/stdlib.hoc
-- Installing: /usr/share/nrn/lib/hoc/import3d.hoc
-- Installing: /usr/share/nrn/lib/hoc/movierun.hoc
-- Installing: /usr/share/nrn/lib/hoc/shapebox.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/celbild
-- Installing: /usr/share/nrn/lib/hoc/celbild/celmemb.hoc
-- Installing: /usr/share/nrn/lib/hoc/celbild/inhomofn.hoc
-- Installing: /usr/share/nrn/lib/hoc/celbild/celbild1.hoc
-- Installing: /usr/share/nrn/lib/hoc/celbild/celtopol.hoc
-- Installing: /usr/share/nrn/lib/hoc/celbild/celgeom.hoc
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-- Installing: /usr/share/nrn/lib/hoc/stdrun.hoc
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-- Installing: /usr/share/nrn/lib/hoc/stdgui.hoc
-- Installing: /usr/share/nrn/lib/hoc/mulfit.hoc
-- Installing: /usr/share/nrn/lib/hoc/pointgrp.hoc
-- Installing: /usr/share/nrn/lib/hoc/nrngui1.hoc
-- Installing: /usr/share/nrn/lib/hoc/impedanx.hoc
-- Installing: /usr/share/nrn/lib/hoc/prcellstate.hoc
-- Installing: /usr/share/nrn/lib/hoc/chanbild.hoc
-- Installing: /usr/share/nrn/lib/hoc/mknrndll.hoc
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-- Installing: /usr/share/nrn/lib/hoc/nrngui.hoc
-- Installing: /usr/share/nrn/lib/hoc/vecwrap.hoc
-- Installing: /usr/share/nrn/lib/hoc/kinbuild.hoc
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-- Installing: /usr/share/nrn/lib/hoc/lincir.hoc
-- Installing: /usr/share/nrn/lib/hoc/modlunit.hoc
-- Installing: /usr/share/nrn/lib/hoc/attshape.hoc
-- Installing: /usr/share/nrn/lib/hoc/netbild.hoc
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-- Up-to-date: /usr/share/nrn/lib/hoc/lincir
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-- Installing: /usr/share/nrn/lib/hoc/lincir/elmbase.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/mview
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-- Installing: /usr/share/nrn/lib/hoc/mview/mviewxml.hoc
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-- Installing: /usr/share/nrn/lib/hoc/mview/realcell.hoc
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-- Installing: /usr/share/nrn/lib/hoc/mview/ncview.hoc
-- Installing: /usr/share/nrn/lib/hoc/mview/ppanal.hoc
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-- Installing: /usr/share/nrn/lib/hoc/mview/treeview.hoc
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-- Installing: /usr/share/nrn/lib/hoc/mview/secanal.hoc
-- Installing: /usr/share/nrn/lib/hoc/mview/allpp.hoc
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-- Installing: /usr/share/nrn/lib/hoc/mview/artview.hoc
-- Installing: /usr/share/nrn/lib/hoc/mview/rcclasses.hoc
-- Installing: /usr/share/nrn/lib/hoc/mview/distinct.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/chanbild
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-- Installing: /usr/share/nrn/lib/hoc/chanbild/const.hoc
-- Installing: /usr/share/nrn/lib/hoc/chanbild/gategui.hoc
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-- Installing: /usr/share/nrn/lib/hoc/chanbild/exp.hoc
-- Installing: /usr/share/nrn/lib/hoc/chanbild/kstgui.hoc
-- Installing: /usr/share/nrn/lib/hoc/chanbild/sigmoid.hoc
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-- Installing: /usr/share/nrn/lib/hoc/chanbild/table.hoc
-- Installing: /usr/share/nrn/lib/hoc/corenrn.hoc
-- Installing: /usr/share/nrn/lib/hoc/pcchdir.hoc
-- Installing: /usr/share/nrn/lib/hoc/vplay.hoc
-- Installing: /usr/share/nrn/lib/hoc/loadbal.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/import3d
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-- Installing: /usr/share/nrn/lib/hoc/import3d/import3d_gui.hoc
-- Installing: /usr/share/nrn/lib/hoc/import3d/import3d_sec.hoc
-- Installing: /usr/share/nrn/lib/hoc/import3d/read_nts.hoc
-- Installing: /usr/share/nrn/lib/hoc/atoltool.hoc
-- Installing: /usr/share/nrn/lib/hoc/parcom.hoc
-- Installing: /usr/share/nrn/lib/hoc/celbild.hoc
-- Installing: /usr/share/nrn/lib/hoc/single.hoc
-- Installing: /usr/share/nrn/lib/hoc/mkcurve.hoc
-- Installing: /usr/share/nrn/lib/hoc/logax.hoc
-- Installing: /usr/share/nrn/lib/hoc/singlech.hoc
-- Installing: /usr/share/nrn/lib/hoc/impratio.hoc
-- Installing: /usr/share/nrn/lib/hoc/family.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/netbild
-- Installing: /usr/share/nrn/lib/hoc/netbild/spkplot.hoc
-- Installing: /usr/share/nrn/lib/hoc/netbild/edgegui.hoc
-- Installing: /usr/share/nrn/lib/hoc/netbild/netdata.hoc
-- Installing: /usr/share/nrn/lib/hoc/netbild/artcel.hoc
-- Installing: /usr/share/nrn/lib/hoc/netbild/syntypes.hoc
-- Installing: /usr/share/nrn/lib/hoc/netbild/netgui.hoc
-- Installing: /usr/share/nrn/lib/hoc/netbild/grstrlst.hoc
-- Installing: /usr/share/nrn/lib/hoc/netbild/netready.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/mulfit
-- Installing: /usr/share/nrn/lib/hoc/mulfit/fitparm.hoc
-- Installing: /usr/share/nrn/lib/hoc/mulfit/eonerun.hoc
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-- Installing: /usr/share/nrn/lib/hoc/mulfit/e_norm.hoc
-- Installing: /usr/share/nrn/lib/hoc/mulfit/eparmlst.hoc
-- Installing: /usr/share/nrn/lib/hoc/mulfit/e_actpot.hoc
-- Installing: /usr/share/nrn/lib/hoc/mulfit/e_xy.hoc
-- Installing: /usr/share/nrn/lib/hoc/mulfit/eoneprim.hoc
-- Installing: /usr/share/nrn/lib/hoc/mulfit/mulfit1.hoc
-- Installing: /usr/share/nrn/lib/hoc/mulfit/clampfit.hoc
-- Installing: /usr/share/nrn/lib/hoc/mulfit/eonefunc.hoc
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-- Installing: /usr/share/nrn/lib/hoc/mulfit/protorun.hoc
-- Installing: /usr/share/nrn/lib/nrnunits.lib.in
-- Up-to-date: /usr/share/nrn/lib/auditscripts
-- Installing: /usr/share/nrn/lib/auditscripts/saveaudit
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-- Installing: /usr/share/nrn/lib/auditscripts/notes
-- Installing: /usr/share/nrn/lib/auditscripts/hocaudit.sh
-- Installing: /usr/share/nrn/lib/auditscripts/gettarname
-- Installing: /usr/share/nrn/lib/shape.cm2
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-- Installing: /usr/share/nrn/lib/prologue.id
-- Installing: /usr/share/nrn/lib/nrn.defaults.in
-- Up-to-date: /usr/share/nrn/demo
-- Installing: /usr/share/nrn/demo/hh.hoc
-- Installing: /usr/share/nrn/demo/reconst.hoc
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-- Installing: /usr/share/nrn/demo/nomodel.hoc
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-- Up-to-date: /usr/share/nrn/demo/sync
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-- Up-to-date: /usr/share/nrn/demo/release
-- Installing: /usr/share/nrn/demo/release/invlfire.mod
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-- Installing: /usr/share/nrn/demo/release/camchan.mod
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-- Installing: /usr/share/nrn/demo/release/mcna.mod
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-- Installing: /usr/share/nrn/demo/demo.hoc
-- Up-to-date: /usr/share/nrn/demo/dend3
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-- Installing: /usr/share/nrn/demo/dend3.ses
-- Installing: /usr/share/nrn/lib/nrnunits.lib
-- Installing: /usr/share/nrn/lib/nrn.defaults
-- Up-to-date: /usr/share/nrn/lib/cleanup
-- Up-to-date: /usr/include
-- Installing: /usr/include/nrnisaac.h
-- Installing: /usr/include/nrncvode
-- Installing: /usr/include/nrncvode/nrnneosm.h
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-- Installing: /usr/include/nrnconf.h
-- Installing: /usr/include/ivstream.h
-- Installing: /usr/include/nrnoc_ml.h
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-- Installing: /usr/include/nrnran123.h
-- Installing: /usr/include/multicore.h
-- Installing: /usr/include/cspredef.h
-- Installing: /usr/include/nrniv_mf.h
-- Installing: /usr/include/nrnjava.h
-- Installing: /usr/include/nrnmpiuse.h
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-- Installing: /usr/include/Random123/ReinterpretCtr.hpp
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-- Installing: /usr/include/Random123/boxmuller.hpp
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-- Installing: /usr/include/Random123/conventional/Engine.hpp
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-- Installing: /usr/include/Random123/features/sse.h
-- Installing: /usr/include/Random123/features/msvcfeatures.h
-- Installing: /usr/include/Random123/features/pgccfeatures.h
-- Installing: /usr/include/coreneuron
-- Installing: /usr/include/coreneuron/membrane_definitions.h
-- Installing: /usr/include/coreneuron/mpi
-- Installing: /usr/include/coreneuron/mpi/nrnmpi_def_cinc.h
-- Installing: /usr/include/coreneuron/mpi/mpispike.hpp
-- Installing: /usr/include/coreneuron/mpi/nrnmpiuse.h
-- Installing: /usr/include/coreneuron/mpi/nrnmpi.h
-- Installing: /usr/include/coreneuron/mpi/nrnmpidec.h
-- Installing: /usr/include/coreneuron/mpi/nrnmpi_impl.h
-- Installing: /usr/include/coreneuron/apps
-- Installing: /usr/include/coreneuron/apps/corenrn_parameters.hpp
-- Installing: /usr/include/coreneuron/nrnconf.h
-- Installing: /usr/include/coreneuron/sim
-- Installing: /usr/include/coreneuron/sim/fast_imem.hpp
-- Installing: /usr/include/coreneuron/sim/multicore.hpp
-- Installing: /usr/include/coreneuron/sim/scopmath
-- Installing: /usr/include/coreneuron/sim/scopmath/errcodes.h
-- Installing: /usr/include/coreneuron/sim/scopmath/newton_struct.h
-- Installing: /usr/include/coreneuron/mechanism
-- Installing: /usr/include/coreneuron/mechanism/mech_mapping.hpp
-- Installing: /usr/include/coreneuron/mechanism/register_mech.hpp
-- Installing: /usr/include/coreneuron/mechanism/eion.hpp
-- Installing: /usr/include/coreneuron/mechanism/mech
-- Installing: /usr/include/coreneuron/mechanism/mech/cfile
-- Installing: /usr/include/coreneuron/mechanism/mech/cfile/scoplib.h
-- Installing: /usr/include/coreneuron/mechanism/mech/cfile/cabvars.h
-- Installing: /usr/include/coreneuron/mechanism/mech/mod2c_core_thread.hpp
-- Installing: /usr/include/coreneuron/mechanism/mechanism.hpp
-- Installing: /usr/include/coreneuron/mechanism/nrnoc_ml.ispc
-- Installing: /usr/include/coreneuron/mechanism/membfunc.hpp
-- Installing: /usr/include/coreneuron/utils
-- Installing: /usr/include/coreneuron/utils/ivocvect.hpp
-- Installing: /usr/include/coreneuron/utils/nrnmutdec.h
-- Installing: /usr/include/coreneuron/utils/progressbar
-- Installing: /usr/include/coreneuron/utils/progressbar/progressbar.h
-- Installing: /usr/include/coreneuron/utils/vrecitem.h
-- Installing: /usr/include/coreneuron/utils/memory.h
-- Installing: /usr/include/coreneuron/utils/lpt.hpp
-- Installing: /usr/include/coreneuron/utils/string_utils.h
-- Installing: /usr/include/coreneuron/utils/nrnoc_aux.hpp
-- Installing: /usr/include/coreneuron/utils/randoms
-- Installing: /usr/include/coreneuron/utils/randoms/nrnran123.h
-- Installing: /usr/include/coreneuron/utils/nrn_assert.h
-- Installing: /usr/include/coreneuron/utils/profile
-- Installing: /usr/include/coreneuron/utils/profile/cuda_profile.h
-- Installing: /usr/include/coreneuron/utils/profile/profiler_interface.h
-- Installing: /usr/include/coreneuron/utils/memory_utils.h
-- Installing: /usr/include/coreneuron/utils/nrn_stats.h
-- Installing: /usr/include/coreneuron/network
-- Installing: /usr/include/coreneuron/network/have2want.h
-- Installing: /usr/include/coreneuron/network/partrans.hpp
-- Installing: /usr/include/coreneuron/network/tqueue.hpp
-- Installing: /usr/include/coreneuron/network/tnode.hpp
-- Installing: /usr/include/coreneuron/network/netpar.hpp
-- Installing: /usr/include/coreneuron/network/netcvode.hpp
-- Installing: /usr/include/coreneuron/network/netcon.hpp
-- Installing: /usr/include/coreneuron/network/multisend.hpp
-- Installing: /usr/include/coreneuron/nrnoc
-- Installing: /usr/include/coreneuron/nrnoc/md1redef.h
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-- Installing: /usr/include/coreneuron/nrnoc/md2redef.h
-- Installing: /usr/include/coreneuron/config
-- Installing: /usr/include/coreneuron/config/config.h
-- Installing: /usr/include/coreneuron/engine.h
-- Installing: /usr/include/coreneuron/io
-- Installing: /usr/include/coreneuron/io/core2nrn_data_return.hpp
-- Installing: /usr/include/coreneuron/io/lfp.hpp
-- Installing: /usr/include/coreneuron/io/file_utils.hpp
-- Installing: /usr/include/coreneuron/io/phase2.hpp
-- Installing: /usr/include/coreneuron/io/setup_fornetcon.hpp
-- Installing: /usr/include/coreneuron/io/prcellstate.hpp
-- Installing: /usr/include/coreneuron/io/nrn_setup.hpp
-- Installing: /usr/include/coreneuron/io/user_params.hpp
-- Installing: /usr/include/coreneuron/io/mech_report.h
-- Installing: /usr/include/coreneuron/io/nrnsection_mapping.hpp
-- Installing: /usr/include/coreneuron/io/mem_layout_util.hpp
-- Installing: /usr/include/coreneuron/io/reports
-- Installing: /usr/include/coreneuron/io/reports/report_handler.hpp
-- Installing: /usr/include/coreneuron/io/reports/report_event.hpp
-- Installing: /usr/include/coreneuron/io/reports/binary_report_handler.hpp
-- Installing: /usr/include/coreneuron/io/reports/sonata_report_handler.hpp
-- Installing: /usr/include/coreneuron/io/reports/nrnreport.hpp
-- Installing: /usr/include/coreneuron/io/nrn2core_direct.h
-- Installing: /usr/include/coreneuron/io/nrn_filehandler.hpp
-- Installing: /usr/include/coreneuron/io/output_spikes.hpp
-- Installing: /usr/include/coreneuron/io/nrn_checkpoint.hpp
-- Installing: /usr/include/coreneuron/io/phase1.hpp
-- Installing: /usr/include/coreneuron/permute
-- Installing: /usr/include/coreneuron/permute/node_permute.h
-- Installing: /usr/include/coreneuron/permute/cellorder.hpp
-- Installing: /usr/include/coreneuron/permute/data_layout.hpp
-- Installing: /usr/include/coreneuron/gpu
-- Installing: /usr/include/coreneuron/gpu/nrn_acc_manager.hpp
-- Installing: /usr/include/coreneuron/coreneuron.hpp
-- Installing: /usr/include/coreneuron/nrniv
-- Installing: /usr/include/coreneuron/nrniv/profiler_interface.h
-- Installing: /usr/include/coreneuron/nrniv/nrniv_decl.h
-- Installing: /usr/include/nrnapi.h
-- Installing: /usr/include/spconfig.h
-- Installing: /usr/include/nrnassrt.h
-- Installing: /usr/include/scoplib.h
-- Installing: /usr/include/hoclist.h
-- Installing: /usr/include/nrnmpidec.h
-- Installing: /usr/include/scoplib_ansi.h
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-- Installing: /usr/include/md1redef.h
-- Installing: /usr/include/membfunc.h
-- Installing: /usr/include/hocassrt.h
-- Installing: /usr/include/hocdec.h
-- Installing: /usr/include/oc_ansi.h
-- Installing: /usr/include/nrnpthread.h
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-- Installing: /usr/include/options.h
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-- Installing: /usr/include/nrnredef.h
-- Installing: /usr/include/spmatrix.h
-- Installing: /usr/include/hoc_membf.h
-- Installing: /usr/include/membdef.h
-- Installing: /usr/include/nrn_ansi.h
-- Installing: /usr/include/md2redef.h
-- Installing: /usr/include/hocparse.h
-- Installing: /usr/include/section.h
-- Installing: /usr/include/nrnpy_hoc.h
-- Installing: /usr/include/cabvars.h
-- Installing: /usr/include/neuron.h
-- Installing: /usr/include/hocgetsym.h
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-- Installing: /usr/include/cspmatrix.h
-- Installing: /usr/include/hoc.h
-- Installing: /usr/share/cmake/coreneuron-config.cmake
-- Installing: /usr/share/cmake/coreneuron.cmake
-- Installing: /usr/share/cmake/coreneuron-relwithdebinfo.cmake
-- Installing: /usr/share/mod2c/nrnunits.lib
-- Installing: /usr/bin/mod2c_core
-- Installing: /usr/lib/libcoreneuron.a
-- Installing: /usr/lib/libcudacoreneuron.a
-- Installing: /usr/lib/libscopmath.a
-- Up-to-date: /usr/include//coreneuron
-- Up-to-date: /usr/include//coreneuron/membrane_definitions.h
-- Up-to-date: /usr/include//coreneuron/mpi
-- Up-to-date: /usr/include//coreneuron/mpi/nrnmpi_def_cinc.h
-- Up-to-date: /usr/include//coreneuron/mpi/mpispike.hpp
-- Up-to-date: /usr/include//coreneuron/mpi/nrnmpiuse.h
-- Up-to-date: /usr/include//coreneuron/mpi/nrnmpi.h
-- Up-to-date: /usr/include//coreneuron/mpi/nrnmpidec.h
-- Up-to-date: /usr/include//coreneuron/mpi/nrnmpi_impl.h
-- Up-to-date: /usr/include//coreneuron/apps
-- Up-to-date: /usr/include//coreneuron/apps/corenrn_parameters.hpp
-- Up-to-date: /usr/include//coreneuron/nrnconf.h
-- Up-to-date: /usr/include//coreneuron/sim
-- Up-to-date: /usr/include//coreneuron/sim/fast_imem.hpp
-- Up-to-date: /usr/include//coreneuron/sim/multicore.hpp
-- Up-to-date: /usr/include//coreneuron/sim/scopmath
-- Up-to-date: /usr/include//coreneuron/sim/scopmath/errcodes.h
-- Up-to-date: /usr/include//coreneuron/sim/scopmath/newton_struct.h
-- Up-to-date: /usr/include//coreneuron/mechanism
-- Up-to-date: /usr/include//coreneuron/mechanism/mech_mapping.hpp
-- Up-to-date: /usr/include//coreneuron/mechanism/register_mech.hpp
-- Up-to-date: /usr/include//coreneuron/mechanism/eion.hpp
-- Up-to-date: /usr/include//coreneuron/mechanism/mech
-- Up-to-date: /usr/include//coreneuron/mechanism/mech/cfile
-- Up-to-date: /usr/include//coreneuron/mechanism/mech/cfile/scoplib.h
-- Up-to-date: /usr/include//coreneuron/mechanism/mech/cfile/cabvars.h
-- Up-to-date: /usr/include//coreneuron/mechanism/mech/mod2c_core_thread.hpp
-- Up-to-date: /usr/include//coreneuron/mechanism/mechanism.hpp
-- Up-to-date: /usr/include//coreneuron/mechanism/nrnoc_ml.ispc
-- Up-to-date: /usr/include//coreneuron/mechanism/membfunc.hpp
-- Up-to-date: /usr/include//coreneuron/utils
-- Up-to-date: /usr/include//coreneuron/utils/ivocvect.hpp
-- Up-to-date: /usr/include//coreneuron/utils/nrnmutdec.h
-- Up-to-date: /usr/include//coreneuron/utils/progressbar
-- Up-to-date: /usr/include//coreneuron/utils/progressbar/progressbar.h
-- Up-to-date: /usr/include//coreneuron/utils/vrecitem.h
-- Up-to-date: /usr/include//coreneuron/utils/memory.h
-- Up-to-date: /usr/include//coreneuron/utils/lpt.hpp
-- Up-to-date: /usr/include//coreneuron/utils/string_utils.h
-- Up-to-date: /usr/include//coreneuron/utils/nrnoc_aux.hpp
-- Up-to-date: /usr/include//coreneuron/utils/randoms
-- Up-to-date: /usr/include//coreneuron/utils/randoms/nrnran123.h
-- Up-to-date: /usr/include//coreneuron/utils/nrn_assert.h
-- Up-to-date: /usr/include//coreneuron/utils/profile
-- Up-to-date: /usr/include//coreneuron/utils/profile/cuda_profile.h
-- Up-to-date: /usr/include//coreneuron/utils/profile/profiler_interface.h
-- Up-to-date: /usr/include//coreneuron/utils/memory_utils.h
-- Up-to-date: /usr/include//coreneuron/utils/nrn_stats.h
-- Up-to-date: /usr/include//coreneuron/network
-- Up-to-date: /usr/include//coreneuron/network/have2want.h
-- Up-to-date: /usr/include//coreneuron/network/partrans.hpp
-- Up-to-date: /usr/include//coreneuron/network/tqueue.hpp
-- Up-to-date: /usr/include//coreneuron/network/tnode.hpp
-- Up-to-date: /usr/include//coreneuron/network/netpar.hpp
-- Up-to-date: /usr/include//coreneuron/network/netcvode.hpp
-- Up-to-date: /usr/include//coreneuron/network/netcon.hpp
-- Up-to-date: /usr/include//coreneuron/network/multisend.hpp
-- Up-to-date: /usr/include//coreneuron/nrnoc
-- Up-to-date: /usr/include//coreneuron/nrnoc/md1redef.h
-- Up-to-date: /usr/include//coreneuron/nrnoc/nrnunits_modern.h
-- Up-to-date: /usr/include//coreneuron/nrnoc/md2redef.h
-- Up-to-date: /usr/include//coreneuron/config
-- Up-to-date: /usr/include//coreneuron/config/config.h
-- Up-to-date: /usr/include//coreneuron/engine.h
-- Up-to-date: /usr/include//coreneuron/io
-- Up-to-date: /usr/include//coreneuron/io/core2nrn_data_return.hpp
-- Up-to-date: /usr/include//coreneuron/io/lfp.hpp
-- Up-to-date: /usr/include//coreneuron/io/file_utils.hpp
-- Up-to-date: /usr/include//coreneuron/io/phase2.hpp
-- Up-to-date: /usr/include//coreneuron/io/setup_fornetcon.hpp
-- Up-to-date: /usr/include//coreneuron/io/prcellstate.hpp
-- Up-to-date: /usr/include//coreneuron/io/nrn_setup.hpp
-- Up-to-date: /usr/include//coreneuron/io/user_params.hpp
-- Up-to-date: /usr/include//coreneuron/io/mech_report.h
-- Up-to-date: /usr/include//coreneuron/io/nrnsection_mapping.hpp
-- Up-to-date: /usr/include//coreneuron/io/mem_layout_util.hpp
-- Up-to-date: /usr/include//coreneuron/io/reports
-- Up-to-date: /usr/include//coreneuron/io/reports/report_handler.hpp
-- Up-to-date: /usr/include//coreneuron/io/reports/report_event.hpp
-- Up-to-date: /usr/include//coreneuron/io/reports/binary_report_handler.hpp
-- Up-to-date: /usr/include//coreneuron/io/reports/sonata_report_handler.hpp
-- Up-to-date: /usr/include//coreneuron/io/reports/nrnreport.hpp
-- Up-to-date: /usr/include//coreneuron/io/nrn2core_direct.h
-- Up-to-date: /usr/include//coreneuron/io/nrn_filehandler.hpp
-- Up-to-date: /usr/include//coreneuron/io/output_spikes.hpp
-- Up-to-date: /usr/include//coreneuron/io/nrn_checkpoint.hpp
-- Up-to-date: /usr/include//coreneuron/io/phase1.hpp
-- Up-to-date: /usr/include//coreneuron/permute
-- Up-to-date: /usr/include//coreneuron/permute/node_permute.h
-- Up-to-date: /usr/include//coreneuron/permute/cellorder.hpp
-- Up-to-date: /usr/include//coreneuron/permute/data_layout.hpp
-- Up-to-date: /usr/include//coreneuron/gpu
-- Up-to-date: /usr/include//coreneuron/gpu/nrn_acc_manager.hpp
-- Up-to-date: /usr/include//coreneuron/coreneuron.hpp
-- Up-to-date: /usr/include//coreneuron/nrniv
-- Up-to-date: /usr/include//coreneuron/nrniv/profiler_interface.h
-- Up-to-date: /usr/include//coreneuron/nrniv/nrniv_decl.h
-- Installing: /usr/share/coreneuron/kinderiv.py
-- Installing: /usr/share/coreneuron/mod_func.c.pl
-- Installing: /usr/share/coreneuron/dimplic.cpp
-- Installing: /usr/share/coreneuron/enginemech.cpp
-- Up-to-date: /usr/bin/mod2c_core
-- Up-to-date: /usr/share/mod2c/nrnunits.lib
-- Installing: /usr/bin/nrniv-core
-- Installing: /usr/share/coreneuron/coreneuron.cpp
-- Up-to-date: /usr/include
-- Up-to-date: /usr/include/nrnisaac.h
-- Up-to-date: /usr/include/nrncvode
-- Up-to-date: /usr/include/nrncvode/nrnneosm.h
-- Up-to-date: /usr/include/ocfunc.h
-- Up-to-date: /usr/include/nrnconf.h
-- Up-to-date: /usr/include/ivstream.h
-- Up-to-date: /usr/include/nrnoc_ml.h
-- Up-to-date: /usr/include/nmodlmutex.h
-- Up-to-date: /usr/include/nrnran123.h
-- Up-to-date: /usr/include/multicore.h
-- Up-to-date: /usr/include/cspredef.h
-- Up-to-date: /usr/include/nrniv_mf.h
-- Up-to-date: /usr/include/nrnjava.h
-- Up-to-date: /usr/include/nrnmpiuse.h
-- Up-to-date: /usr/include/nrnmpi.h
-- Up-to-date: /usr/include/Random123
-- Up-to-date: /usr/include/Random123/aes.h
-- Up-to-date: /usr/include/Random123/u01fixedpt.h
-- Up-to-date: /usr/include/Random123/threefry.h
-- Up-to-date: /usr/include/Random123/ars.h
-- Up-to-date: /usr/include/Random123/philox.h
-- Up-to-date: /usr/include/Random123/ReinterpretCtr.hpp
-- Up-to-date: /usr/include/Random123/gsl_microrng.h
-- Up-to-date: /usr/include/Random123/boxmuller.hpp
-- Up-to-date: /usr/include/Random123/MicroURNG.hpp
-- Up-to-date: /usr/include/Random123/array.h
-- Up-to-date: /usr/include/Random123/uniform.hpp
-- Up-to-date: /usr/include/Random123/conventional
-- Up-to-date: /usr/include/Random123/conventional/Engine.hpp
-- Up-to-date: /usr/include/Random123/conventional/gsl_cbrng.h
-- Up-to-date: /usr/include/Random123/features
-- Up-to-date: /usr/include/Random123/features/xlcfeatures.h
-- Up-to-date: /usr/include/Random123/features/open64features.h
-- Up-to-date: /usr/include/Random123/features/clangfeatures.h
-- Up-to-date: /usr/include/Random123/features/nvccfeatures.h
-- Up-to-date: /usr/include/Random123/features/iccfeatures.h
-- Up-to-date: /usr/include/Random123/features/fujitsufeatures.h
-- Up-to-date: /usr/include/Random123/features/metalfeatures.h
-- Up-to-date: /usr/include/Random123/features/sunprofeatures.h
-- Up-to-date: /usr/include/Random123/features/gccfeatures.h
-- Up-to-date: /usr/include/Random123/features/compilerfeatures.h
-- Up-to-date: /usr/include/Random123/features/crayfeatures.h
-- Up-to-date: /usr/include/Random123/features/openclfeatures.h
-- Up-to-date: /usr/include/Random123/features/sse.h
-- Up-to-date: /usr/include/Random123/features/msvcfeatures.h
-- Up-to-date: /usr/include/Random123/features/pgccfeatures.h
-- Up-to-date: /usr/include/coreneuron
-- Up-to-date: /usr/include/coreneuron/membrane_definitions.h
-- Up-to-date: /usr/include/coreneuron/mpi
-- Up-to-date: /usr/include/coreneuron/mpi/nrnmpi_def_cinc.h
-- Up-to-date: /usr/include/coreneuron/mpi/mpispike.hpp
-- Up-to-date: /usr/include/coreneuron/mpi/nrnmpiuse.h
-- Up-to-date: /usr/include/coreneuron/mpi/nrnmpi.h
-- Up-to-date: /usr/include/coreneuron/mpi/nrnmpidec.h
-- Up-to-date: /usr/include/coreneuron/mpi/nrnmpi_impl.h
-- Up-to-date: /usr/include/coreneuron/apps
-- Up-to-date: /usr/include/coreneuron/apps/corenrn_parameters.hpp
-- Up-to-date: /usr/include/coreneuron/nrnconf.h
-- Up-to-date: /usr/include/coreneuron/sim
-- Up-to-date: /usr/include/coreneuron/sim/fast_imem.hpp
-- Up-to-date: /usr/include/coreneuron/sim/multicore.hpp
-- Up-to-date: /usr/include/coreneuron/sim/scopmath
-- Up-to-date: /usr/include/coreneuron/sim/scopmath/errcodes.h
-- Up-to-date: /usr/include/coreneuron/sim/scopmath/newton_struct.h
-- Up-to-date: /usr/include/coreneuron/mechanism
-- Up-to-date: /usr/include/coreneuron/mechanism/mech_mapping.hpp
-- Up-to-date: /usr/include/coreneuron/mechanism/register_mech.hpp
-- Up-to-date: /usr/include/coreneuron/mechanism/eion.hpp
-- Up-to-date: /usr/include/coreneuron/mechanism/mech
-- Up-to-date: /usr/include/coreneuron/mechanism/mech/cfile
-- Up-to-date: /usr/include/coreneuron/mechanism/mech/cfile/scoplib.h
-- Up-to-date: /usr/include/coreneuron/mechanism/mech/cfile/cabvars.h
-- Up-to-date: /usr/include/coreneuron/mechanism/mech/mod2c_core_thread.hpp
-- Up-to-date: /usr/include/coreneuron/mechanism/mechanism.hpp
-- Up-to-date: /usr/include/coreneuron/mechanism/nrnoc_ml.ispc
-- Up-to-date: /usr/include/coreneuron/mechanism/membfunc.hpp
-- Up-to-date: /usr/include/coreneuron/utils
-- Up-to-date: /usr/include/coreneuron/utils/ivocvect.hpp
-- Up-to-date: /usr/include/coreneuron/utils/nrnmutdec.h
-- Up-to-date: /usr/include/coreneuron/utils/progressbar
-- Up-to-date: /usr/include/coreneuron/utils/progressbar/progressbar.h
-- Up-to-date: /usr/include/coreneuron/utils/vrecitem.h
-- Up-to-date: /usr/include/coreneuron/utils/memory.h
-- Up-to-date: /usr/include/coreneuron/utils/lpt.hpp
-- Up-to-date: /usr/include/coreneuron/utils/string_utils.h
-- Up-to-date: /usr/include/coreneuron/utils/nrnoc_aux.hpp
-- Up-to-date: /usr/include/coreneuron/utils/randoms
-- Up-to-date: /usr/include/coreneuron/utils/randoms/nrnran123.h
-- Up-to-date: /usr/include/coreneuron/utils/nrn_assert.h
-- Up-to-date: /usr/include/coreneuron/utils/profile
-- Up-to-date: /usr/include/coreneuron/utils/profile/cuda_profile.h
-- Up-to-date: /usr/include/coreneuron/utils/profile/profiler_interface.h
-- Up-to-date: /usr/include/coreneuron/utils/memory_utils.h
-- Up-to-date: /usr/include/coreneuron/utils/nrn_stats.h
-- Up-to-date: /usr/include/coreneuron/network
-- Up-to-date: /usr/include/coreneuron/network/have2want.h
-- Up-to-date: /usr/include/coreneuron/network/partrans.hpp
-- Up-to-date: /usr/include/coreneuron/network/tqueue.hpp
-- Up-to-date: /usr/include/coreneuron/network/tnode.hpp
-- Up-to-date: /usr/include/coreneuron/network/netpar.hpp
-- Up-to-date: /usr/include/coreneuron/network/netcvode.hpp
-- Up-to-date: /usr/include/coreneuron/network/netcon.hpp
-- Up-to-date: /usr/include/coreneuron/network/multisend.hpp
-- Up-to-date: /usr/include/coreneuron/nrnoc
-- Up-to-date: /usr/include/coreneuron/nrnoc/md1redef.h
-- Up-to-date: /usr/include/coreneuron/nrnoc/nrnunits_modern.h
-- Up-to-date: /usr/include/coreneuron/nrnoc/md2redef.h
-- Up-to-date: /usr/include/coreneuron/config
-- Up-to-date: /usr/include/coreneuron/config/config.h
-- Up-to-date: /usr/include/coreneuron/engine.h
-- Up-to-date: /usr/include/coreneuron/io
-- Up-to-date: /usr/include/coreneuron/io/core2nrn_data_return.hpp
-- Up-to-date: /usr/include/coreneuron/io/lfp.hpp
-- Up-to-date: /usr/include/coreneuron/io/file_utils.hpp
-- Up-to-date: /usr/include/coreneuron/io/phase2.hpp
-- Up-to-date: /usr/include/coreneuron/io/setup_fornetcon.hpp
-- Up-to-date: /usr/include/coreneuron/io/prcellstate.hpp
-- Up-to-date: /usr/include/coreneuron/io/nrn_setup.hpp
-- Up-to-date: /usr/include/coreneuron/io/user_params.hpp
-- Up-to-date: /usr/include/coreneuron/io/mech_report.h
-- Up-to-date: /usr/include/coreneuron/io/nrnsection_mapping.hpp
-- Up-to-date: /usr/include/coreneuron/io/mem_layout_util.hpp
-- Up-to-date: /usr/include/coreneuron/io/reports
-- Up-to-date: /usr/include/coreneuron/io/reports/report_handler.hpp
-- Up-to-date: /usr/include/coreneuron/io/reports/report_event.hpp
-- Up-to-date: /usr/include/coreneuron/io/reports/binary_report_handler.hpp
-- Up-to-date: /usr/include/coreneuron/io/reports/sonata_report_handler.hpp
-- Up-to-date: /usr/include/coreneuron/io/reports/nrnreport.hpp
-- Up-to-date: /usr/include/coreneuron/io/nrn2core_direct.h
-- Up-to-date: /usr/include/coreneuron/io/nrn_filehandler.hpp
-- Up-to-date: /usr/include/coreneuron/io/output_spikes.hpp
-- Up-to-date: /usr/include/coreneuron/io/nrn_checkpoint.hpp
-- Up-to-date: /usr/include/coreneuron/io/phase1.hpp
-- Up-to-date: /usr/include/coreneuron/permute
-- Up-to-date: /usr/include/coreneuron/permute/node_permute.h
-- Up-to-date: /usr/include/coreneuron/permute/cellorder.hpp
-- Up-to-date: /usr/include/coreneuron/permute/data_layout.hpp
-- Up-to-date: /usr/include/coreneuron/gpu
-- Up-to-date: /usr/include/coreneuron/gpu/nrn_acc_manager.hpp
-- Up-to-date: /usr/include/coreneuron/coreneuron.hpp
-- Up-to-date: /usr/include/coreneuron/nrniv
-- Up-to-date: /usr/include/coreneuron/nrniv/profiler_interface.h
-- Up-to-date: /usr/include/coreneuron/nrniv/nrniv_decl.h
-- Up-to-date: /usr/include/nrnapi.h
-- Up-to-date: /usr/include/spconfig.h
-- Up-to-date: /usr/include/nrnassrt.h
-- Up-to-date: /usr/include/scoplib.h
-- Up-to-date: /usr/include/hoclist.h
-- Up-to-date: /usr/include/nrnmpidec.h
-- Up-to-date: /usr/include/scoplib_ansi.h
-- Up-to-date: /usr/include/nrncvode.h
-- Up-to-date: /usr/include/md1redef.h
-- Up-to-date: /usr/include/membfunc.h
-- Up-to-date: /usr/include/hocassrt.h
-- Up-to-date: /usr/include/hocdec.h
-- Up-to-date: /usr/include/oc_ansi.h
-- Up-to-date: /usr/include/nrnpthread.h
-- Up-to-date: /usr/include/multisplit.h
-- Up-to-date: /usr/include/options.h
-- Up-to-date: /usr/include/ocmisc.h
-- Up-to-date: /usr/include/nrnredef.h
-- Up-to-date: /usr/include/spmatrix.h
-- Up-to-date: /usr/include/hoc_membf.h
-- Up-to-date: /usr/include/membdef.h
-- Up-to-date: /usr/include/nrn_ansi.h
-- Up-to-date: /usr/include/md2redef.h
-- Up-to-date: /usr/include/hocparse.h
-- Up-to-date: /usr/include/section.h
-- Up-to-date: /usr/include/nrnpy_hoc.h
-- Up-to-date: /usr/include/cabvars.h
-- Up-to-date: /usr/include/neuron.h
-- Up-to-date: /usr/include/hocgetsym.h
-- Up-to-date: /usr/include/isoc99.h
-- Up-to-date: /usr/include/cspmatrix.h
-- Up-to-date: /usr/include/hoc.h
-- Installing: /usr/share/modfile
-- Installing: /usr/share/modfile/svclmp.mod
-- Installing: /usr/share/modfile/pattern.mod
-- Installing: /usr/share/modfile/netstim.mod
-- Installing: /usr/share/modfile/passive.mod
-- Installing: /usr/share/modfile/exp2syn.mod
-- Installing: /usr/share/modfile/expsyn.mod
-- Installing: /usr/share/modfile/hh.mod
-- Installing: /usr/share/modfile/stim.mod
-- Installing: /usr/share/coreneuron/nrnivmodl_core_makefile
-- Installing: /usr/bin/nrnivmodl-core
-- Installing: /usr/bin/nrniv
-- Set runtime path of "/usr/bin/nrniv" to "/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/lib"
-- Installing: /usr/bin/nocmodl
-- Installing: /usr/bin/modlunit
-- Installing: /usr/lib/libnrniv.so
-- Set runtime path of "/usr/lib/libnrniv.so" to "/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/lib"
-- Installing: /usr/share/nrn/nrnmain.cpp
-- Up-to-date: /usr/include/nrnmpiuse.h
-- Up-to-date: /usr/include/nrncvode/nrnneosm.h
-- Up-to-date: /usr/include/nrnconf.h
-- Installing: /usr/bin/nrngui
-- Installing: /usr/bin/neurondemo
-- Installing: /usr/bin/nrnivmodl
-- Installing: /usr/bin/nrnmech_makefile
-- Installing: /usr/bin/nrnpyenv.sh
-- Installing: /usr/bin/sortspike
-- Installing: /usr/bin/mkthreadsafe
-- Up-to-date: /usr/bin/nrnpyenv.sh
-- Installing: /usr/bin/set_nrnpyenv.sh
-- Installing: /usr/lib/librxdmath.so
Installing python module using:
+ cd /home/jhielson/neuron/nrn/build/src/nrnpython
+ /usr/bin/python3.6 setup.py --quiet build --build-lib=/home/jhielson/neuron/nrn/build/lib/python install --prefix= --home=/usr
(base) jhielson@jhielson-Robotics:~/neuron/nrn/build$ python -c "from neuron import h; from neuron import coreneuron"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'neuron'
(base) jhielson@jhielson-Robotics:~/neuron/nrn/build$ python3 -c "from neuron import h; from neuron import coreneuron"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'neuron'
(base) jhielson@jhielson-Robotics:~/neuron/nrn/build$ python -c "from neuron import h; from neuron import coreneuron"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'neuron'
(base) jhielson@jhielson-Robotics:~/neuron/nrn/build$ sudo make install
[  4%] Built target mod2c_core
[  5%] Built target cudacoreneuron
[  7%] Built target coreneuron-copy-nrnivmodl-core-dependencies
[  7%] Built target nrnivmodl-core
[  7%] Built target kin_deriv_header
[ 17%] Built target coreneuron
[ 18%] Built target scopmath
[ 20%] Built target nrniv-core
[ 24%] Built target nocmodl
[ 27%] Built target modlunit
[ 27%] Built target nrnversion_h
[ 28%] Generating help_data.dat
[ 28%] Built target help_data_dat
[ 28%] Update hh.mod for CoreNEURON compatibility
[ 28%] Built target hh_update
[ 98%] Built target nrniv_lib
[100%] Built target nrniv
Building python module with: /usr/bin/python3.6
[100%] Built target hoc_module
[100%] Built target rxdmath
Install the project...
-- Install configuration: "RelWithDebInfo"
-- Up-to-date: /usr/share/nrn/lib
-- Up-to-date: /usr/share/nrn/lib/helpdict
-- Up-to-date: /usr/share/nrn/lib/hocload.sh
-- Up-to-date: /usr/share/nrn/lib/shape.cm1
-- Up-to-date: /usr/share/nrn/lib/hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/electrod.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/varmeth1.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/impedanc.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/single1.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/showmech.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/stdlib.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/import3d.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/movierun.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/shapebox.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/celbild
-- Up-to-date: /usr/share/nrn/lib/hoc/celbild/celmemb.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/celbild/inhomofn.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/celbild/celbild1.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/celbild/celtopol.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/celbild/celgeom.hoc
-- Up-to-date: /usr/share/nrn/lib/hoc/celbild/celmang.hoc
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-- Up-to-date: /usr/include/scoplib_ansi.h
-- Up-to-date: /usr/include/nrncvode.h
-- Up-to-date: /usr/include/md1redef.h
-- Up-to-date: /usr/include/membfunc.h
-- Up-to-date: /usr/include/hocassrt.h
-- Up-to-date: /usr/include/hocdec.h
-- Up-to-date: /usr/include/oc_ansi.h
-- Up-to-date: /usr/include/nrnpthread.h
-- Up-to-date: /usr/include/multisplit.h
-- Up-to-date: /usr/include/options.h
-- Up-to-date: /usr/include/ocmisc.h
-- Up-to-date: /usr/include/nrnredef.h
-- Up-to-date: /usr/include/spmatrix.h
-- Up-to-date: /usr/include/hoc_membf.h
-- Up-to-date: /usr/include/membdef.h
-- Up-to-date: /usr/include/nrn_ansi.h
-- Up-to-date: /usr/include/md2redef.h
-- Up-to-date: /usr/include/hocparse.h
-- Up-to-date: /usr/include/section.h
-- Up-to-date: /usr/include/nrnpy_hoc.h
-- Up-to-date: /usr/include/cabvars.h
-- Up-to-date: /usr/include/neuron.h
-- Up-to-date: /usr/include/hocgetsym.h
-- Up-to-date: /usr/include/isoc99.h
-- Up-to-date: /usr/include/cspmatrix.h
-- Up-to-date: /usr/include/hoc.h
-- Up-to-date: /usr/share/cmake/coreneuron-config.cmake
-- Up-to-date: /usr/share/cmake/coreneuron.cmake
-- Up-to-date: /usr/share/cmake/coreneuron-relwithdebinfo.cmake
-- Up-to-date: /usr/share/mod2c/nrnunits.lib
-- Installing: /usr/bin/mod2c_core
-- Up-to-date: /usr/lib/libcoreneuron.a
-- Up-to-date: /usr/lib/libcudacoreneuron.a
-- Up-to-date: /usr/lib/libscopmath.a
-- Up-to-date: /usr/include//coreneuron
-- Up-to-date: /usr/include//coreneuron/membrane_definitions.h
-- Up-to-date: /usr/include//coreneuron/mpi
-- Up-to-date: /usr/include//coreneuron/mpi/nrnmpi_def_cinc.h
-- Up-to-date: /usr/include//coreneuron/mpi/mpispike.hpp
-- Up-to-date: /usr/include//coreneuron/mpi/nrnmpiuse.h
-- Up-to-date: /usr/include//coreneuron/mpi/nrnmpi.h
-- Up-to-date: /usr/include//coreneuron/mpi/nrnmpidec.h
-- Up-to-date: /usr/include//coreneuron/mpi/nrnmpi_impl.h
-- Up-to-date: /usr/include//coreneuron/apps
-- Up-to-date: /usr/include//coreneuron/apps/corenrn_parameters.hpp
-- Up-to-date: /usr/include//coreneuron/nrnconf.h
-- Up-to-date: /usr/include//coreneuron/sim
-- Up-to-date: /usr/include//coreneuron/sim/fast_imem.hpp
-- Up-to-date: /usr/include//coreneuron/sim/multicore.hpp
-- Up-to-date: /usr/include//coreneuron/sim/scopmath
-- Up-to-date: /usr/include//coreneuron/sim/scopmath/errcodes.h
-- Up-to-date: /usr/include//coreneuron/sim/scopmath/newton_struct.h
-- Up-to-date: /usr/include//coreneuron/mechanism
-- Up-to-date: /usr/include//coreneuron/mechanism/mech_mapping.hpp
-- Up-to-date: /usr/include//coreneuron/mechanism/register_mech.hpp
-- Up-to-date: /usr/include//coreneuron/mechanism/eion.hpp
-- Up-to-date: /usr/include//coreneuron/mechanism/mech
-- Up-to-date: /usr/include//coreneuron/mechanism/mech/cfile
-- Up-to-date: /usr/include//coreneuron/mechanism/mech/cfile/scoplib.h
-- Up-to-date: /usr/include//coreneuron/mechanism/mech/cfile/cabvars.h
-- Up-to-date: /usr/include//coreneuron/mechanism/mech/mod2c_core_thread.hpp
-- Up-to-date: /usr/include//coreneuron/mechanism/mechanism.hpp
-- Up-to-date: /usr/include//coreneuron/mechanism/nrnoc_ml.ispc
-- Up-to-date: /usr/include//coreneuron/mechanism/membfunc.hpp
-- Up-to-date: /usr/include//coreneuron/utils
-- Up-to-date: /usr/include//coreneuron/utils/ivocvect.hpp
-- Up-to-date: /usr/include//coreneuron/utils/nrnmutdec.h
-- Up-to-date: /usr/include//coreneuron/utils/progressbar
-- Up-to-date: /usr/include//coreneuron/utils/progressbar/progressbar.h
-- Up-to-date: /usr/include//coreneuron/utils/vrecitem.h
-- Up-to-date: /usr/include//coreneuron/utils/memory.h
-- Up-to-date: /usr/include//coreneuron/utils/lpt.hpp
-- Up-to-date: /usr/include//coreneuron/utils/string_utils.h
-- Up-to-date: /usr/include//coreneuron/utils/nrnoc_aux.hpp
-- Up-to-date: /usr/include//coreneuron/utils/randoms
-- Up-to-date: /usr/include//coreneuron/utils/randoms/nrnran123.h
-- Up-to-date: /usr/include//coreneuron/utils/nrn_assert.h
-- Up-to-date: /usr/include//coreneuron/utils/profile
-- Up-to-date: /usr/include//coreneuron/utils/profile/cuda_profile.h
-- Up-to-date: /usr/include//coreneuron/utils/profile/profiler_interface.h
-- Up-to-date: /usr/include//coreneuron/utils/memory_utils.h
-- Up-to-date: /usr/include//coreneuron/utils/nrn_stats.h
-- Up-to-date: /usr/include//coreneuron/network
-- Up-to-date: /usr/include//coreneuron/network/have2want.h
-- Up-to-date: /usr/include//coreneuron/network/partrans.hpp
-- Up-to-date: /usr/include//coreneuron/network/tqueue.hpp
-- Up-to-date: /usr/include//coreneuron/network/tnode.hpp
-- Up-to-date: /usr/include//coreneuron/network/netpar.hpp
-- Up-to-date: /usr/include//coreneuron/network/netcvode.hpp
-- Up-to-date: /usr/include//coreneuron/network/netcon.hpp
-- Up-to-date: /usr/include//coreneuron/network/multisend.hpp
-- Up-to-date: /usr/include//coreneuron/nrnoc
-- Up-to-date: /usr/include//coreneuron/nrnoc/md1redef.h
-- Up-to-date: /usr/include//coreneuron/nrnoc/nrnunits_modern.h
-- Up-to-date: /usr/include//coreneuron/nrnoc/md2redef.h
-- Up-to-date: /usr/include//coreneuron/config
-- Up-to-date: /usr/include//coreneuron/config/config.h
-- Up-to-date: /usr/include//coreneuron/engine.h
-- Up-to-date: /usr/include//coreneuron/io
-- Up-to-date: /usr/include//coreneuron/io/core2nrn_data_return.hpp
-- Up-to-date: /usr/include//coreneuron/io/lfp.hpp
-- Up-to-date: /usr/include//coreneuron/io/file_utils.hpp
-- Up-to-date: /usr/include//coreneuron/io/phase2.hpp
-- Up-to-date: /usr/include//coreneuron/io/setup_fornetcon.hpp
-- Up-to-date: /usr/include//coreneuron/io/prcellstate.hpp
-- Up-to-date: /usr/include//coreneuron/io/nrn_setup.hpp
-- Up-to-date: /usr/include//coreneuron/io/user_params.hpp
-- Up-to-date: /usr/include//coreneuron/io/mech_report.h
-- Up-to-date: /usr/include//coreneuron/io/nrnsection_mapping.hpp
-- Up-to-date: /usr/include//coreneuron/io/mem_layout_util.hpp
-- Up-to-date: /usr/include//coreneuron/io/reports
-- Up-to-date: /usr/include//coreneuron/io/reports/report_handler.hpp
-- Up-to-date: /usr/include//coreneuron/io/reports/report_event.hpp
-- Up-to-date: /usr/include//coreneuron/io/reports/binary_report_handler.hpp
-- Up-to-date: /usr/include//coreneuron/io/reports/sonata_report_handler.hpp
-- Up-to-date: /usr/include//coreneuron/io/reports/nrnreport.hpp
-- Up-to-date: /usr/include//coreneuron/io/nrn2core_direct.h
-- Up-to-date: /usr/include//coreneuron/io/nrn_filehandler.hpp
-- Up-to-date: /usr/include//coreneuron/io/output_spikes.hpp
-- Up-to-date: /usr/include//coreneuron/io/nrn_checkpoint.hpp
-- Up-to-date: /usr/include//coreneuron/io/phase1.hpp
-- Up-to-date: /usr/include//coreneuron/permute
-- Up-to-date: /usr/include//coreneuron/permute/node_permute.h
-- Up-to-date: /usr/include//coreneuron/permute/cellorder.hpp
-- Up-to-date: /usr/include//coreneuron/permute/data_layout.hpp
-- Up-to-date: /usr/include//coreneuron/gpu
-- Up-to-date: /usr/include//coreneuron/gpu/nrn_acc_manager.hpp
-- Up-to-date: /usr/include//coreneuron/coreneuron.hpp
-- Up-to-date: /usr/include//coreneuron/nrniv
-- Up-to-date: /usr/include//coreneuron/nrniv/profiler_interface.h
-- Up-to-date: /usr/include//coreneuron/nrniv/nrniv_decl.h
-- Up-to-date: /usr/share/coreneuron/kinderiv.py
-- Up-to-date: /usr/share/coreneuron/mod_func.c.pl
-- Up-to-date: /usr/share/coreneuron/dimplic.cpp
-- Up-to-date: /usr/share/coreneuron/enginemech.cpp
-- Up-to-date: /usr/bin/mod2c_core
-- Up-to-date: /usr/share/mod2c/nrnunits.lib
-- Up-to-date: /usr/bin/nrniv-core
-- Up-to-date: /usr/share/coreneuron/coreneuron.cpp
-- Up-to-date: /usr/include
-- Up-to-date: /usr/include/nrnisaac.h
-- Up-to-date: /usr/include/nrncvode
-- Up-to-date: /usr/include/nrncvode/nrnneosm.h
-- Up-to-date: /usr/include/ocfunc.h
-- Up-to-date: /usr/include/nrnconf.h
-- Up-to-date: /usr/include/ivstream.h
-- Up-to-date: /usr/include/nrnoc_ml.h
-- Up-to-date: /usr/include/nmodlmutex.h
-- Up-to-date: /usr/include/nrnran123.h
-- Up-to-date: /usr/include/multicore.h
-- Up-to-date: /usr/include/cspredef.h
-- Up-to-date: /usr/include/nrniv_mf.h
-- Up-to-date: /usr/include/nrnjava.h
-- Up-to-date: /usr/include/nrnmpiuse.h
-- Up-to-date: /usr/include/nrnmpi.h
-- Up-to-date: /usr/include/Random123
-- Up-to-date: /usr/include/Random123/aes.h
-- Up-to-date: /usr/include/Random123/u01fixedpt.h
-- Up-to-date: /usr/include/Random123/threefry.h
-- Up-to-date: /usr/include/Random123/ars.h
-- Up-to-date: /usr/include/Random123/philox.h
-- Up-to-date: /usr/include/Random123/ReinterpretCtr.hpp
-- Up-to-date: /usr/include/Random123/gsl_microrng.h
-- Up-to-date: /usr/include/Random123/boxmuller.hpp
-- Up-to-date: /usr/include/Random123/MicroURNG.hpp
-- Up-to-date: /usr/include/Random123/array.h
-- Up-to-date: /usr/include/Random123/uniform.hpp
-- Up-to-date: /usr/include/Random123/conventional
-- Up-to-date: /usr/include/Random123/conventional/Engine.hpp
-- Up-to-date: /usr/include/Random123/conventional/gsl_cbrng.h
-- Up-to-date: /usr/include/Random123/features
-- Up-to-date: /usr/include/Random123/features/xlcfeatures.h
-- Up-to-date: /usr/include/Random123/features/open64features.h
-- Up-to-date: /usr/include/Random123/features/clangfeatures.h
-- Up-to-date: /usr/include/Random123/features/nvccfeatures.h
-- Up-to-date: /usr/include/Random123/features/iccfeatures.h
-- Up-to-date: /usr/include/Random123/features/fujitsufeatures.h
-- Up-to-date: /usr/include/Random123/features/metalfeatures.h
-- Up-to-date: /usr/include/Random123/features/sunprofeatures.h
-- Up-to-date: /usr/include/Random123/features/gccfeatures.h
-- Up-to-date: /usr/include/Random123/features/compilerfeatures.h
-- Up-to-date: /usr/include/Random123/features/crayfeatures.h
-- Up-to-date: /usr/include/Random123/features/openclfeatures.h
-- Up-to-date: /usr/include/Random123/features/sse.h
-- Up-to-date: /usr/include/Random123/features/msvcfeatures.h
-- Up-to-date: /usr/include/Random123/features/pgccfeatures.h
-- Up-to-date: /usr/include/coreneuron
-- Up-to-date: /usr/include/coreneuron/membrane_definitions.h
-- Up-to-date: /usr/include/coreneuron/mpi
-- Up-to-date: /usr/include/coreneuron/mpi/nrnmpi_def_cinc.h
-- Up-to-date: /usr/include/coreneuron/mpi/mpispike.hpp
-- Up-to-date: /usr/include/coreneuron/mpi/nrnmpiuse.h
-- Up-to-date: /usr/include/coreneuron/mpi/nrnmpi.h
-- Up-to-date: /usr/include/coreneuron/mpi/nrnmpidec.h
-- Up-to-date: /usr/include/coreneuron/mpi/nrnmpi_impl.h
-- Up-to-date: /usr/include/coreneuron/apps
-- Up-to-date: /usr/include/coreneuron/apps/corenrn_parameters.hpp
-- Up-to-date: /usr/include/coreneuron/nrnconf.h
-- Up-to-date: /usr/include/coreneuron/sim
-- Up-to-date: /usr/include/coreneuron/sim/fast_imem.hpp
-- Up-to-date: /usr/include/coreneuron/sim/multicore.hpp
-- Up-to-date: /usr/include/coreneuron/sim/scopmath
-- Up-to-date: /usr/include/coreneuron/sim/scopmath/errcodes.h
-- Up-to-date: /usr/include/coreneuron/sim/scopmath/newton_struct.h
-- Up-to-date: /usr/include/coreneuron/mechanism
-- Up-to-date: /usr/include/coreneuron/mechanism/mech_mapping.hpp
-- Up-to-date: /usr/include/coreneuron/mechanism/register_mech.hpp
-- Up-to-date: /usr/include/coreneuron/mechanism/eion.hpp
-- Up-to-date: /usr/include/coreneuron/mechanism/mech
-- Up-to-date: /usr/include/coreneuron/mechanism/mech/cfile
-- Up-to-date: /usr/include/coreneuron/mechanism/mech/cfile/scoplib.h
-- Up-to-date: /usr/include/coreneuron/mechanism/mech/cfile/cabvars.h
-- Up-to-date: /usr/include/coreneuron/mechanism/mech/mod2c_core_thread.hpp
-- Up-to-date: /usr/include/coreneuron/mechanism/mechanism.hpp
-- Up-to-date: /usr/include/coreneuron/mechanism/nrnoc_ml.ispc
-- Up-to-date: /usr/include/coreneuron/mechanism/membfunc.hpp
-- Up-to-date: /usr/include/coreneuron/utils
-- Up-to-date: /usr/include/coreneuron/utils/ivocvect.hpp
-- Up-to-date: /usr/include/coreneuron/utils/nrnmutdec.h
-- Up-to-date: /usr/include/coreneuron/utils/progressbar
-- Up-to-date: /usr/include/coreneuron/utils/progressbar/progressbar.h
-- Up-to-date: /usr/include/coreneuron/utils/vrecitem.h
-- Up-to-date: /usr/include/coreneuron/utils/memory.h
-- Up-to-date: /usr/include/coreneuron/utils/lpt.hpp
-- Up-to-date: /usr/include/coreneuron/utils/string_utils.h
-- Up-to-date: /usr/include/coreneuron/utils/nrnoc_aux.hpp
-- Up-to-date: /usr/include/coreneuron/utils/randoms
-- Up-to-date: /usr/include/coreneuron/utils/randoms/nrnran123.h
-- Up-to-date: /usr/include/coreneuron/utils/nrn_assert.h
-- Up-to-date: /usr/include/coreneuron/utils/profile
-- Up-to-date: /usr/include/coreneuron/utils/profile/cuda_profile.h
-- Up-to-date: /usr/include/coreneuron/utils/profile/profiler_interface.h
-- Up-to-date: /usr/include/coreneuron/utils/memory_utils.h
-- Up-to-date: /usr/include/coreneuron/utils/nrn_stats.h
-- Up-to-date: /usr/include/coreneuron/network
-- Up-to-date: /usr/include/coreneuron/network/have2want.h
-- Up-to-date: /usr/include/coreneuron/network/partrans.hpp
-- Up-to-date: /usr/include/coreneuron/network/tqueue.hpp
-- Up-to-date: /usr/include/coreneuron/network/tnode.hpp
-- Up-to-date: /usr/include/coreneuron/network/netpar.hpp
-- Up-to-date: /usr/include/coreneuron/network/netcvode.hpp
-- Up-to-date: /usr/include/coreneuron/network/netcon.hpp
-- Up-to-date: /usr/include/coreneuron/network/multisend.hpp
-- Up-to-date: /usr/include/coreneuron/nrnoc
-- Up-to-date: /usr/include/coreneuron/nrnoc/md1redef.h
-- Up-to-date: /usr/include/coreneuron/nrnoc/nrnunits_modern.h
-- Up-to-date: /usr/include/coreneuron/nrnoc/md2redef.h
-- Up-to-date: /usr/include/coreneuron/config
-- Up-to-date: /usr/include/coreneuron/config/config.h
-- Up-to-date: /usr/include/coreneuron/engine.h
-- Up-to-date: /usr/include/coreneuron/io
-- Up-to-date: /usr/include/coreneuron/io/core2nrn_data_return.hpp
-- Up-to-date: /usr/include/coreneuron/io/lfp.hpp
-- Up-to-date: /usr/include/coreneuron/io/file_utils.hpp
-- Up-to-date: /usr/include/coreneuron/io/phase2.hpp
-- Up-to-date: /usr/include/coreneuron/io/setup_fornetcon.hpp
-- Up-to-date: /usr/include/coreneuron/io/prcellstate.hpp
-- Up-to-date: /usr/include/coreneuron/io/nrn_setup.hpp
-- Up-to-date: /usr/include/coreneuron/io/user_params.hpp
-- Up-to-date: /usr/include/coreneuron/io/mech_report.h
-- Up-to-date: /usr/include/coreneuron/io/nrnsection_mapping.hpp
-- Up-to-date: /usr/include/coreneuron/io/mem_layout_util.hpp
-- Up-to-date: /usr/include/coreneuron/io/reports
-- Up-to-date: /usr/include/coreneuron/io/reports/report_handler.hpp
-- Up-to-date: /usr/include/coreneuron/io/reports/report_event.hpp
-- Up-to-date: /usr/include/coreneuron/io/reports/binary_report_handler.hpp
-- Up-to-date: /usr/include/coreneuron/io/reports/sonata_report_handler.hpp
-- Up-to-date: /usr/include/coreneuron/io/reports/nrnreport.hpp
-- Up-to-date: /usr/include/coreneuron/io/nrn2core_direct.h
-- Up-to-date: /usr/include/coreneuron/io/nrn_filehandler.hpp
-- Up-to-date: /usr/include/coreneuron/io/output_spikes.hpp
-- Up-to-date: /usr/include/coreneuron/io/nrn_checkpoint.hpp
-- Up-to-date: /usr/include/coreneuron/io/phase1.hpp
-- Up-to-date: /usr/include/coreneuron/permute
-- Up-to-date: /usr/include/coreneuron/permute/node_permute.h
-- Up-to-date: /usr/include/coreneuron/permute/cellorder.hpp
-- Up-to-date: /usr/include/coreneuron/permute/data_layout.hpp
-- Up-to-date: /usr/include/coreneuron/gpu
-- Up-to-date: /usr/include/coreneuron/gpu/nrn_acc_manager.hpp
-- Up-to-date: /usr/include/coreneuron/coreneuron.hpp
-- Up-to-date: /usr/include/coreneuron/nrniv
-- Up-to-date: /usr/include/coreneuron/nrniv/profiler_interface.h
-- Up-to-date: /usr/include/coreneuron/nrniv/nrniv_decl.h
-- Up-to-date: /usr/include/nrnapi.h
-- Up-to-date: /usr/include/spconfig.h
-- Up-to-date: /usr/include/nrnassrt.h
-- Up-to-date: /usr/include/scoplib.h
-- Up-to-date: /usr/include/hoclist.h
-- Up-to-date: /usr/include/nrnmpidec.h
-- Up-to-date: /usr/include/scoplib_ansi.h
-- Up-to-date: /usr/include/nrncvode.h
-- Up-to-date: /usr/include/md1redef.h
-- Up-to-date: /usr/include/membfunc.h
-- Up-to-date: /usr/include/hocassrt.h
-- Up-to-date: /usr/include/hocdec.h
-- Up-to-date: /usr/include/oc_ansi.h
-- Up-to-date: /usr/include/nrnpthread.h
-- Up-to-date: /usr/include/multisplit.h
-- Up-to-date: /usr/include/options.h
-- Up-to-date: /usr/include/ocmisc.h
-- Up-to-date: /usr/include/nrnredef.h
-- Up-to-date: /usr/include/spmatrix.h
-- Up-to-date: /usr/include/hoc_membf.h
-- Up-to-date: /usr/include/membdef.h
-- Up-to-date: /usr/include/nrn_ansi.h
-- Up-to-date: /usr/include/md2redef.h
-- Up-to-date: /usr/include/hocparse.h
-- Up-to-date: /usr/include/section.h
-- Up-to-date: /usr/include/nrnpy_hoc.h
-- Up-to-date: /usr/include/cabvars.h
-- Up-to-date: /usr/include/neuron.h
-- Up-to-date: /usr/include/hocgetsym.h
-- Up-to-date: /usr/include/isoc99.h
-- Up-to-date: /usr/include/cspmatrix.h
-- Up-to-date: /usr/include/hoc.h
-- Up-to-date: /usr/share/modfile
-- Up-to-date: /usr/share/modfile/svclmp.mod
-- Up-to-date: /usr/share/modfile/pattern.mod
-- Up-to-date: /usr/share/modfile/netstim.mod
-- Up-to-date: /usr/share/modfile/passive.mod
-- Up-to-date: /usr/share/modfile/exp2syn.mod
-- Up-to-date: /usr/share/modfile/expsyn.mod
-- Up-to-date: /usr/share/modfile/hh.mod
-- Up-to-date: /usr/share/modfile/stim.mod
-- Up-to-date: /usr/share/coreneuron/nrnivmodl_core_makefile
-- Up-to-date: /usr/bin/nrnivmodl-core
-- Up-to-date: /usr/bin/nrniv
-- Installing: /usr/bin/nocmodl
-- Installing: /usr/bin/modlunit
-- Up-to-date: /usr/lib/libnrniv.so
-- Up-to-date: /usr/share/nrn/nrnmain.cpp
-- Up-to-date: /usr/include/nrnmpiuse.h
-- Up-to-date: /usr/include/nrncvode/nrnneosm.h
-- Up-to-date: /usr/include/nrnconf.h
-- Up-to-date: /usr/bin/nrngui
-- Up-to-date: /usr/bin/neurondemo
-- Up-to-date: /usr/bin/nrnivmodl
-- Up-to-date: /usr/bin/nrnmech_makefile
-- Up-to-date: /usr/bin/nrnpyenv.sh
-- Up-to-date: /usr/bin/sortspike
-- Up-to-date: /usr/bin/mkthreadsafe
-- Up-to-date: /usr/bin/nrnpyenv.sh
-- Up-to-date: /usr/bin/set_nrnpyenv.sh
-- Installing: /usr/lib/librxdmath.so
Installing python module using:
+ cd /home/jhielson/neuron/nrn/build/src/nrnpython
+ /usr/bin/python3.6 setup.py --quiet build --build-lib=/home/jhielson/neuron/nrn/build/lib/python install --prefix= --home=/usr
jhielson commented 3 years ago

Hi,

Sorry to take your time with this issue. I have changed the pythonpath on my bashrc file to:

export PATH=$HOME/neuron/nrn/bin:$PATH
export PYTHONPATH=/usr/local/nrn/share/nrn/lib/python:$PYTHONPATH
export PYTHONPATH=/usr/local/nrn/lib/python/neuron:$PYTHONPATH

And, Python continues to not recognizing neuron:

ModuleNotFoundError: No module named 'neuron.hoc37'

Not sure how to fix that.

pramodk commented 3 years ago

@jhielson : in the top comment yo have posted:

...
-- --------------+--------------------------------------------------------------
-- Build option | Status
-- --------------+--------------------------------------------------------------
-- C COMPILER | /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc
-- CXX COMPILER | /opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc++
-- BUILD_TYPE | RelWithDebInfo (allowed: Custom;Debug;Release;RelWithDebInfo;Fast)
....
-- DYNAMIC | OFF
-- Python | ON
-- EXE | /usr/bin/python3.6
-- INC | /usr/include/python3.6m
-- LIB | /usr/lib/x86_64-linux-gnu/libpython3.6m.so

i.e. python detected by CMake is /usr/bin/python3.6. Are you using same python version 3.6 to test neuron?

And just another recommendation - seems like you haven't set -DCMAKE_INSTALL_PREFIX=/install/dir/path option. Without this, neuron is installed in system directories like /usr/local, /usr/include, /usr/bin. This is not a good idea when installing multiple versions or using different python versions. So, I would recommend to remove all the installed files (mentioned in your previous comments) and do fresh installation in home directory (e.g. -DCMAKE_INSTALL_PREFIX=$HOME/nrn-install).

jhielson commented 3 years ago

Thanks! I have done that, but it does not recognize coreneuron:

Python 3.6.9 (default, Jan 26 2021, 15:33:00) 
[GCC 8.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import neuron
>>> from neuron import coreneuron
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: cannot import name 'coreneuron'
>>> from neuron import h
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: cannot import name 'h'
>>>

My .bashrc file:

export PYTHONPATH=$HOME/nrn-install:$PYTHONPATH
export PATH=$HOME/nrn-install/bin:$PATH

The directory and paths:

$ cd ~/nrn-install/
$ ls
bin  include  lib  share  x86_64
$ echo $PYTHONPATH 
/home/jhielson/nrn-install:
$ echo $PATH
/usr/local/cuda-11.3/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/mpi/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin:/home/jhielson/nrn-install/bin:/home/jhielson/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/webots
jhielson commented 3 years ago

Sorry. I did not mean to close it

jhielson commented 3 years ago

Hi,

I have managed to install the package by following your suggestions. When I execute the command:

$ python3 -c "from neuron import h; from neuron import coreneuron"

the output is clean without any import error.

The package was installed at $HOME/nrn-install and my bash file containing the following export commands:

#coreNEURON
export PYTHONPATH=$HOME/nrn-install:$PYTHONPATH
export PATH=$HOME/nrn-install/bin:$PATH
export PYTHONPATH=$HOME/neuron/nrn/build/lib/python:$PYTHONPATH
export PYTHONPATH=/usr/local/nrn/share/nrn/lib/python:$PYTHONPATH
export PYTHONPATH=/usr/local/nrn/lib/python/neuron:$PYTHONPATH

#nvidia
export MANPATH=$MANPATH:/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/man 
export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin:$PATH 
export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/mpi/bin:$PATH
export MANPATH=$MANPATH:/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/mpi/man
export NVHPCSDK=/opt/nvidia/hpc_sdk

But, I can not compile any mod file. I get the following output:

$ nrnivmodl -coreneuron izhi2007b.mod 
/home/jhielson/netpyneExample/spdemo
Mod files: "./izhi2007b.mod"

COBJS=''
FATAL: Invalid mods directory: 'izhi2007b.mod'

$ nrnivmodl -coreneuron spikeout.mod 
/home/jhielson/netpyneExample/spdemo
Mod files: "./spikeout.mod"

COBJS=''
FATAL: Invalid mods directory: 'spikeout.mod'

Am I doing something wrong?

olupton commented 3 years ago

You should run nrnivmodl -coreneuron directory_containing_mod_files/, not nrnivmodl -coreneuron path/to/file.mod. See: https://nrn.readthedocs.io/en/latest/coreneuron/how-to/coreneuron.html#building-mod-files

jhielson commented 3 years ago

Sorry, my bad. I have three different mod files and I get the following error:

Mod files: "./spdemo/izhi2007b.mod" "./spdemo/spikeout.mod" "./spdemo/SynExp2NMDA.mod"

Creating x86_64 directory for .o files.

COBJS=''
[INFO] Running: make -j4 -f /usr/share/coreneuron/nrnivmodl_core_makefile ROOT=/usr MODS_PATH=x86_64/corenrn/mod2c BUILD_TYPE=STATIC
Default NMODL flags: 
diff: x86_64/corenrn/mod2c/_mod_func.cpp: No such file or directory
Translating x86_64/corenrn/mod2c/SynExp2NMDA.mod into x86_64/corenrn/mod2c//SynExp2NMDA.cpp
Translating x86_64/corenrn/mod2c/expsyn.mod into x86_64/corenrn/mod2c//expsyn.cpp
Translating x86_64/corenrn/mod2c/exp2syn.mod into x86_64/corenrn/mod2c//exp2syn.cpp
cvode_emit=0 cvode_not_allowed=0
cvode_emit=0 cvode_not_allowed=0
Thread Safe
Translating x86_64/corenrn/mod2c/hh.mod into x86_64/corenrn/mod2c//hh.cpp
Thread Safe
cvode_emit=0 cvode_not_allowed=0
Thread Safe
cvode_emit=0 cvode_not_allowed=0
Thread Safe
Translating x86_64/corenrn/mod2c/izhi2007b.mod into x86_64/corenrn/mod2c//izhi2007b.cpp
Translating x86_64/corenrn/mod2c/netstim.mod into x86_64/corenrn/mod2c//netstim.cpp
Translating x86_64/corenrn/mod2c/passive.mod into x86_64/corenrn/mod2c//passive.cpp
cvode_emit=0 cvode_not_allowed=0
Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it
only affects and is affected by discrete events. As such it is not
located in a section and is not associated with an integrator
Thread Safe
cvode_emit=0 cvode_not_allowed=0
Thread Safe
Translating x86_64/corenrn/mod2c/pattern.mod into x86_64/corenrn/mod2c//pattern.cpp
Notice: VERBATIM blocks are not thread safe
cvode_emit=0 cvode_not_allowed=0
Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it
only affects and is affected by discrete events. As such it is not
located in a section and is not associated with an integrator
Thread Safe
cvode_emit=0 cvode_not_allowed=0
Error : x86_64/corenrn/mod2c/izhi2007b.mod is not thread safe and incompatible with CoreNEURON
See details at https://neuron.yale.edu/neuron/docs/multithread-parallelizationTranslating x86_64/corenrn/mod2c/spikeout.mod into x86_64/corenrn/mod2c//spikeout.cpp
cvode_emit=0 cvode_not_allowed=0
Translating x86_64/corenrn/mod2c/stim.mod into x86_64/corenrn/mod2c//stim.cpp
Thread Safe
Translating x86_64/corenrn/mod2c/svclmp.mod into x86_64/corenrn/mod2c//svclmp.cpp
cvode_emit=0 cvode_not_allowed=0
Thread Safe
cvode_emit=0 cvode_not_allowed=0
Thread Safe
"/usr/include/c++/7/cstdlib", line 75: catastrophic error: cannot open source file "stdlib.h"
  #include_next <stdlib.h>
                          ^

1 catastrophic error detected in the compilation of "/usr/share/coreneuron/enginemech.cpp".
Compilation terminated.
/usr/share/coreneuron/nrnivmodl_core_makefile:195: recipe for target 'x86_64/corenrn/build/enginemech.o' failed
make: *** [x86_64/corenrn/build/enginemech.o] Error 2
make: *** Waiting for unfinished jobs....
Aborted (core dumped)
/usr/share/coreneuron/nrnivmodl_core_makefile:225: recipe for target 'x86_64/corenrn/mod2c/izhi2007b.cpp' failed
make: *** [x86_64/corenrn/mod2c/izhi2007b.cpp] Error 134
make: *** Deleting file 'x86_64/corenrn/mod2c/izhi2007b.cpp'

Should I close this issue and open a new one? Maybe this error is related to the version of my gcc.

jhielson commented 3 years ago

Hi @olupton ,

Sorry for taking your time again but I could not solve the last compilation issue. When I try to compile my models (mod files) I get the following error:

$ nrnivmodl -coreneuron .
/home/jhielson/netpyneExample/spdemo
Mod files: "./spikeout.mod" "./SynExp2NMDA.mod"

COBJS=''
[INFO] Running: make -j4 -f /usr/share/coreneuron/nrnivmodl_core_makefile ROOT=/usr MODS_PATH=x86_64/corenrn/mod2c BUILD_TYPE=STATIC
Default NMODL flags: 
"/usr/include/c++/7/cstdlib", line 75: catastrophic error: cannot open source file "stdlib.h"
  #include_next <stdlib.h>
                          ^

1 catastrophic error detected in the compilation of "/usr/share/coreneuron/enginemech.cpp".
Compilation terminated.
/usr/share/coreneuron/nrnivmodl_core_makefile:195: recipe for target 'x86_64/corenrn/build/enginemech.o' failed
make: *** [x86_64/corenrn/build/enginemech.o] Error 2
make: *** Waiting for unfinished jobs....
"/usr/include/c++/7/cmath", line 45: catastrophic error: cannot open source file "math.h"
  #include_next <math.h>
                        ^

1 catastrophic error detected in the compilation of "x86_64/corenrn/mod2c/_dimplic.cpp".
Compilation terminated.
/usr/share/coreneuron/nrnivmodl_core_makefile:213: recipe for target 'x86_64/corenrn/build/_dimplic.o' failed
make: *** [x86_64/corenrn/build/_dimplic.o] Error 2
"/usr/include/c++/7/cstdlib", line 75: catastrophic error: cannot open source file "stdlib.h"
  #include_next <stdlib.h>
                          ^

1 catastrophic error detected in the compilation of "x86_64/corenrn/mod2c/SynExp2NMDA.cpp".
Compilation terminated.
/usr/share/coreneuron/nrnivmodl_core_makefile:213: recipe for target 'x86_64/corenrn/build/SynExp2NMDA.o' failed
make: *** [x86_64/corenrn/build/SynExp2NMDA.o] Error 2

Please, can you help me with that?

olupton commented 3 years ago

Can you attach the full log of VERBOSE=1 nrnivmodl -coreneuron . please?

jhielson commented 3 years ago

That is the output : 

/home/jhielson/netpyneExample/spdemo
Mod files: "./spikeout.mod" "./SynExp2NMDA.mod"

COBJS=''
[INFO] Running: make -j4 -f /usr/share/coreneuron/nrnivmodl_core_makefile ROOT=/usr MODS_PATH=x86_64/corenrn/mod2c BUILD_TYPE=STATIC
Default NMODL flags: 
/usr/bin/perl /usr/share/coreneuron/mod_func.c.pl SynExp2NMDA.mod exp2syn.mod expsyn.mod hh.mod netstim.mod passive.mod pattern.mod spikeout.mod stim.mod svclmp.mod > x86_64/corenrn/mod2c/_mod_func.cpp.tmp
cd x86_64/corenrn/mod2c; \
/usr/bin/python3.6 /usr/share/coreneuron/kinderiv.py;
/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc++ -O3 -g -acc -gpu=cuda11.3,cc60,cc70 --diag_suppress 161,177,550 -mp   -g  -O2  --c++14 -fPIC  -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DCORENEURON_BUILD -DHAVE_MALLOC_H -DEIGEN_DONT_VECTORIZE=1 -DNRNMPI=1 -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DLAYOUT=0 -DDISABLE_HOC_EXP -DENABLE_SPLAYTREE_QUEUING  -I/usr/include -I/usr/include/coreneuron/utils/randoms  -I/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/include  -c -DADDITIONAL_MECHS /usr/share/coreneuron/enginemech.cpp -o x86_64/corenrn/build/enginemech.o
diff -q x86_64/corenrn/mod2c/_mod_func.cpp.tmp x86_64/corenrn/mod2c/_mod_func.cpp || \
mv x86_64/corenrn/mod2c/_mod_func.cpp.tmp x86_64/corenrn/mod2c/_mod_func.cpp
/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc++ -O3 -g -acc -gpu=cuda11.3,cc60,cc70 --diag_suppress 161,177,550 -mp   -g  -O2  --c++14 -fPIC  -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DCORENEURON_BUILD -DHAVE_MALLOC_H -DEIGEN_DONT_VECTORIZE=1 -DNRNMPI=1 -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DLAYOUT=0 -DDISABLE_HOC_EXP -DENABLE_SPLAYTREE_QUEUING  -I/usr/include -I/usr/include/coreneuron/utils/randoms  -I/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/include  -c x86_64/corenrn/mod2c/_dimplic.cpp -o x86_64/corenrn/build/_dimplic.o
/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc++ -O3 -g -acc -gpu=cuda11.3,cc60,cc70 --diag_suppress 161,177,550 -mp   -g  -O2  --c++14 -fPIC  -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DCORENEURON_BUILD -DHAVE_MALLOC_H -DEIGEN_DONT_VECTORIZE=1 -DNRNMPI=1 -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DLAYOUT=0 -DDISABLE_HOC_EXP -DENABLE_SPLAYTREE_QUEUING  -I/usr/include -I/usr/include/coreneuron/utils/randoms  -I/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/include  -c x86_64/corenrn/mod2c/SynExp2NMDA.cpp -o x86_64/corenrn/build/SynExp2NMDA.o
/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc++ -O3 -g -acc -gpu=cuda11.3,cc60,cc70 --diag_suppress 161,177,550 -mp   -g  -O2  --c++14 -fPIC  -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DCORENEURON_BUILD -DHAVE_MALLOC_H -DEIGEN_DONT_VECTORIZE=1 -DNRNMPI=1 -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DLAYOUT=0 -DDISABLE_HOC_EXP -DENABLE_SPLAYTREE_QUEUING  -I/usr/include -I/usr/include/coreneuron/utils/randoms  -I/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/include  -c x86_64/corenrn/mod2c/exp2syn.cpp -o x86_64/corenrn/build/exp2syn.o
"/usr/include/c++/7/cstdlib", line 75: catastrophic error: cannot open source file "stdlib.h"
  #include_next <stdlib.h>
                          ^

1 catastrophic error detected in the compilation of "/usr/share/coreneuron/enginemech.cpp".
Compilation terminated.
/usr/share/coreneuron/nrnivmodl_core_makefile:195: recipe for target 'x86_64/corenrn/build/enginemech.o' failed
make: *** [x86_64/corenrn/build/enginemech.o] Error 2
make: *** Waiting for unfinished jobs....
"/usr/include/c++/7/cmath", line 45: catastrophic error: cannot open source file "math.h"
  #include_next <math.h>
                        ^

1 catastrophic error detected in the compilation of "x86_64/corenrn/mod2c/_dimplic.cpp".
Compilation terminated.
/usr/share/coreneuron/nrnivmodl_core_makefile:213: recipe for target 'x86_64/corenrn/build/_dimplic.o' failed
make: *** [x86_64/corenrn/build/_dimplic.o] Error 2
"/usr/include/c++/7/cstdlib", line 75: catastrophic error: cannot open source file "stdlib.h"
  #include_next <stdlib.h>
                          ^

1 catastrophic error detected in the compilation of "x86_64/corenrn/mod2c/SynExp2NMDA.cpp".
Compilation terminated.
"/usr/include/c++/7/cstdlib", line 75: catastrophic error: cannot open source file "stdlib.h"
  #include_next <stdlib.h>
                          ^

1 catastrophic error detected in the compilation of "x86_64/corenrn/mod2c/exp2syn.cpp".
Compilation terminated.
/usr/share/coreneuron/nrnivmodl_core_makefile:213: recipe for target 'x86_64/corenrn/build/SynExp2NMDA.o' failed
make: *** [x86_64/corenrn/build/SynExp2NMDA.o] Error 2
/usr/share/coreneuron/nrnivmodl_core_makefile:213: recipe for target 'x86_64/corenrn/build/exp2syn.o' failed
make: *** [x86_64/corenrn/build/exp2syn.o] Error 2
olupton commented 3 years ago

The problem seems to come from NVHPC's handling of include directories, here is a tiny example:

$ echo "#include <cstdlib>" > foo.cpp && nvc++ -I/usr/include -o foo foo.cpp
"[snipped]/gcc-9.3.0-45gzrp/include/c++/9.3.0/cstdlib", line 75: catastrophic error: cannot open source file "stdlib.h"
  #include_next <stdlib.h>
                          ^
1 catastrophic error detected in the compilation of "foo.cpp".
Compilation terminated.

and we can see above you have:

nvc++ ... -I/usr/include -I/usr/include/coreneuron/utils/randoms ... -c /usr/share/coreneuron/enginemech.cpp -o x86_64/corenrn/build/enginemech.o

which looks like you still have CMAKE_INSTALL_PREFIX=/usr. Can you try a clean build? I understood from the comments above that you had changed to installing into a folder in your home directory, so I guess this is an accident?

jhielson commented 3 years ago

Thanks. I had an old pythonpath in my bashfile. After removing it, the compilation completed with warnings:

VERBOSE=1 nrnivmodl -coreneuron
/home/jhielson/netpyneExample/spdemo
Mod files: "./spikeout.mod" "./SynExp2NMDA.mod"

COBJS=''
[INFO] Running: make -j4 -f /home/jhielson/nrn-install/share/coreneuron/nrnivmodl_core_makefile ROOT=/home/jhielson/nrn-install MODS_PATH=x86_64/corenrn/mod2c BUILD_TYPE=STATIC
Default NMODL flags: 
/usr/bin/perl /home/jhielson/nrn-install/share/coreneuron/mod_func.c.pl SynExp2NMDA.mod exp2syn.mod expsyn.mod hh.mod netstim.mod passive.mod pattern.mod spikeout.mod stim.mod svclmp.mod > x86_64/corenrn/mod2c/_mod_func.cpp.tmp
cd x86_64/corenrn/mod2c; \
/usr/bin/python3.6 /home/jhielson/nrn-install/share/coreneuron/kinderiv.py;
/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc++ -O3 -g -acc -gpu=cuda11.3,cc60,cc70 --diag_suppress 161,177,550 -mp   -g  -O2  --c++14 -fPIC  -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DCORENEURON_BUILD -DHAVE_MALLOC_H -DEIGEN_DONT_VECTORIZE=1 -DNRNMPI=1 -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DLAYOUT=0 -DDISABLE_HOC_EXP -DENABLE_SPLAYTREE_QUEUING  -I/home/jhielson/nrn-install/include -I/home/jhielson/nrn-install/include/coreneuron/utils/randoms  -I/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/include  -c -DADDITIONAL_MECHS /home/jhielson/nrn-install/share/coreneuron/enginemech.cpp -o x86_64/corenrn/build/enginemech.o
diff -q x86_64/corenrn/mod2c/_mod_func.cpp.tmp x86_64/corenrn/mod2c/_mod_func.cpp || \
mv x86_64/corenrn/mod2c/_mod_func.cpp.tmp x86_64/corenrn/mod2c/_mod_func.cpp
/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc++ -O3 -g -acc -gpu=cuda11.3,cc60,cc70 --diag_suppress 161,177,550 -mp   -g  -O2  --c++14 -fPIC  -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DCORENEURON_BUILD -DHAVE_MALLOC_H -DEIGEN_DONT_VECTORIZE=1 -DNRNMPI=1 -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DLAYOUT=0 -DDISABLE_HOC_EXP -DENABLE_SPLAYTREE_QUEUING  -I/home/jhielson/nrn-install/include -I/home/jhielson/nrn-install/include/coreneuron/utils/randoms  -I/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/include  -c x86_64/corenrn/mod2c/_dimplic.cpp -o x86_64/corenrn/build/_dimplic.o
/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc++ -O3 -g -acc -gpu=cuda11.3,cc60,cc70 --diag_suppress 161,177,550 -mp   -g  -O2  --c++14 -fPIC  -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DCORENEURON_BUILD -DHAVE_MALLOC_H -DEIGEN_DONT_VECTORIZE=1 -DNRNMPI=1 -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DLAYOUT=0 -DDISABLE_HOC_EXP -DENABLE_SPLAYTREE_QUEUING  -I/home/jhielson/nrn-install/include -I/home/jhielson/nrn-install/include/coreneuron/utils/randoms  -I/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/include  -c x86_64/corenrn/mod2c/SynExp2NMDA.cpp -o x86_64/corenrn/build/SynExp2NMDA.o
/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc++ -O3 -g -acc -gpu=cuda11.3,cc60,cc70 --diag_suppress 161,177,550 -mp   -g  -O2  --c++14 -fPIC  -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DCORENEURON_BUILD -DHAVE_MALLOC_H -DEIGEN_DONT_VECTORIZE=1 -DNRNMPI=1 -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DLAYOUT=0 -DDISABLE_HOC_EXP -DENABLE_SPLAYTREE_QUEUING  -I/home/jhielson/nrn-install/include -I/home/jhielson/nrn-install/include/coreneuron/utils/randoms  -I/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/include  -c x86_64/corenrn/mod2c/exp2syn.cpp -o x86_64/corenrn/build/exp2syn.o
/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/compilers/bin/nvc++ -O3 -g -acc -gpu=cuda11.3,cc60,cc70 --diag_suppress 161,177,550 -mp   -g  -O2  --c++14 -fPIC  -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DCORENEURON_BUILD -DHAVE_MALLOC_H -DEIGEN_DONT_VECTORIZE=1 -DNRNMPI=1 -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DLAYOUT=0 -DDISABLE_HOC_EXP -DENABLE_SPLAYTREE_QUEUING  -I/home/jhielson/nrn-install/include -I/home/jhielson/nrn-install/include/coreneuron/utils/randoms  -I/opt/nvidia/hpc_sdk/Linux_x86_64/21.5/comm_libs/openmpi/openmpi-3.1.5/include  -c x86_64/corenrn/mod2c/expsyn.cpp -o x86_64/corenrn/build/expsyn.o
NVC++-S-1053-External and Static variables are not supported in acc routine - _ZN58_INTERNAL_36_x86_64_corenrn_mod2c_SynExp2NMDA_cpp_cc3caf8a10coreneuron1FE (x86_64/corenrn/mod2c/SynExp2NMDA.cpp: 453)
NVC++/x86-64 Linux 21.5-0: compilation completed with severe errors
/home/jhielson/nrn-install/share/coreneuron/nrnivmodl_core_makefile:213: recipe for target 'x86_64/corenrn/build/SynExp2NMDA.o' failed
make: *** [x86_64/corenrn/build/SynExp2NMDA.o] Error 2
make: *** Waiting for unfinished jobs....
NVC++-W-1053-External and Static variables are not supported in acc routine - _ZN10coreneuron11nrn_threadsE (x86_64/corenrn/mod2c/expsyn.cpp: 378)
NVC++-W-1053-External and Static variables are not supported in acc routine - _ZN10coreneuron11nrn_threadsE (x86_64/corenrn/mod2c/exp2syn.cpp: 396)
NVC++/x86-64 Linux 21.5-0: compilation completed with warnings
NVC++/x86-64 Linux 21.5-0: compilation completed with warnings
olupton commented 3 years ago

I see

NVC++/x86-64 Linux 21.5-0: compilation completed with severe errors
/home/jhielson/nrn-install/share/coreneuron/nrnivmodl_core_makefile:213: recipe for target 'x86_64/corenrn/build/SynExp2NMDA.o' failed
make: *** [x86_64/corenrn/build/SynExp2NMDA.o] Error 2
make: *** Waiting for unfinished jobs....

there. Can you check for other errors?

Did you rebuild in and reinstall to a clean directory, or is this just with a change to your Python path?

jhielson commented 3 years ago

Hi,

I rebuilt the package from a clean directory. But it only worked after removing the wrong python path inside the bashrc file.

It also says:

NVC++-S-1053-External and Static variables are not supported in acc routine - _ZN58_INTERNAL_36_x86_64_corenrn_mod2c_SynExp2NMDA_cpp_cc3caf8a10coreneuron1FE (x86_64/corenrn/mod2c/SynExp2NMDA.cpp: 453)
olupton commented 3 years ago

OK, that is normally only a warning, but it seems that with this SynExp2NMDA.mod mechanism it's an error. I can reproduce it locally (with this file, hopefully it's the same one you're using). I'll have a look.

jhielson commented 3 years ago

Thanks! It is the same mod file.

olupton commented 3 years ago

This seems to be a problem with the combination of OpenACC/GPU support, the MOD2C translator, and this mechanism -- specifically that it contains a CONSTANT { ... } block.

For me it works locally if we merge the CONSTANT block into the PARAMETER block and add GLOBAL T, F, R, z to the NEURON block:

--- SynExp2NMDA.mod  2021-06-28 16:39:32.672863000 +0200
+++ SynExp2NMDA.mod  2021-06-28 16:39:12.146030000 +0200
@@ -39,6 +39,7 @@
 NEURON {
        POINT_PROCESS Exp2NMDA
        NONSPECIFIC_CURRENT i
+       GLOBAL T, F, R, z
        RANGE tau1, tau2, e, i, Mg, K0, delta, wf
        THREADSAFE
 }
@@ -66,9 +67,6 @@
        delta = 0.8     (1)             : the electrical distance of the Mg2+ binding site from the outside of the membrane from Spruston95
 : Parameter Controls Ohm's law in NMDAR
        e = -0.7                (mV)    : in CA1-CA3 region = -0.7 from Spruston95
-}
-
-CONSTANT {
        T = 273.16      (degC)
        F = 9.648e4     (coul)  : Faraday's constant (coulombs/mol)
        R = 8.315       (J/degC): universal gas constant (joules/mol/K)

hopefully you can use this workaround for the moment.

jhielson commented 3 years ago

Thanks! It works. I am gonna create a network using those models to test.

jhielson commented 3 years ago

Hi,

Do you known if there are commands to activate the package, like bellow, but for NetpyNE models?

  1. Enable cache efficiency :

    from neuron import h h.cvode.cache_efficient(1)

  2. Enable CoreNEURON :

    from neuron import coreneuron coreneuron.enable = True

  3. If GPU support is enabled during build, enable GPU execution using:

    coreneuron.gpu = True

    :warning: In this case you must launch your script using the special binary! This is explained in more detail below.

  4. Use psolve to run simulation after initialization :

    h.stdinit() pc.psolve(h.tstop)

iomaganaris commented 3 years ago

Hello @jhielson ,

Currently we're working with NetPyNE developers to integrate CoreNEURON support in NetPyNE. It would be helpful if you could create a ticket in the NetPyNE repo about that and we can check how to make a version of NetPyNE available with this feature.

Thank you very much!

jhielson commented 3 years ago

Thank you! I will create a ticket there.

(https://github.com/Neurosim-lab/netpyne/issues/611#issue-931776912)