BlueBrain / CoreNeuron

Simulator optimized for large scale neural network simulations.
BSD 3-Clause "New" or "Revised" License
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CMake Error at external/coreneuron/coreneuron/CMakeLists.txt:37:: file COPY cannot find external/Random123/include/Random123 #601

Closed pramodk closed 3 years ago

pramodk commented 3 years ago

Describe the issue

While building NEURON on Juelich's JUSUF system I get following error:


[kumbhar1@jsfl01 build]$ cmake .. -DCMAKE_INSTALL_PREFIX=`pwd`/install -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_RX3D=ON -DNRN_ENABLE_CORENEURON=ON
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /p/software/jusuf/stages/2020/software/GCCcore/9.3.0/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /p/software/jusuf/stages/2020/software/GCCcore/9.3.0/bin/c++ - skipped
-- 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 "2.5.37")
-- Found Readline: /p/software/jusuf/stages/2020/software/libreadline/8.0-GCCcore-9.3.0/include
-- Found PythonInterp: /p/software/jusuf/stages/2020/software/Python/3.8.5-GCCcore-9.3.0/bin/python3 (found version "3.8.5")
-- Found Cython: /p/software/jusuf/stages/2020/software/Python/3.8.5-GCCcore-9.3.0/bin/cython (found version "0.29.21")
-- Found MPI_C: /opt/ddn/ime/lib/libim_client.so (found version "3.1")
-- Found MPI_CXX: /opt/ddn/ime/lib/libim_client.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Found PythonInterp: /p/software/jusuf/stages/2020/software/Python/3.8.5-GCCcore-9.3.0/bin/python3 (found suitable version "3.8.5", minimum required is "3.6")
-- Found PythonInterp: /p/software/jusuf/stages/2020/software/Python/3.8.5-GCCcore-9.3.0/bin/python3 (found suitable version "3.8.5", minimum required is "3")
-- Found PythonLibs: /p/software/jusuf/stages/2020/software/Python/3.8.5-GCCcore-9.3.0/lib/libpython3.8.so
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Found Threads: TRUE
-- Building CoreNEURON from submodule
-- Sub-module : missing /p/home/jusers/kumbhar1/jusuf/nrn/external/coreneuron : running git submodule update --init
Submodule 'external/coreneuron' (https://github.com/BlueBrain/CoreNeuron.git) registered for path 'external/coreneuron'
Cloning into 'external/coreneuron'...
Submodule path 'external/coreneuron': checked out '864b7120b28900c28d606cfff9434b63f5c70d6d'
-- 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 '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
-- Found Random123: /p/software/jusuf/stages/2020/software/Java/1.8_292-b10-OpenJDK
-- Could NOT find CLI11 (missing: CLI11_PROJ)
-- Sub-module CLI11 missing: running git submodule update --init
Submodule 'external/CLI11' (https://github.com/CLIUtils/CLI11.git) registered for path 'external/CLI11'
Cloning into 'external/CLI11'...
Submodule path 'external/CLI11': checked out 'dd0d8e4fe729e5b1110232c7a5c9566dad884686'
-- Found Git: /usr/bin/git (found version "1.8.3.1")
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.5") found components: doxygen missing components: dot
-- Found PythonInterp: /p/software/jusuf/stages/2020/software/Python/3.8.5-GCCcore-9.3.0/bin/python3 (found version "3.8.5")
-- Found Perl: /usr/bin/perl (found version "5.16.3")
-- Could NOT find MOD2C (missing: MOD2C_PROJ)
-- Sub-module mod2c missing : running git submodule update --init --recursive
Submodule 'external/mod2c' (https://github.com/BlueBrain/mod2c) registered for path 'external/mod2c'
Cloning into 'external/mod2c'...
Submodule path 'external/mod2c': checked out '9b474e903028cf5512f6998c428fa03c4f3c326f'
-- mod2c is used as APPLICATION_NAME
CMake Error at external/coreneuron/coreneuron/CMakeLists.txt:37 (file):
  file COPY cannot find
  "/p/home/jusers/kumbhar1/jusuf/nrn/external/coreneuron/external/Random123/include/Random123":
  No such file or directory.

--
-- Configured CoreNEURON 0.21.0
--
-- Some things you can do now:
-- --------------------+--------------------------------------------------------
-- Command             |   Description
-- --------------------+--------------------------------------------------------
-- make install        | Will install CoreNEURON to: /p/home/jusers/kumbhar1/jusuf/nrn/build/install
-- make docs           | Build full docs. Calls targets: doxygen, sphinx
-- --------------------+--------------------------------------------------------
--  Build option       | Status
-- --------------------+--------------------------------------------------------
-- C COMPILER          | /p/software/jusuf/stages/2020/software/GCCcore/9.3.0/bin/cc
-- CXX COMPILER        | /p/software/jusuf/stages/2020/software/GCCcore/9.3.0/bin/c++
-- COMPILE FLAGS       |  -fopenmp  -Wno-unknown-pragmas -g  -O2 -Wno-write-strings -std=c++14
-- Build Type          | SHARED
-- MPI                 | ON
--   INC               | /opt/ddn/ime/include;/p/software/jusuf/stages/2020/software/psmpi/5.4.7-1-GCC-9.3.0/include
-- OpenMP              | ON
-- Use legacy units    | OFF
-- NMODL               | OFF
-- MOD2CPP PATH        | /p/home/jusers/kumbhar1/jusuf/nrn/build/bin/mod2c_core
-- GPU Support         | OFF
-- 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/
-- --------------+--------------------------------------------------------------
--
Using Target in compiling and linking, you should take care of it if
                    it fail miserabily (CODE: 1234567890)
-- Sub-module : missing external/coding-conventions : running git submodule update --init
Submodule 'external/coding-conventions' (https://github.com/BlueBrain/hpc-coding-conventions.git) registered for path 'external/coding-conventions'
Cloning into 'external/coding-conventions'...
Submodule path 'external/coding-conventions': checked out '91c5d922a1b45943c6d2eca719088b547243f75c'
--
-- Configured NEURON 8.0
--
-- You can now build NEURON using:
--   cmake --build . --parallel 8 [--target TARGET]
-- 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: /p/home/jusers/kumbhar1/jusuf/nrn/build/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    | /p/software/jusuf/stages/2020/software/GCCcore/9.3.0/bin/cc
-- CXX COMPILER  | /p/software/jusuf/stages/2020/software/GCCcore/9.3.0/bin/c++
-- BUILD_TYPE    | RelWithDebInfo (allowed: Custom;Debug;Release;RelWithDebInfo;Fast)
-- COMPILE FLAGS | -g  -O2 -Wno-write-strings
-- Shared        | ON
-- Default units | modern units (2019 nist constants)
-- MPI           | ON
--   INC         | /p/software/jusuf/stages/2020/software/psmpi/5.4.7-1-GCC-9.3.0/include
--   LIB         | /opt/ddn/ime/lib/libim_client.so
--   DYNAMIC     | OFF
-- Python        | ON
--   EXE         | /p/software/jusuf/stages/2020/software/Python/3.8.5-GCCcore-9.3.0/bin/python3
--   INC         | /p/software/jusuf/stages/2020/software/Python/3.8.5-GCCcore-9.3.0/include/python3.8
--   LIB         | /p/software/jusuf/stages/2020/software/Python/3.8.5-GCCcore-9.3.0/lib/libpython3.8.so
--   MODULE      | ON
--   DYNAMIC     | OFF
-- Readline      | /p/software/jusuf/stages/2020/software/libreadline/8.0-GCCcore-9.3.0/lib/libreadline.so
-- Curses        | /p/software/jusuf/stages/2020/software/ncurses/6.2-GCCcore-9.3.0/lib/libcurses.so;/p/software/jusuf/stages/2020/software/ncurses/6.2-GCCcore-9.3.0/lib/libform.so
-- RX3D          | ON
--   OptLevel    | 0
-- Interviews    | OFF
-- CoreNEURON    | ON
--   PATH        | /p/home/jusers/kumbhar1/jusuf/nrn/external/coreneuron
--   LINK FLAGS  | -Lx86_64 -lcorenrnmech
--   Legacy Units| OFF
-- --------------+--------------------------------------------------------------
--  See documentation : https://www.neuron.yale.edu/neuron/
-- --------------+--------------------------------------------------------------
--
-- Configuring incomplete, errors occurred!
See also "/p/home/jusers/kumbhar1/jusuf/nrn/build/CMakeFiles/CMakeOutput.log".
See also "/p/home/jusers/kumbhar1/jusuf/nrn/build/CMakeFiles/CMakeError.log".

To Reproduce

Expected behavior

Cmake should finish fine even without --recursive option

System (please complete the following information)

Additional context

This is on external system. I haven't tried to reproduce this locally/BB5.

pramodk commented 3 years ago

Submodule of coreneuron is not cloned automatically:

$ tree /p/home/jusers/kumbhar1/jusuf/nrn/external/coreneuron/external/Random123/
/p/home/jusers/kumbhar1/jusuf/nrn/external/coreneuron/external/Random123/

0 directories, 0 files

and that's because:

-- Found Random123: /p/software/jusuf/stages/2020/software/Java/1.8_292-b10-OpenJDK

Oops!!