Re: [Yade-dev] [Yade-users] [Question #665387]: Compile error JointedCohesiveFrictionalPM

William Chèvremont Wed, 14 Mar 2018 10:44:12 -0700

Hi Robert,

Here is my output if I run cmake with clean cache:

-- The C compiler identification is GNU 7.2.0
-- The CXX compiler identification is GNU 7.2.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- 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: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found PythonInterp: /usr/bin/python (found version "2.7.14")

CMake Warning (dev) at/usr/share/cmake-3.9/Modules/FindOpenMP.cmake:200 (if):

  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy

details. Use the cmake_policy command to set the policy andsuppress this

  warning.

Quoted variables like "c" will no longer be dereferenced when thepolicy is

  set to NEW.  Since the policy is not set the OLD behavior will be used.
Call Stack (most recent call first):
  /usr/share/cmake-3.9/Modules/FindOpenMP.cmake:324 (_OPENMP_GET_FLAGS)
  CMakeLists.txt:37 (INCLUDE)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found
-- Found Qt4: /usr/bin/qmake (found version "4.8.7")
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
-- Version is set to 2018-03-14.git-45c88e0
-- Found OpenGL: /lib/x86_64-linux-gnu/libglib-2.0.so.0
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Found GL2PS: /usr/lib/x86_64-linux-gnu/libgl2ps.so
-- Found CGAL: /usr/local/include, /usr/local/lib/libCGAL.so

-- Found NumPy: version "1.12.1"/usr/lib/python2.7/dist-packages/numpy/core/include

-- Found Loki: /usr/include
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0
-- GCC Version >= 4.9. Adding -fstack-protector-strong
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   python
--   thread
--   filesystem
--   iostreams
--   regex
--   serialization
--   system
--   date_time
--   chrono
--   atomic
--   Boost_VERSION: 106200
--   Boost_LIB_VERSION: 1_62
--   Boost_INCLUDE_DIRS: /usr/include

-- Boost_LIBRARIES:/usr/lib/x86_64-linux-gnu/libboost_python.so/usr/lib/x86_64-linux-gnu/libboost_thread.so/usr/lib/x86_64-linux-gnu/libboost_filesystem.so/usr/lib/x86_64-linux-gnu/libboost_iostreams.so/usr/lib/x86_64-linux-gnu/libboost_regex.so/usr/lib/x86_64-linux-gnu/libboost_serialization.so/usr/lib/x86_64-linux-gnu/libboost_system.so/usr/lib/x86_64-linux-gnu/libboost_date_time.so/usr/lib/x86_64-linux-gnu/libboost_chrono.so/usr/lib/x86_64-linux-gnu/libboost_atomic.so/usr/lib/x86_64-linux-gnu/libpthread.so-- Found Eigen3: /usr/include/eigen3 (Required is at least version"2.91.0")

-- Found BZip2: /lib/x86_64-linux-gnu/libbz2.so.1 (found version "1.0.6")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Found ZLIB: /lib/x86_64-linux-gnu/libz.so.1 (found version "1.2.11")

-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (foundversion "2.7.14")

-- Found Eigen3, version: 3.3.4
-- Disable vectorization
-- Found VTK
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Checking for one of the modules 'glib-2.0'

-- Found GLib2: glib-2.0/usr/include/glib-2.0;/usr/lib/x86_64-linux-gnu/glib-2.0/include

-- Looking for include file glib/gregex.h
-- Looking for include file glib/gregex.h - not found
-- Found GTS
-- Found GLUT: /usr/lib/x86_64-linux-gnu/libglut.so
-- USE QT5
-- Found QGLVIEWER-qt5: /usr/include/QGLViewer
-- Found GUI-Qt5-LIBS

-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so/usr/lib/x86_64-linux-gnu/libgmpxx.so-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so/usr/lib/x86_64-linux-gnu/libgmpxx.so

-- Found CGAL

-- SuiteSparse version 4.5.5 found, CHOLMOD direct solver for CPUactivated.

-- Found Cholmod: /usr/lib/x86_64-linux-gnu/libcholmod.so
-- Found OpenBlas: /usr/lib/x86_64-linux-gnu/libopenblas.so
-- Found Metis: /usr/include
-- Found Cholmod in /usr/lib/x86_64-linux-gnu/libcholmod.so
-- Found OpenBlas in /usr/lib/x86_64-linux-gnu/libopenblas.so
-- Found Metis in /usr/lib/x86_64-linux-gnu/libmetis.so
-- Found GL2PS

LBMFLOW is still experimental, building and running LBM engine are atyour own risk!

Yade will be installed to /media/datas/Yade/install
-- Suffix is set to -2018-03-14.git-45c88e0
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /media/datas/Yade2/install
-- Found gts: /usr/lib/python2.7/dist-packages/gts
-- Use system gts version
-- Found minieigen: /usr/lib/python2.7/dist-packages/minieigen.so
-- Found Tkinter: /usr/lib/python2.7/lib-tk/Tkinter.pyc
-- VTK version >5 is found
-- ===========================================================

-- Yade configured with following features: Odeint VTK OpenMP GTSGUI-Qt5 CGAL PFVFLOW TWOPHASEFLOW LINSOLV GL2PS LBMFLOW-- Disabled features: CHOLMOD_GPU SPH DEFORM LIQMIGRATIONMASK_ARBITRARY PROFILING PotentialParticles PotentialBlocks

-- Debug build
-- ===========================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /media/datas/Yade/build


William.


Le 14/03/2018 à 18:35, Robert Caulk a écrit :

Hello William,

There seems to be a deeper issue and the #include <random> is no morethan a bandaid that helps us narrow down the possible causes. I have afeeling this might track back to CMakeLists.txt. Do you mind providingthe output of your:


cmake -DCMAKE_INSTALL_PREFIX=../install ../trunk

command?

Cheers,

Robert

On Tue, Mar 13, 2018 at 2:06 AM, William Chèvremont<william.chevrem...@univ-grenoble-alpes.fr<mailto:william.chevrem...@univ-grenoble-alpes.fr>> wrote:


    Thanks Robert, that solved my issue.


    Le 12/03/2018 à 18:27, Robert Caulk a écrit :

    Hey Will,

    Looks like Thomas Chauve is encountering the same issue. I am
    unable to recreate this problem so will one of you please try adding:

    #include <random>

    to JointedCohesiveFrictionalpm.hpp and then recompiling?

    Thanks!

    Robert


    On Fri, Mar 9, 2018 at 10:51 AM, William Chèvremont
    <william.chevrem...@univ-grenoble-alpes.fr
    <mailto:william.chevrem...@univ-grenoble-alpes.fr>> wrote:

        In fact, for the git rebase, I updade py computer and forget
        to run this command again. Now fixed.

        For the compile error, my linux and compiler are following:

        >$ gcc --version
        gcc (Ubuntu 7.2.0-8ubuntu3.2) 7.2.0

        >$ lsb_release -a
        LSB Version:
        
core-9.20160110ubuntu5-amd64:core-9.20160110ubuntu5-noarch:security-9.20160110ubuntu5-amd64:security-9.20160110ubuntu5-noarch
        Distributor ID: Ubuntu
        Description:    Ubuntu 17.10
        Release:        17.10
        Codename:       artful

        I also get the same error on the cluster with this compiler:
        gcc (Debian 5.4.1-3) 5.4.1 20161019

        William.


        Le 09/03/2018 à 18:42, Bruno Chareyre a écrit :

        This being said I don't think the merge can be the cause of
        William's compile error.
        The question is why gcc can't find std::random_device.
        Just weird.
        B
        /
        /
        On 03/09/2018 06:35 PM, Bruno Chareyre wrote:

        Let us continue the discussion here on yade-dev, William is
        member.
        Merge commits are painful, as you suggest Robert it applies
        the upstream changes on the local trunk then it commits the
        merged code.
        In the log it looks like reapplying the same changes, the
        problem is if it's not reapplying exactly the same thing it
        can go unnoticed.
        This is known as "merge bubble" on the git forums.

        It can be avoided manually or, more simply, by changing the
        default behavior of git once for all (on a given machine):|
        git config branch.autosetuprebase always|

        Please always consider the above command before any commit
        to yade trunk.

        Cheers

        Bruno



        On 03/09/2018 06:08 PM, Robert Caulk wrote:

        Question #665387 on Yade changed:
        https://answers.launchpad.net/yade/+question/665387
        <https://answers.launchpad.net/yade/+question/665387>

             Status: Open => Answered

        Robert Caulk proposed the following answer:
        Hello William,

        Which linux distribution are you running? Which compiler are you using
        (gcc --version)?

        As Bruno mentions on yade-dev, your most recent build passes the
        buildbot [1] - so it may be a local problem. (I think Bruno's message
        [2] was not posted here as intended. He suggests you join yade-dev list
        serv [3] and send compiler questions there).

        Although it seems unlikely - is it possible this has something to do
        with this unusual merge of master with itself [4]? Is that a merge into
        your local repository? Perhaps you are you working off a read-only
        clone? Do you have duplicated commits on your local machine? I can't
        quite figure out what is going on there, the "merge" seems to simply add
        commits that are already committed to the repository.

        Cheers,

        Robert

        [1]https://yade-dem.org/buildbot/builders/yade-full/builds/4507
        <https://yade-dem.org/buildbot/builders/yade-full/builds/4507>
        [2]https://lists.launchpad.net/yade-dev/msg13755.html
        <https://lists.launchpad.net/yade-dev/msg13755.html>
        [3]https://launchpad.net/~yade-dev
        <https://launchpad.net/%7Eyade-dev>
        
[4]https://github.com/yade/trunk/commit/921bb17079fea51385fe620526f9bc48c055918e
        
<https://github.com/yade/trunk/commit/921bb17079fea51385fe620526f9bc48c055918e>




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Re: [Yade-dev] [Yade-users] [Question #665387]: Compile error JointedCohesiveFrictionalPM

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