'failed to import hit' and 'undefined symbol: MPI_UNWEIGHTED', even after uninstall/reinstall.
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Walter Kou
Jul 6, 2018, 12:36:19 PM7/6/18
to moose...@googlegroups.com
Hi all,
wkou@yogapad:~/projects/moose/test$ ./run_tests -j8
failed to import hit - try running "make hit" in the $MOOSE_DIR/test directory.
failed to import hit - try running "make hit" in the $MOOSE_DIR/test directory.
I encountered this error (again) even I first uninstall a) moose-environment and b) remove the whole repository:
sudo -E dpkg -r moose-environment
# See note below before performing the next command
sudo -E dpkg -r moose-framework # error on no this packagerm -rf ~/projects
Then I reinstall the environment: Ubuntu 16.04 Package version: Build 74, and setup module, module list
Currently Loaded Modulefiles:
1) miniconda 5) moose/.petsc-3.8.3_mpich-3.2_gcc-7.3.0-opt
2) moose-tools 6) moose/.tbb-2018_U3
3) moose/.gcc-7.3.0 7) moose/.cppunit-1.12.1_gcc-7.3.0
4) moose/.mpich-3.2_gcc-7.3.0 8) moose-dev-gcc
1) miniconda 5) moose/.petsc-3.8.3_mpich-3.2_gcc-7.3.0-opt
2) moose-tools 6) moose/.tbb-2018_U3
3) moose/.gcc-7.3.0 7) moose/.cppunit-1.12.1_gcc-7.3.0
4) moose/.mpich-3.2_gcc-7.3.0 8) moose-dev-gcc
I pull the master branch and rebuild it based on instruction, no error! But in the last step on 'run_tests', I get the above error on 'failed to import hit'.
I also tested some modules and get error on 'undefined symbol'
wkou@yogapad:~/projects/moose/modules/solid_mechanics/examples/bridge$ ../../solid_mechanics-opt -i bridge.i
../../solid_mechanics-opt: symbol lookup error: /opt/moose/mpich-3.2/gcc-7.3.0/lib/libmpifort.so.12: undefined symbol: MPI_UNWEIGHTED
../../solid_mechanics-opt: symbol lookup error: /opt/moose/mpich-3.2/gcc-7.3.0/lib/libmpifort.so.12: undefined symbol: MPI_UNWEIGHTED
My moose environment is: ~/projects/moose/test$ env
GCC_MAN=/opt/moose/gcc-7.3.0/share/man
CPLUS_INCLUDE_PATH=/opt/moose/mpich-3.2/gcc-7.3.0/include
MODULE_VERSION_STACK=3.2.10
XDG_VTNR=7
LC_PAPER=en_US.UTF-8
MANPATH=/opt/moose/mpich-3.2/gcc-7.3.0/share/man:/opt/moose/gcc-7.3.0/share/man:/opt/moose/gnuplot-4.6.5/share/man:/opt/moose/lcov-1.11/usr/share/man:/opt/moose/graphviz-2.38.0/share/man:/opt/moose/doxygen-1.8.11/man:/opt/moose/seacas/share/man:/home/wkou/SOFTWARES/LIBRARIESIBAMR/OPENMPI/share/man:/home/wkou/SOFTWARES/LIBRARIESIBAMR/OPENMPI/share/man:
LC_ADDRESS=en_US.UTF-8
XDG_SESSION_ID=c2
XDG_GREETER_DATA_DIR=/var/lib/lightdm-data/wkou
LC_MONETARY=en_US.UTF-8
CLUTTER_IM_MODULE=xim
DBUS_STARTER_ADDRESS=unix:abstract=/tmp/dbus-2hhDHgADcz,guid=59a44f58516b908887dd3d3a5b3f7b76
GPG_AGENT_INFO=/home/wkou/.gnupg/S.gpg-agent:0:1
ACCESS=/opt/moose/seacas
TERM=xterm-256color
VTE_VERSION=4205
XDG_MENU_PREFIX=gnome-
SHELL=/bin/bash
DERBY_HOME=/usr/lib/jvm/java-8-oracle/db
LIBRARY_PATH=/opt/moose/tbb-2018_U3/lib
QT_LINUX_ACCESSIBILITY_ALWAYS_ON=1
FPATH=/opt/moose/mpich-3.2/gcc-7.3.0/include
WINDOWID=37750342
LC_NUMERIC=en_US.UTF-8
TBB_DIR=/opt/moose/tbb-2018_U3
UPSTART_SESSION=unix:abstract=/com/ubuntu/upstart-session/1000/1837
GNOME_KEYRING_CONTROL=
visit210=/home/wkou/SOFTWARES/VISIT210/visit_install/bin/visit
GTK_MODULES=gail:atk-bridge
USER=wkou
MOOSE_JOBS=4
LD_LIBRARY_PATH=/opt/moose/tbb-2018_U3/lib:/opt/moose/gcc-7.3.0/lib64:/opt/moose/gcc-7.3.0/lib:/opt/moose/gcc-7.3.0/lib/i386:/opt/moose/seacas/lib:/home/wkou/SOFTWARES/GSL/gsl_install/lib:/home/wkou/SOFTWARES/LIBRARIESIBAMR/OPENMPI/lib:/usr/local/lib
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
QT_ACCESSIBILITY=1
LC_TELEPHONE=en_US.UTF-8
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
CPATH=/opt/moose/tbb-2018_U3/include
SSH_AUTH_SOCK=/run/user/1000/keyring/ssh
ZEITGEIST_DATA_PATH=/home/wkou/.local/share/zeitgeist
SESSION_MANAGER=local/yogapad:@/tmp/.ICE-unix/2033,unix/yogapad:/tmp/.ICE-unix/2033
DEFAULTS_PATH=/usr/share/gconf/gnome.default.path
XDG_CONFIG_DIRS=/etc/xdg/xdg-gnome:/usr/share/upstart/xdg:/etc/xdg
MODULE_VERSION=3.2.10
DESKTOP_SESSION=gnome
PATH=/opt/moose/cppunit-1.12.1/gcc-7.3.0/bin:/opt/moose/mpich-3.2/gcc-7.3.0/bin:/opt/moose/llvm-5.0.1/bin:/opt/moose/gcc-7.3.0/bin:/opt/moose/miniconda/bin:/opt/moose/gnuplot-4.6.5/bin:/opt/moose/lcov-1.11/usr/bin:/opt/moose/graphviz-2.38.0/bin:/opt/moose/doxygen-1.8.11/bin:/opt/moose/seacas/bin:/opt/moose/seacas/etc:/home/wkou/node-v6.11.3-linux-x64/bin:/home/wkou/SOFTWARES/SOFTWARES/GSL/gsl_install/bin:/home/wkou/SOFTWARES/LIBRARIESIBAMR/OPENMPI/bin:/home/wkou/node-v6.11.3-linux-x64/bin:/home/wkou/SOFTWARES/SOFTWARES/GSL/gsl_install/bin:/home/wkou/SOFTWARES/LIBRARIESIBAMR/OPENMPI/bin:/opt/texbin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/usr/local/texlive/2015/bin/x86_64-linux/:/usr/local/lib/:/home/wkou/SOFTWARES/VISIT210/visit_install/bin:/usr/local/lib/:/home/wkou/SOFTWARES/VISIT210/visit_install/bin
GCC_BIN=/opt/moose/gcc-7.3.0/bin
QT_IM_MODULE=ibus
QT_QPA_PLATFORMTHEME=appmenu-qt5
TBBROOT=/opt/moose/tbb-2018_U3
C_INCLUDE_PATH=/opt/moose/mpich-3.2/gcc-7.3.0/include
LC_IDENTIFICATION=en_US.UTF-8
F90=mpif90
XDG_SESSION_TYPE=x11
PWD=/home/wkou/projects/moose/test
JOB=xsession-init
_LMFILES_=/opt/moose/Modules/3.2.10/modulefiles/miniconda:/opt/moose/Modules/3.2.10/modulefiles/moose-tools:/opt/moose/Modules/3.2.10/modulefiles/moose/.gcc-7.3.0:/opt/moose/Modules/3.2.10/modulefiles/moose/.mpich-3.2_gcc-7.3.0:/opt/moose/Modules/3.2.10/modulefiles/moose/.petsc-3.8.3_mpich-3.2_gcc-7.3.0-opt:/opt/moose/Modules/3.2.10/modulefiles/moose/.tbb-2018_U3:/opt/moose/Modules/3.2.10/modulefiles/moose/.cppunit-1.12.1_gcc-7.3.0:/opt/moose/Modules/3.2.10/modulefiles/moose-dev-gcc
XMODIFIERS=@im
JAVA_HOME=/usr/lib/jvm/java-8-oracle
MPLBACKEND=qt5Agg
GNOME_KEYRING_PID=
LANG=en_US.UTF-8
MODULEPATH=/opt/moose/Modules/versions:/opt/moose/Modules/$MODULE_VERSION/modulefiles:/opt/moose/Modules/modulefiles
GDM_LANG=en_US
MANDATORY_PATH=/usr/share/gconf/gnome.mandatory.path
LOADEDMODULES=miniconda:moose-tools:moose/.gcc-7.3.0:moose/.mpich-3.2_gcc-7.3.0:moose/.petsc-3.8.3_mpich-3.2_gcc-7.3.0-opt:moose/.tbb-2018_U3:moose/.cppunit-1.12.1_gcc-7.3.0:moose-dev-gcc
LC_MEASUREMENT=en_US.UTF-8
IM_CONFIG_PHASE=1
F77=mpif77
PAPERSIZE=letter
GDMSESSION=gnome
CXX=mpicxx
SESSIONTYPE=gnome-session
DBUS_STARTER_BUS_TYPE=session
GTK2_MODULES=overlay-scrollbar
SHLVL=1
HOME=/home/wkou
XDG_SEAT=seat0
LANGUAGE=en_US:en
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
GCC_LIB=/opt/moose/gcc-7.3.0/lib:/opt/moose/gcc-7.3.0/lib/i386
FC=mpif90
CPPUNIT_DIR=/opt/moose/cppunit-1.12.1/gcc-7.3.0
UPSTART_INSTANCE=
UPSTART_EVENTS=starting
XDG_SESSION_DESKTOP=gnome
LOGNAME=wkou
J2SDKDIR=/usr/lib/jvm/java-8-oracle
XDG_DATA_DIRS=/usr/share/gnome:/usr/local/share:/usr/share:/var/lib/snapd/desktop:/var/lib/snapd/desktop
QT4_IM_MODULE=xim
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-2hhDHgADcz,guid=59a44f58516b908887dd3d3a5b3f7b76
MPI_HOME=/opt/moose/mpich-3.2/gcc-7.3.0
MODULESHOME=/opt/moose/Modules/3.2.10
LESSOPEN=| /usr/bin/lesspipe %s
INSTANCE=
UPSTART_JOB=dbus
CC=mpicc
DBUS_DEBUG_OUTPUT=1
XDG_RUNTIME_DIR=/run/user/1000
DISPLAY=:0
INCLUDE=/opt/moose/cppunit-1.12.1/gcc-7.3.0/include
MOOSE_PPS_WIDTH=180
XDG_CURRENT_DESKTOP=GNOME
GTK_IM_MODULE=ibus
J2REDIR=/usr/lib/jvm/java-8-oracle/jre
PETSC_DIR=/opt/moose/petsc-3.8.3/mpich-3.2_gcc-7.3.0-opt
LESSCLOSE=/usr/bin/lesspipe %s %s
LC_TIME=en_US.UTF-8
LC_NAME=en_US.UTF-8
XAUTHORITY=/home/wkou/.Xauthority
BASH_FUNC_module%%=() { eval `/opt/moose/Modules/$MODULE_VERSION/bin/modulecmd bash $*`
}
_=/usr/bin/env
OLDPWD=/home/wkou/projects/moose
CPLUS_INCLUDE_PATH=/opt/moose/mpich-3.2/gcc-7.3.0/include
MODULE_VERSION_STACK=3.2.10
XDG_VTNR=7
LC_PAPER=en_US.UTF-8
MANPATH=/opt/moose/mpich-3.2/gcc-7.3.0/share/man:/opt/moose/gcc-7.3.0/share/man:/opt/moose/gnuplot-4.6.5/share/man:/opt/moose/lcov-1.11/usr/share/man:/opt/moose/graphviz-2.38.0/share/man:/opt/moose/doxygen-1.8.11/man:/opt/moose/seacas/share/man:/home/wkou/SOFTWARES/LIBRARIESIBAMR/OPENMPI/share/man:/home/wkou/SOFTWARES/LIBRARIESIBAMR/OPENMPI/share/man:
LC_ADDRESS=en_US.UTF-8
XDG_SESSION_ID=c2
XDG_GREETER_DATA_DIR=/var/lib/lightdm-data/wkou
LC_MONETARY=en_US.UTF-8
CLUTTER_IM_MODULE=xim
DBUS_STARTER_ADDRESS=unix:abstract=/tmp/dbus-2hhDHgADcz,guid=59a44f58516b908887dd3d3a5b3f7b76
GPG_AGENT_INFO=/home/wkou/.gnupg/S.gpg-agent:0:1
ACCESS=/opt/moose/seacas
TERM=xterm-256color
VTE_VERSION=4205
XDG_MENU_PREFIX=gnome-
SHELL=/bin/bash
DERBY_HOME=/usr/lib/jvm/java-8-oracle/db
LIBRARY_PATH=/opt/moose/tbb-2018_U3/lib
QT_LINUX_ACCESSIBILITY_ALWAYS_ON=1
FPATH=/opt/moose/mpich-3.2/gcc-7.3.0/include
WINDOWID=37750342
LC_NUMERIC=en_US.UTF-8
TBB_DIR=/opt/moose/tbb-2018_U3
UPSTART_SESSION=unix:abstract=/com/ubuntu/upstart-session/1000/1837
GNOME_KEYRING_CONTROL=
visit210=/home/wkou/SOFTWARES/VISIT210/visit_install/bin/visit
GTK_MODULES=gail:atk-bridge
USER=wkou
MOOSE_JOBS=4
LD_LIBRARY_PATH=/opt/moose/tbb-2018_U3/lib:/opt/moose/gcc-7.3.0/lib64:/opt/moose/gcc-7.3.0/lib:/opt/moose/gcc-7.3.0/lib/i386:/opt/moose/seacas/lib:/home/wkou/SOFTWARES/GSL/gsl_install/lib:/home/wkou/SOFTWARES/LIBRARIESIBAMR/OPENMPI/lib:/usr/local/lib
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
QT_ACCESSIBILITY=1
LC_TELEPHONE=en_US.UTF-8
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
CPATH=/opt/moose/tbb-2018_U3/include
SSH_AUTH_SOCK=/run/user/1000/keyring/ssh
ZEITGEIST_DATA_PATH=/home/wkou/.local/share/zeitgeist
SESSION_MANAGER=local/yogapad:@/tmp/.ICE-unix/2033,unix/yogapad:/tmp/.ICE-unix/2033
DEFAULTS_PATH=/usr/share/gconf/gnome.default.path
XDG_CONFIG_DIRS=/etc/xdg/xdg-gnome:/usr/share/upstart/xdg:/etc/xdg
MODULE_VERSION=3.2.10
DESKTOP_SESSION=gnome
PATH=/opt/moose/cppunit-1.12.1/gcc-7.3.0/bin:/opt/moose/mpich-3.2/gcc-7.3.0/bin:/opt/moose/llvm-5.0.1/bin:/opt/moose/gcc-7.3.0/bin:/opt/moose/miniconda/bin:/opt/moose/gnuplot-4.6.5/bin:/opt/moose/lcov-1.11/usr/bin:/opt/moose/graphviz-2.38.0/bin:/opt/moose/doxygen-1.8.11/bin:/opt/moose/seacas/bin:/opt/moose/seacas/etc:/home/wkou/node-v6.11.3-linux-x64/bin:/home/wkou/SOFTWARES/SOFTWARES/GSL/gsl_install/bin:/home/wkou/SOFTWARES/LIBRARIESIBAMR/OPENMPI/bin:/home/wkou/node-v6.11.3-linux-x64/bin:/home/wkou/SOFTWARES/SOFTWARES/GSL/gsl_install/bin:/home/wkou/SOFTWARES/LIBRARIESIBAMR/OPENMPI/bin:/opt/texbin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/usr/local/texlive/2015/bin/x86_64-linux/:/usr/local/lib/:/home/wkou/SOFTWARES/VISIT210/visit_install/bin:/usr/local/lib/:/home/wkou/SOFTWARES/VISIT210/visit_install/bin
GCC_BIN=/opt/moose/gcc-7.3.0/bin
QT_IM_MODULE=ibus
QT_QPA_PLATFORMTHEME=appmenu-qt5
TBBROOT=/opt/moose/tbb-2018_U3
C_INCLUDE_PATH=/opt/moose/mpich-3.2/gcc-7.3.0/include
LC_IDENTIFICATION=en_US.UTF-8
F90=mpif90
XDG_SESSION_TYPE=x11
PWD=/home/wkou/projects/moose/test
JOB=xsession-init
_LMFILES_=/opt/moose/Modules/3.2.10/modulefiles/miniconda:/opt/moose/Modules/3.2.10/modulefiles/moose-tools:/opt/moose/Modules/3.2.10/modulefiles/moose/.gcc-7.3.0:/opt/moose/Modules/3.2.10/modulefiles/moose/.mpich-3.2_gcc-7.3.0:/opt/moose/Modules/3.2.10/modulefiles/moose/.petsc-3.8.3_mpich-3.2_gcc-7.3.0-opt:/opt/moose/Modules/3.2.10/modulefiles/moose/.tbb-2018_U3:/opt/moose/Modules/3.2.10/modulefiles/moose/.cppunit-1.12.1_gcc-7.3.0:/opt/moose/Modules/3.2.10/modulefiles/moose-dev-gcc
XMODIFIERS=@im
JAVA_HOME=/usr/lib/jvm/java-8-oracle
MPLBACKEND=qt5Agg
GNOME_KEYRING_PID=
LANG=en_US.UTF-8
MODULEPATH=/opt/moose/Modules/versions:/opt/moose/Modules/$MODULE_VERSION/modulefiles:/opt/moose/Modules/modulefiles
GDM_LANG=en_US
MANDATORY_PATH=/usr/share/gconf/gnome.mandatory.path
LOADEDMODULES=miniconda:moose-tools:moose/.gcc-7.3.0:moose/.mpich-3.2_gcc-7.3.0:moose/.petsc-3.8.3_mpich-3.2_gcc-7.3.0-opt:moose/.tbb-2018_U3:moose/.cppunit-1.12.1_gcc-7.3.0:moose-dev-gcc
LC_MEASUREMENT=en_US.UTF-8
IM_CONFIG_PHASE=1
F77=mpif77
PAPERSIZE=letter
GDMSESSION=gnome
CXX=mpicxx
SESSIONTYPE=gnome-session
DBUS_STARTER_BUS_TYPE=session
GTK2_MODULES=overlay-scrollbar
SHLVL=1
HOME=/home/wkou
XDG_SEAT=seat0
LANGUAGE=en_US:en
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
GCC_LIB=/opt/moose/gcc-7.3.0/lib:/opt/moose/gcc-7.3.0/lib/i386
FC=mpif90
CPPUNIT_DIR=/opt/moose/cppunit-1.12.1/gcc-7.3.0
UPSTART_INSTANCE=
UPSTART_EVENTS=starting
XDG_SESSION_DESKTOP=gnome
LOGNAME=wkou
J2SDKDIR=/usr/lib/jvm/java-8-oracle
XDG_DATA_DIRS=/usr/share/gnome:/usr/local/share:/usr/share:/var/lib/snapd/desktop:/var/lib/snapd/desktop
QT4_IM_MODULE=xim
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-2hhDHgADcz,guid=59a44f58516b908887dd3d3a5b3f7b76
MPI_HOME=/opt/moose/mpich-3.2/gcc-7.3.0
MODULESHOME=/opt/moose/Modules/3.2.10
LESSOPEN=| /usr/bin/lesspipe %s
INSTANCE=
UPSTART_JOB=dbus
CC=mpicc
DBUS_DEBUG_OUTPUT=1
XDG_RUNTIME_DIR=/run/user/1000
DISPLAY=:0
INCLUDE=/opt/moose/cppunit-1.12.1/gcc-7.3.0/include
MOOSE_PPS_WIDTH=180
XDG_CURRENT_DESKTOP=GNOME
GTK_IM_MODULE=ibus
J2REDIR=/usr/lib/jvm/java-8-oracle/jre
PETSC_DIR=/opt/moose/petsc-3.8.3/mpich-3.2_gcc-7.3.0-opt
LESSCLOSE=/usr/bin/lesspipe %s %s
LC_TIME=en_US.UTF-8
LC_NAME=en_US.UTF-8
XAUTHORITY=/home/wkou/.Xauthority
BASH_FUNC_module%%=() { eval `/opt/moose/Modules/$MODULE_VERSION/bin/modulecmd bash $*`
}
_=/usr/bin/env
OLDPWD=/home/wkou/projects/moose
Walter
Walter Kou
Jul 6, 2018, 6:01:27 PM7/6/18
to moose...@googlegroups.com
The two issues were fixed, after looking into the module files. I wrote it in detail as below to save other's time.
1) symbol lookup error: libmpifort.so.12?, as below:
wkou@yogapad:~/projects/moose/modules/solid_mechanics/examples/bridge$ ../../solid_mechanics-opt -i bridge.i
../../solid_mechanics-opt: symbol lookup error: /opt/moose/mpich-3.2/gcc-7.3.0/lib/libmpifort.so.12: undefined symbol: MPI_UNWEIGHTED
../../solid_mechanics-opt: symbol lookup error: /opt/moose/mpich-3.2/gcc-7.3.0/lib/libmpifort.so.12: undefined symbol: MPI_UNWEIGHTED
This is actually because 'LD_LIBRARY_PATH' from loaded module does not prepend '/opt/moose/mpich-3.2/gcc-7.3.0/lib', but other libs (like gcc..) are added by the module load. Therefore, my built-in openmpi library is linked instead.
One can test it: $ echo $LD_LIBRARY_PATH
fix: export LD_LIBRARY_PATH=/opt/moose/mpich-3.2/gcc-7.3.0/lib:$LD_LIBRARY_PATH
suggestion: prepend this library in module file.
2) 'failed to import hit - try running "make hit" in the $MOOSE_DIR/test directory.'
I check the several module files in /opt/moose/Module and found $MOOSE_DIR, if it exists, can 'help' to find/add $MOOSE_DIR/python
So what I did is to
1) first add below lines in '~/.bashrc'
module unload moose-tools moose-dev-gcc
alias load_moose='module load moose-tools moose-dev-gcc'
alias unload_moose='module unload moose-tools moose-dev-gcc'
export LD_LIBRARY_PATH=/opt/moose/mpich-3.2/gcc-7.3.0/lib:$LD_LIBRARY_PATH
export MOOSE_DIR=~/projects/moose
alias load_moose='module load moose-tools moose-dev-gcc'
alias unload_moose='module unload moose-tools moose-dev-gcc'
export LD_LIBRARY_PATH=/opt/moose/mpich-3.2/gcc-7.3.0/lib:$LD_LIBRARY_PATH
export MOOSE_DIR=~/projects/moose
## By default, moose module is unloaded, as I need to use native libs. to run other applications sometime to avoid conflict.
## one need to run 'load_moose' before using moose.
2) $ load_moose
# this will load moose with $MOOSE_DIR set and openmpi library path prepended
3) cd $MOOSE_DIR/test
make clean # remove old built in my case
make -j8
4) ./run_test -j8
# got error on 'failed to import hit'
5) make hit
6) ./run_test -j8
# Everything is OK
Thanks,
Walter
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