symbol lookup error
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Gyan
Nov 4, 2015, 1:50:07 PM11/4/15
to moose-users
Hi,
I am getting the following error when I include mpiexec. Earlier this example used to run fine and I have not updated Bison recently. So, it appears that something has changed on my computer, but I cannot figure it out.
~/projects/bison/examples/2D-RZ_rodlet_10pellets$ mpiexec -n 16 ../../bison-opt -i input.i
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
--------------------------------------------------------------------------
mpiexec noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
Please note that these are 16 error statements for 16 processors. When I specify 8 processor, it gives 8 error statements.
Without mpiexec it runs fine.
Thanks,
Gyan
I am getting the following error when I include mpiexec. Earlier this example used to run fine and I have not updated Bison recently. So, it appears that something has changed on my computer, but I cannot figure it out.
~/projects/bison/examples/2D-RZ_rodlet_10pellets$ mpiexec -n 16 ../../bison-opt -i input.i
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
../../bison-opt: symbol lookup error: /opt/moose/openmpi/openmpi-1.8.1/gcc-opt/lib/libmpi_mpifh.so.2: undefined symbol: mpi_fortran_weights_empty
--------------------------------------------------------------------------
mpiexec noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
Please note that these are 16 error statements for 16 processors. When I specify 8 processor, it gives 8 error statements.
Without mpiexec it runs fine.
Thanks,
Gyan
Cody Permann
Nov 4, 2015, 2:15:35 PM11/4/15
to moose-users
Did you update your MOOSE package recently?
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Gyan
Nov 4, 2015, 2:23:44 PM11/4/15
to moose-users
No, I did not update it since several months.
After this error showed up today, I updated libmesh and recompiled the Bison code again, but that didn't help.
Gyan
After this error showed up today, I updated libmesh and recompiled the Bison code again, but that didn't help.
Gyan
Miller, Jason M
Nov 4, 2015, 2:27:08 PM11/4/15
to moose...@googlegroups.com
Is this on Linux or Mac? Also, what is the package version you currently have installed:
cat /opt/moose/build
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Gyan
Nov 4, 2015, 2:38:13 PM11/4/15
to moose-users
This is on Linux (Ubuntu 14.04). Package version is 1.1-13.
Gyan
Gyan
Miller, Jason M
Nov 4, 2015, 3:08:06 PM11/4/15
to moose...@googlegroups.com
Its possible a system update has caused the underlying GNU implementation to change enough, where that specific version of our package is requiring some symbol no longer available.
The only easy solution I know of to get around this, is to try and use the latest available version of the package (1.1-24). However, if your system was updated recently, there is no guarantee that the latest available package will work (because the latest available package was built earlier in Jun of this year).
If you decide to try the latest available version, please let us know if that worked or not!
Jason
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Derek Gaston
Nov 5, 2015, 8:37:34 AM11/5/15
to moose...@googlegroups.com
Maybe he accidentally installed a system MPI? It could have come in as a dependency on something else he installed...
We REALLY need to figure out how to ignore system MPI...
Derek
We REALLY need to figure out how to ignore system MPI...
Derek
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Gyan
Nov 5, 2015, 10:16:40 AM11/5/15
to moose-users
Here is the log of the system update after which things stopped working:
Start-Date: 2015-11-04 10:02:22
Commandline: aptdaemon role='role-commit-packages' sender=':1.73568'
Upgrade: libvte-2.90-9:amd64 (0.34.9-1ubuntu1, 0.34.9-1ubuntu2), gir1.2-vte-2.90:amd64 (0.34.9-1ubuntu1, 0.34.9-1ubuntu2), shotwell-common:amd64 (0.18.0-0ubuntu4.3, 0.18.0-0ubuntu4.4), shotwell:amd64 (0.18.0-0ubuntu4.3, 0.18.0-0ubuntu4.4), libvte-2.90-common:amd64 (0.34.9-1ubuntu1, 0.34.9-1ubuntu2), libmtp9:amd64 (1.1.6-20-g1b9f164-1ubuntu2, 1.1.6-20-g1b9f164-1ubuntu2.1), libmtp-common:amd64 (1.1.6-20-g1b9f164-1ubuntu2, 1.1.6-20-g1b9f164-1ubuntu2.1), linux-firmware:amd64 (1.127.15, 1.127.16), libmtp-runtime:amd64 (1.1.6-20-g1b9f164-1ubuntu2, 1.1.6-20-g1b9f164-1ubuntu2.1)
End-Date: 2015-11-04 10:02:39
Can't directly see something related to MPI here, but it might be included. I think there is something in this update which has caused it; after this update the error showed up.
I will try to update Bison and see if that fixes anything. I am assuming that latest version of Bison will come with latest version of Moose.
Thanks,
Gyan
Start-Date: 2015-11-04 10:02:22
Commandline: aptdaemon role='role-commit-packages' sender=':1.73568'
Upgrade: libvte-2.90-9:amd64 (0.34.9-1ubuntu1, 0.34.9-1ubuntu2), gir1.2-vte-2.90:amd64 (0.34.9-1ubuntu1, 0.34.9-1ubuntu2), shotwell-common:amd64 (0.18.0-0ubuntu4.3, 0.18.0-0ubuntu4.4), shotwell:amd64 (0.18.0-0ubuntu4.3, 0.18.0-0ubuntu4.4), libvte-2.90-common:amd64 (0.34.9-1ubuntu1, 0.34.9-1ubuntu2), libmtp9:amd64 (1.1.6-20-g1b9f164-1ubuntu2, 1.1.6-20-g1b9f164-1ubuntu2.1), libmtp-common:amd64 (1.1.6-20-g1b9f164-1ubuntu2, 1.1.6-20-g1b9f164-1ubuntu2.1), linux-firmware:amd64 (1.127.15, 1.127.16), libmtp-runtime:amd64 (1.1.6-20-g1b9f164-1ubuntu2, 1.1.6-20-g1b9f164-1ubuntu2.1)
End-Date: 2015-11-04 10:02:39
Can't directly see something related to MPI here, but it might be included. I think there is something in this update which has caused it; after this update the error showed up.
I will try to update Bison and see if that fixes anything. I am assuming that latest version of Bison will come with latest version of Moose.
Thanks,
Gyan
Gyan
Nov 5, 2015, 3:52:51 PM11/5/15
to moose-users
I updated Bison and Moose (1.1-24). Now it shows a different error:
~/projects/bison/examples/2D-RZ_rodlet_10pellets$ mpiexec -n 16 ../../bison-opt -i input.i
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
../../bison-opt: error while loading shared libraries: libpetsc.so.3.5: cannot open shared object file: No such file or directory
--------------------------------------------------------------------------
mpiexec noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
Gyan
Miller, Jason M
Nov 5, 2015, 4:33:29 PM11/5/15
to moose...@googlegroups.com
Can you get me the results of the following commands:
module list
env
cat ~/projects/bison/moose/libmesh/build/config.log
ldd ~/projects/bison/bison-opt
Thanks!
Jason
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Gyan
Nov 6, 2015, 9:59:32 AM11/6/15
to moose-users
Here is the output:
~$ echo $PETSC_DIR
/opt/moose/petsc/openmpi_petsc-3.6.0/gcc-opt-superlu
~$ module list
Currently Loaded Modulefiles:
1) moose/.gcc_4.9.1
2) moose/.tbb
3) moose/.openmpi-1.8.4_gcc
4) moose/.openmpi_petsc-3.6.0-gcc-superlu
5) moose-tools
6) moose/.vtk6
7) moose-dev-gcc
~$ env
GCC_MAN=/opt/moose/gcc_4.9.1/share/man
CPLUS_INCLUDE_PATH=/opt/moose/openmpi/openmpi-1.8.4/gcc-opt/include
MODULE_VERSION_STACK=3.2.10
XDG_VTNR=7
MANPATH=/opt/moose/openmpi/openmpi-1.8.4/gcc-opt/share/man:/opt/moose/gcc_4.9.1/share/man:/usr/share/man
XDG_SESSION_ID=c2
VTKINCLUDE_DIR=/opt/moose/vtk-6.1/include/vtk-6.1
CLUTTER_IM_MODULE=xim
SELINUX_INIT=YES
XDG_GREETER_DATA_DIR=/var/lib/lightdm-data/g********
GPG_AGENT_INFO=/run/user/8158/keyring-YUTyh6/gpg:0:1
ACCESS=/opt/moose/SEACAS
TERM=xterm
SHELL=/bin/bash
VTE_VERSION=3409
LIBRARY_PATH=/opt/moose/tbb/lib/intel64/cc4.1.0_libc2.4_kernel2.6.16.21
FPATH=/opt/moose/openmpi/openmpi-1.8.4/gcc-opt/include
WINDOWID=56623116
TBB_DIR=/opt/moose/tbb
UPSTART_SESSION=unix:abstract=/com/ubuntu/upstart-session/8158/2527
GNOME_KEYRING_CONTROL=/run/user/8158/keyring-YUTyh6
INCLUDE_PATH=/opt/moose/vtk-6.1/include/vtk-6.1
GTK_MODULES=overlay-scrollbar:unity-gtk-module
XLIB_SKIP_ARGB_VISUALS=1
USER=g********
LD_LIBRARY_PATH=/opt/moose/vtk-6.1/lib:/opt/moose/openmpi/openmpi-1.8.4/gcc-opt/lib:/opt/moose/tbb/lib/intel64/cc4.1.0_libc2.4_kernel2.6.16.21:/opt/moose/gcc_4.9.1/lib64
MOOSE_JOBS=16
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: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:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=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:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=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:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=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:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
CPATH=/opt/moose/tbb/include
SSH_AUTH_SOCK=/run/user/8158/keyring-YUTyh6/ssh
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/usr/share/upstart/xdg:/etc/xdg
MODULE_VERSION=3.2.10
PATH=/media/g********/SIM_Abaqus_Extend.AllOS/IsightSEE5.9-2-Linux:/home/g********/Downloads/Cubit-15.0-Lin64-sculpt/bin:/home/g********/Downloads/ParaView-4.3.1-Linux-64bit/bin:/opt/intel/bin:/home/g********/SIMULIA/Commands:/home/g********/projects/moose/gui:/opt/moose/SEACAS/bin:/opt/moose/SEACAS/etc:/opt/moose/miniconda/bin:/opt/moose/openmpi/openmpi-1.8.4/gcc-opt/bin:/opt/moose/gcc_4.9.1/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
DESKTOP_SESSION=ubuntu
GCC_BIN=/opt/moose/gcc_4.9.1/bin
QT_IM_MODULE=ibus
QT_QPA_PLATFORMTHEME=appmenu-qt5
TBBROOT=/opt/moose/tbb
C_INCLUDE_PATH=/opt/moose/openmpi/openmpi-1.8.4/gcc-opt/include
F90=mpif90
JOB=gnome-session
PWD=/home/g********
_LMFILES_=/opt/moose/Modules/3.2.10/modulefiles/moose/.gcc_4.9.1:/opt/moose/Modules/3.2.10/modulefiles/moose/.tbb:/opt/moose/Modules/3.2.10/modulefiles/moose/.openmpi-1.8.4_gcc:/opt/moose/Modules/3.2.10/modulefiles/moose/.openmpi_petsc-3.6.0-gcc-superlu:/opt/moose/Modules/3.2.10/modulefiles/moose-tools:/opt/moose/Modules/3.2.10/modulefiles/moose/.vtk6:/opt/moose/Modules/3.2.10/modulefiles/moose-dev-gcc
XMODIFIERS=@im=ibus
GNOME_KEYRING_PID=2524
LANG=en_US.UTF-8
MODULEPATH=/opt/moose/Modules/versions:/opt/moose/Modules/$MODULE_VERSION/modulefiles:/opt/moose/Modules/modulefiles:/opt/moose/Modules/3.2.10/openmpi_gcc
GDM_LANG=en
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
LOADEDMODULES=moose/.gcc_4.9.1:moose/.tbb:moose/.openmpi-1.8.4_gcc:moose/.openmpi_petsc-3.6.0-gcc-superlu:moose-tools:moose/.vtk6:moose-dev-gcc
IM_CONFIG_PHASE=1
COMPIZ_CONFIG_PROFILE=ubuntu
F77=mpif77
GDMSESSION=ubuntu
CXX=mpicxx
SESSIONTYPE=gnome-session
HOME=/home/g********
XDG_SEAT=seat0
SHLVL=1
QT_API=pyside
LANGUAGE=en_US:
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
GCC_LIB=/opt/moose/gcc_4.9.1/lib64
FC=mpif90
UPSTART_INSTANCE=
VTKLIB_DIR=/opt/moose/vtk-6.1/lib
PYTHONPATH=/home/g********/Downloads/Cubit-14.1-Lin64/bin:
UPSTART_EVENTS=started starting
LOGNAME=g********
QT4_IM_MODULE=xim
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/share/gnome:/usr/local/share/:/usr/share/
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-ZqpjaTDrpq
MPI_HOME=/opt/moose/openmpi/openmpi-1.8.4/gcc-opt
MODULESHOME=/opt/moose/Modules/3.2.10
LESSOPEN=| /usr/bin/lesspipe %s
INSTANCE=Unity
UPSTART_JOB=unity-settings-daemon
TEXTDOMAIN=im-config
CC=mpicc
XDG_RUNTIME_DIR=/run/user/8158
DISPLAY=:0
MOOSE_PPS_WIDTH=180
XDG_CURRENT_DESKTOP=Unity
GTK_IM_MODULE=ibus
PETSC_DIR=/opt/moose/petsc/openmpi_petsc-3.6.0/gcc-opt-superlu
LESSCLOSE=/usr/bin/lesspipe %s %s
TEXTDOMAINDIR=/usr/share/locale/
COLORTERM=gnome-terminal
XAUTHORITY=/home/g********/.Xauthority
BASH_FUNC_module%%=() { eval `/opt/moose/Modules/$MODULE_VERSION/bin/modulecmd bash $*`
}
_=/usr/bin/env
~$ ldd ~/projects/bison/bison-opt
linux-vdso.so.1 => (0x00007ffec3de1000)
libbison-opt.so.0 => /home/g********/projects/bison/lib/libbison-opt.so.0 (0x00007f9dc55e9000)
libwater_steam_eos-opt.so.0 => /home/g********/projects/bison/moose/modules/water_steam_eos/lib/libwater_steam_eos-opt.so.0 (0x00007f9dc53c5000)
libsolid_mechanics-opt.so.0 => /home/g********/projects/bison/moose/modules/solid_mechanics/lib/libsolid_mechanics-opt.so.0 (0x00007f9dc4f2c000)
libtensor_mechanics-opt.so.0 => /home/g********/projects/bison/moose/modules/tensor_mechanics/lib/libtensor_mechanics-opt.so.0 (0x00007f9dc4a9b000)
libmisc-opt.so.0 => /home/g********/projects/bison/moose/modules/misc/lib/libmisc-opt.so.0 (0x00007f9dc4814000)
liblinear_elasticity-opt.so.0 => /home/g********/projects/bison/moose/modules/linear_elasticity/lib/liblinear_elasticity-opt.so.0 (0x00007f9dc45d2000)
libheat_conduction-opt.so.0 => /home/g********/projects/bison/moose/modules/heat_conduction/lib/libheat_conduction-opt.so.0 (0x00007f9dc431a000)
libcontact-opt.so.0 => /home/g********/projects/bison/moose/modules/contact/lib/libcontact-opt.so.0 (0x00007f9dc4040000)
libmoose-opt.so.0 => /home/g********/projects/bison/moose/framework/libmoose-opt.so.0 (0x00007f9dc315e000)
libpcre-opt.so.0 => /home/g********/projects/bison/moose/framework/contrib/pcre/libpcre-opt.so.0 (0x00007f9dc2f32000)
libice_updater-opt.so.0 => /home/g********/projects/bison/moose/framework/contrib/ice_updater/libice_updater-opt.so.0 (0x00007f9dc2d04000)
libgcc_s.so.1 => /opt/moose/gcc_4.9.1/lib64/libgcc_s.so.1 (0x00007f9dc2aee000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f9dc28d0000)
libmesh_opt.so.0 => /home/g********/projects/bison/moose/scripts/../libmesh/installed/lib/libmesh_opt.so.0 (0x00007f9dc16ee000)
libnetcdf.so.7 => /home/g********/projects/bison/moose/scripts/../libmesh/installed/lib/libnetcdf.so.7 (0x00007f9dc1408000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f9dc11ef000)
libtbb.so.2 => /opt/moose/tbb/lib/intel64/cc4.1.0_libc2.4_kernel2.6.16.21/libtbb.so.2 (0x00007f9dc5c99000)
libtbbmalloc.so.2 => /opt/moose/tbb/lib/intel64/cc4.1.0_libc2.4_kernel2.6.16.21/libtbbmalloc.so.2 (0x00007f9dc10a0000)
libpetsc.so.3.5 => not found
libparmetis.so => not found
libmetis.so => not found
libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f9dc0d6b000)
libmpi_usempi.so.1 => /opt/moose/openmpi/openmpi-1.8.4/gcc-opt/lib/libmpi_usempi.so.1 (0x00007f9dc0b6a000)
libmpi_mpifh.so.2 => /opt/moose/openmpi/openmpi-1.8.4/gcc-opt/lib/libmpi_mpifh.so.2 (0x00007f9dc0911000)
libgfortran.so.3 => /opt/moose/gcc_4.9.1/lib64/libgfortran.so.3 (0x00007f9dc05f4000)
libquadmath.so.0 => /opt/moose/gcc_4.9.1/lib64/libquadmath.so.0 (0x00007f9dc03b7000)
libgomp.so.1 => /opt/moose/gcc_4.9.1/lib64/libgomp.so.1 (0x00007f9dc01a2000)
libmpi_cxx.so.1 => /opt/moose/openmpi/openmpi-1.8.4/gcc-opt/lib/libmpi_cxx.so.1 (0x00007f9dbff88000)
libmpi.so.1 => /opt/moose/openmpi/openmpi-1.8.4/gcc-opt/lib/libmpi.so.1 (0x00007f9dbfca8000)
libopen-rte.so.7 => /opt/moose/openmpi/openmpi-1.8.4/gcc-opt/lib/libopen-rte.so.7 (0x00007f9dbfa2c000)
libopen-pal.so.6 => /opt/moose/openmpi/openmpi-1.8.4/gcc-opt/lib/libopen-pal.so.6 (0x00007f9dbf746000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f9dbf542000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f9dbf33a000)
libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x00007f9dbf120000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f9dbef1d000)
libstdc++.so.6 => /opt/moose/gcc_4.9.1/lib64/libstdc++.so.6 (0x00007f9dbec13000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f9dbe90d000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f9dbe548000)
/lib64/ld-linux-x86-64.so.2 (0x00007f9dc5bcc000)
libpetsc.so.3.5 => not found
libparmetis.so => not found
libmetis.so => not found
libpetsc.so.3.5 => not found
libparmetis.so => not found
libmetis.so => not found
libpetsc.so.3.5 => not found
libparmetis.so => not found
libmetis.so => not found
libpetsc.so.3.5 => not found
libparmetis.so => not found
libmetis.so => not found
libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f9dbe329000)
libmpi_usempi_ignore_tkr.so.0 => /opt/moose/openmpi/openmpi-1.8.4/gcc-opt/lib/libmpi_usempi_ignore_tkr.so.0 (0x00007f9dbe123000)
libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f9dbdf1f000)
libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007f9dbdd19000)
~$ cat ~/projects/bison/moose/libmesh/build/config.log
<output, greater than 4500 lines, in the attached text file>
Thanks,
Gyan
~$ echo $PETSC_DIR
/opt/moose/petsc/openmpi_petsc-3.6.0/gcc-opt-superlu
~$ module list
Currently Loaded Modulefiles:
1) moose/.gcc_4.9.1
2) moose/.tbb
3) moose/.openmpi-1.8.4_gcc
4) moose/.openmpi_petsc-3.6.0-gcc-superlu
5) moose-tools
6) moose/.vtk6
7) moose-dev-gcc
~$ env
GCC_MAN=/opt/moose/gcc_4.9.1/share/man
CPLUS_INCLUDE_PATH=/opt/moose/openmpi/openmpi-1.8.4/gcc-opt/include
MODULE_VERSION_STACK=3.2.10
XDG_VTNR=7
MANPATH=/opt/moose/openmpi/openmpi-1.8.4/gcc-opt/share/man:/opt/moose/gcc_4.9.1/share/man:/usr/share/man
XDG_SESSION_ID=c2
VTKINCLUDE_DIR=/opt/moose/vtk-6.1/include/vtk-6.1
CLUTTER_IM_MODULE=xim
SELINUX_INIT=YES
XDG_GREETER_DATA_DIR=/var/lib/lightdm-data/g********
GPG_AGENT_INFO=/run/user/8158/keyring-YUTyh6/gpg:0:1
ACCESS=/opt/moose/SEACAS
TERM=xterm
SHELL=/bin/bash
VTE_VERSION=3409
LIBRARY_PATH=/opt/moose/tbb/lib/intel64/cc4.1.0_libc2.4_kernel2.6.16.21
FPATH=/opt/moose/openmpi/openmpi-1.8.4/gcc-opt/include
WINDOWID=56623116
TBB_DIR=/opt/moose/tbb
UPSTART_SESSION=unix:abstract=/com/ubuntu/upstart-session/8158/2527
GNOME_KEYRING_CONTROL=/run/user/8158/keyring-YUTyh6
INCLUDE_PATH=/opt/moose/vtk-6.1/include/vtk-6.1
GTK_MODULES=overlay-scrollbar:unity-gtk-module
XLIB_SKIP_ARGB_VISUALS=1
USER=g********
LD_LIBRARY_PATH=/opt/moose/vtk-6.1/lib:/opt/moose/openmpi/openmpi-1.8.4/gcc-opt/lib:/opt/moose/tbb/lib/intel64/cc4.1.0_libc2.4_kernel2.6.16.21:/opt/moose/gcc_4.9.1/lib64
MOOSE_JOBS=16
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: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:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=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:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=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:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=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:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
CPATH=/opt/moose/tbb/include
SSH_AUTH_SOCK=/run/user/8158/keyring-YUTyh6/ssh
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/usr/share/upstart/xdg:/etc/xdg
MODULE_VERSION=3.2.10
PATH=/media/g********/SIM_Abaqus_Extend.AllOS/IsightSEE5.9-2-Linux:/home/g********/Downloads/Cubit-15.0-Lin64-sculpt/bin:/home/g********/Downloads/ParaView-4.3.1-Linux-64bit/bin:/opt/intel/bin:/home/g********/SIMULIA/Commands:/home/g********/projects/moose/gui:/opt/moose/SEACAS/bin:/opt/moose/SEACAS/etc:/opt/moose/miniconda/bin:/opt/moose/openmpi/openmpi-1.8.4/gcc-opt/bin:/opt/moose/gcc_4.9.1/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
DESKTOP_SESSION=ubuntu
GCC_BIN=/opt/moose/gcc_4.9.1/bin
QT_IM_MODULE=ibus
QT_QPA_PLATFORMTHEME=appmenu-qt5
TBBROOT=/opt/moose/tbb
C_INCLUDE_PATH=/opt/moose/openmpi/openmpi-1.8.4/gcc-opt/include
F90=mpif90
JOB=gnome-session
PWD=/home/g********
_LMFILES_=/opt/moose/Modules/3.2.10/modulefiles/moose/.gcc_4.9.1:/opt/moose/Modules/3.2.10/modulefiles/moose/.tbb:/opt/moose/Modules/3.2.10/modulefiles/moose/.openmpi-1.8.4_gcc:/opt/moose/Modules/3.2.10/modulefiles/moose/.openmpi_petsc-3.6.0-gcc-superlu:/opt/moose/Modules/3.2.10/modulefiles/moose-tools:/opt/moose/Modules/3.2.10/modulefiles/moose/.vtk6:/opt/moose/Modules/3.2.10/modulefiles/moose-dev-gcc
XMODIFIERS=@im=ibus
GNOME_KEYRING_PID=2524
LANG=en_US.UTF-8
MODULEPATH=/opt/moose/Modules/versions:/opt/moose/Modules/$MODULE_VERSION/modulefiles:/opt/moose/Modules/modulefiles:/opt/moose/Modules/3.2.10/openmpi_gcc
GDM_LANG=en
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
LOADEDMODULES=moose/.gcc_4.9.1:moose/.tbb:moose/.openmpi-1.8.4_gcc:moose/.openmpi_petsc-3.6.0-gcc-superlu:moose-tools:moose/.vtk6:moose-dev-gcc
IM_CONFIG_PHASE=1
COMPIZ_CONFIG_PROFILE=ubuntu
F77=mpif77
GDMSESSION=ubuntu
CXX=mpicxx
SESSIONTYPE=gnome-session
HOME=/home/g********
XDG_SEAT=seat0
SHLVL=1
QT_API=pyside
LANGUAGE=en_US:
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
GCC_LIB=/opt/moose/gcc_4.9.1/lib64
FC=mpif90
UPSTART_INSTANCE=
VTKLIB_DIR=/opt/moose/vtk-6.1/lib
PYTHONPATH=/home/g********/Downloads/Cubit-14.1-Lin64/bin:
UPSTART_EVENTS=started starting
LOGNAME=g********
QT4_IM_MODULE=xim
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/share/gnome:/usr/local/share/:/usr/share/
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-ZqpjaTDrpq
MPI_HOME=/opt/moose/openmpi/openmpi-1.8.4/gcc-opt
MODULESHOME=/opt/moose/Modules/3.2.10
LESSOPEN=| /usr/bin/lesspipe %s
INSTANCE=Unity
UPSTART_JOB=unity-settings-daemon
TEXTDOMAIN=im-config
CC=mpicc
XDG_RUNTIME_DIR=/run/user/8158
DISPLAY=:0
MOOSE_PPS_WIDTH=180
XDG_CURRENT_DESKTOP=Unity
GTK_IM_MODULE=ibus
PETSC_DIR=/opt/moose/petsc/openmpi_petsc-3.6.0/gcc-opt-superlu
LESSCLOSE=/usr/bin/lesspipe %s %s
TEXTDOMAINDIR=/usr/share/locale/
COLORTERM=gnome-terminal
XAUTHORITY=/home/g********/.Xauthority
BASH_FUNC_module%%=() { eval `/opt/moose/Modules/$MODULE_VERSION/bin/modulecmd bash $*`
}
_=/usr/bin/env
~$ ldd ~/projects/bison/bison-opt
linux-vdso.so.1 => (0x00007ffec3de1000)
libbison-opt.so.0 => /home/g********/projects/bison/lib/libbison-opt.so.0 (0x00007f9dc55e9000)
libwater_steam_eos-opt.so.0 => /home/g********/projects/bison/moose/modules/water_steam_eos/lib/libwater_steam_eos-opt.so.0 (0x00007f9dc53c5000)
libsolid_mechanics-opt.so.0 => /home/g********/projects/bison/moose/modules/solid_mechanics/lib/libsolid_mechanics-opt.so.0 (0x00007f9dc4f2c000)
libtensor_mechanics-opt.so.0 => /home/g********/projects/bison/moose/modules/tensor_mechanics/lib/libtensor_mechanics-opt.so.0 (0x00007f9dc4a9b000)
libmisc-opt.so.0 => /home/g********/projects/bison/moose/modules/misc/lib/libmisc-opt.so.0 (0x00007f9dc4814000)
liblinear_elasticity-opt.so.0 => /home/g********/projects/bison/moose/modules/linear_elasticity/lib/liblinear_elasticity-opt.so.0 (0x00007f9dc45d2000)
libheat_conduction-opt.so.0 => /home/g********/projects/bison/moose/modules/heat_conduction/lib/libheat_conduction-opt.so.0 (0x00007f9dc431a000)
libcontact-opt.so.0 => /home/g********/projects/bison/moose/modules/contact/lib/libcontact-opt.so.0 (0x00007f9dc4040000)
libmoose-opt.so.0 => /home/g********/projects/bison/moose/framework/libmoose-opt.so.0 (0x00007f9dc315e000)
libpcre-opt.so.0 => /home/g********/projects/bison/moose/framework/contrib/pcre/libpcre-opt.so.0 (0x00007f9dc2f32000)
libice_updater-opt.so.0 => /home/g********/projects/bison/moose/framework/contrib/ice_updater/libice_updater-opt.so.0 (0x00007f9dc2d04000)
libgcc_s.so.1 => /opt/moose/gcc_4.9.1/lib64/libgcc_s.so.1 (0x00007f9dc2aee000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f9dc28d0000)
libmesh_opt.so.0 => /home/g********/projects/bison/moose/scripts/../libmesh/installed/lib/libmesh_opt.so.0 (0x00007f9dc16ee000)
libnetcdf.so.7 => /home/g********/projects/bison/moose/scripts/../libmesh/installed/lib/libnetcdf.so.7 (0x00007f9dc1408000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f9dc11ef000)
libtbb.so.2 => /opt/moose/tbb/lib/intel64/cc4.1.0_libc2.4_kernel2.6.16.21/libtbb.so.2 (0x00007f9dc5c99000)
libtbbmalloc.so.2 => /opt/moose/tbb/lib/intel64/cc4.1.0_libc2.4_kernel2.6.16.21/libtbbmalloc.so.2 (0x00007f9dc10a0000)
libpetsc.so.3.5 => not found
libparmetis.so => not found
libmetis.so => not found
libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f9dc0d6b000)
libmpi_usempi.so.1 => /opt/moose/openmpi/openmpi-1.8.4/gcc-opt/lib/libmpi_usempi.so.1 (0x00007f9dc0b6a000)
libmpi_mpifh.so.2 => /opt/moose/openmpi/openmpi-1.8.4/gcc-opt/lib/libmpi_mpifh.so.2 (0x00007f9dc0911000)
libgfortran.so.3 => /opt/moose/gcc_4.9.1/lib64/libgfortran.so.3 (0x00007f9dc05f4000)
libquadmath.so.0 => /opt/moose/gcc_4.9.1/lib64/libquadmath.so.0 (0x00007f9dc03b7000)
libgomp.so.1 => /opt/moose/gcc_4.9.1/lib64/libgomp.so.1 (0x00007f9dc01a2000)
libmpi_cxx.so.1 => /opt/moose/openmpi/openmpi-1.8.4/gcc-opt/lib/libmpi_cxx.so.1 (0x00007f9dbff88000)
libmpi.so.1 => /opt/moose/openmpi/openmpi-1.8.4/gcc-opt/lib/libmpi.so.1 (0x00007f9dbfca8000)
libopen-rte.so.7 => /opt/moose/openmpi/openmpi-1.8.4/gcc-opt/lib/libopen-rte.so.7 (0x00007f9dbfa2c000)
libopen-pal.so.6 => /opt/moose/openmpi/openmpi-1.8.4/gcc-opt/lib/libopen-pal.so.6 (0x00007f9dbf746000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f9dbf542000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f9dbf33a000)
libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x00007f9dbf120000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f9dbef1d000)
libstdc++.so.6 => /opt/moose/gcc_4.9.1/lib64/libstdc++.so.6 (0x00007f9dbec13000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f9dbe90d000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f9dbe548000)
/lib64/ld-linux-x86-64.so.2 (0x00007f9dc5bcc000)
libpetsc.so.3.5 => not found
libparmetis.so => not found
libmetis.so => not found
libpetsc.so.3.5 => not found
libparmetis.so => not found
libmetis.so => not found
libpetsc.so.3.5 => not found
libparmetis.so => not found
libmetis.so => not found
libpetsc.so.3.5 => not found
libparmetis.so => not found
libmetis.so => not found
libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f9dbe329000)
libmpi_usempi_ignore_tkr.so.0 => /opt/moose/openmpi/openmpi-1.8.4/gcc-opt/lib/libmpi_usempi_ignore_tkr.so.0 (0x00007f9dbe123000)
libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f9dbdf1f000)
libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007f9dbdd19000)
~$ cat ~/projects/bison/moose/libmesh/build/config.log
<output, greater than 4500 lines, in the attached text file>
Thanks,
Gyan
Miller, Jason M
Nov 6, 2015, 10:32:38 AM11/6/15
to moose...@googlegroups.com
A couple things that I am seeing:
PATH=/media/g********/SIM_Abaqus_Extend.AllOS/IsightSEE5.9-2-Linux:/home/g********/Downloads/Cubit-15.0-Lin64-sculpt/bin:/home/g********/Downloads/ParaView-4.3.1-Linux-64bit/bin:/opt/intel/bin:/home/g********/SIMULIA/Commands:/home/g********/projects/moose/gui:/opt/moose/SEACAS/bin:/opt/moose/SEACAS/etc:/opt/moose/miniconda/bin:/opt/moose/openmpi/openmpi-1.8.4/gcc-opt/bin:/opt/moose/gcc_4.9.1/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
Any Intel compilers being made available before the compilers in /opt/moose/gcc_4.9.1 may cause some issues. Not sure if there are even compilers in /opt/intel/bin, but its worth mentioning.
Your libMesh config, suggests you have not run the update_and_rebuild_libmesh.sh script after you installed the latest moose package (from your libMesh config.log):
PETSCINCLUDEDIRS='-I/opt/moose/petsc/openmpi_petsc-3.5.2/gcc-opt-superlu/include -I/opt/moose/petsc/openmpi_petsc-3.5.2/gcc-opt-superlu//include -I/opt/moose/petsc/openmpi_petsc-3.5.2/gcc-opt-superlu/include -I/opt/moose/petsc/openmpi_petsc-3.5.2/gcc-opt-superlu/include -I/opt/moose/petsc/openmpi_petsc-3.5.2/gcc-opt-superlu/include -I/opt/moose/openmpi/openmpi-1.8.1/gcc-opt/include'
Your `env` suggests you should be seeing PETSc pointing to: /opt/moose/petsc/openmpi_petsc-3.6.0/gcc-opt-superlu
And the results of `ldd bison-opt` supports this (library not found).
Please note; When ever you re-install the MOOSE environment package, you need to close and re-open all opened terminals. This is necessary to clear out an old environment with possible incorrect PATHs to non-existent things (like PETSc libraries).
What you probably need to do is;
1. cd ~/projects/bison/moose/scripts; ./update_and_rebuild_libmesh.sh
2. cd ~/projects/bison; make clobber
3. make
The `make clobber` command should clean out any stale .o files possibly still wanting to link against those missing PETSc libraries.
Hope this helps!
Jason
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Gyan
Nov 6, 2015, 4:05:09 PM11/6/15
to moose-users
Followed the steps; the petsc error is resolved but the error, mentioned at the beginning of this thread, has returned back. So, updating to latest Bison and Moose did not resolve the error.
Probably I am left with the only option of setting up a different Linux OS, may be CentOS, and try running the package on that.
Interestingly, other Ubuntu users did not report this problem, which indicates that it is not an entirely OS-update issue.
Thanks,
Gyan
Probably I am left with the only option of setting up a different Linux OS, may be CentOS, and try running the package on that.
Interestingly, other Ubuntu users did not report this problem, which indicates that it is not an entirely OS-update issue.
Thanks,
Gyan
Miller, Jason M
Nov 6, 2015, 4:12:11 PM11/6/15
to moose...@googlegroups.com
I am no expert in any of the other applications you have binaries for in your home directory... but have you tried removing those from your PATH? Just to see if its something being caused be a second set of compilers/libraries possibly lying around? I would ask that you try the following, just to see if 'something' different happens:
export PATH=/opt/moose/SEACAS/bin:/opt/moose/SEACAS/etc:/opt/moose/miniconda/bin:/opt/moose/openmpi/openmpi-1.8.4/gcc-opt/bin:/opt/moose/gcc_4.9.1/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
And attempt to run_tests again. If that fails, try rebuilding libMesh with the above alteration to your PATH...
Jason
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Gyan
Nov 6, 2015, 5:07:20 PM11/6/15
to moose-users
Will get back to it on Monday and post how things go. Thanks.
Gyan
Gyan
Gyan
Nov 9, 2015, 10:09:20 AM11/9/15
to moose-users
When I remove the path for Cubit-15.0 from .bashrc, it runs fine. I had updated to 15.0 version few days back. It is surprising that path for Cubit-15.0 is interfering; I had path for Cubit-14.1 in .bashrc for a long time and did not encounter this symbol lookup error ever before.
The problem seems to be solved now, except that I will need to keep altering the .bashrc every now and then to comment and uncomment the Cubit path. Thanks very much Jason, appreciate your help.
Gyan
The problem seems to be solved now, except that I will need to keep altering the .bashrc every now and then to comment and uncomment the Cubit path. Thanks very much Jason, appreciate your help.
Gyan
Miller, Jason M
Nov 9, 2015, 10:23:44 AM11/9/15
to moose...@googlegroups.com
Glad to hear it! And you're welcome!
However, hmmm.. that is weird that Cubit would get in the way. It may be possible to keep your path to Cubit in your environment. Try to have PATH to cubit come _after_ the path to anything MOOSE related... Hopefully though, doing that won't make Cubit stop working!
Jason
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Cody Permann
Nov 9, 2015, 10:43:08 AM11/9/15
to moose-users
There has to be a better explanation. Cubit 15 certainly doesn't have any direct impact on our libraries. I'm using Cubit 15 and have no issues. Is it installed in its own path or some common area?
You could always consider setting up a module for cubit then you could load and unload it at will.
You could always consider setting up a module for cubit then you could load and unload it at will.
Cody
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Gyan
Nov 9, 2015, 12:06:00 PM11/9/15
to moose-users
The entire Cubit code is in the /home/g*********/Downloads directory, which may not be the best way to set up Cubit. The last few lines of my .bashrc, specifying paths for different applications, are:
export PATH=/home/g********/projects/moose/gui:$PATH
export XLIB_SKIP_ARGB_VISUALS=1
export PATH=/home/g********/SIMULIA/Commands:$PATH
export PATH=/opt/intel/bin:$PATH
export PATH=/home/g********/Downloads/ParaView-4.3.1-Linux-64bit/bin:$PATH
#export PATH=/home/g********/Downloads/Cubit-15.0-Lin64-sculpt/bin:$PATH
export PATH=/media/g********/SIM_Abaqus_Extend.AllOS/IsightSEE5.9-2-Linux:$PATH
Gyan
export PATH=/home/g********/projects/moose/gui:$PATH
export XLIB_SKIP_ARGB_VISUALS=1
export PATH=/home/g********/SIMULIA/Commands:$PATH
export PATH=/opt/intel/bin:$PATH
export PATH=/home/g********/Downloads/ParaView-4.3.1-Linux-64bit/bin:$PATH
#export PATH=/home/g********/Downloads/Cubit-15.0-Lin64-sculpt/bin:$PATH
export PATH=/media/g********/SIM_Abaqus_Extend.AllOS/IsightSEE5.9-2-Linux:$PATH
Gyan
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