not able to run peacock

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harsh soni

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Jan 30, 2018, 12:46:26 AM1/30/18
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Hi,
I installed moose on my computer (ubuntu 14.04). everything is done but i am not able to open peacock. I get the following error when I run $peacock
  

Error starting peacock: Could not import matplotlib

You need to use the miniconda module. Run:
module load miniconda

I run the command $module load miniconda but I still get the same error.

Please help!

Thanks
Harsh Soni

Miller, Jason M

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Jan 30, 2018, 8:29:22 AM1/30/18
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Harsh,

Can you list the results of the following commands?


which python
module list
env


Thanks!
Jason



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harsh soni

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Jan 30, 2018, 9:43:30 AM1/30/18
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Hi Jason,
Here are the results of the commands you requested:

$ which python
/opt/moose/miniconda/bin/python


$ module list
Currently Loaded Modulefiles:
  1) moose/.gcc-7.2.0                             4) moose/.tbb44_20150728                        7) miniconda
  2) moose/.mpich-3.2_gcc-7.2.0                   5) moose/.cppunit-1.12.1_gcc-7.2.0              8) moose-tools
  3) moose/.petsc-3.7.6_mpich-3.2_gcc-7.2.0-opt   6) moose-dev-gcc


$ env
GCC_MAN=/opt/moose/gcc-7.2.0/share/man
CPLUS_INCLUDE_PATH=/opt/moose/mpich-3.2/gcc-7.2.0/include
MODULE_VERSION_STACK=3.2.10
XDG_VTNR=7
LC_PAPER=en_US.UTF-8
MANPATH=/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:/opt/moose/mpich-3.2/gcc-7.2.0/share/man:/opt/moose/gcc-7.2.0/share/man:/opt/intel/man/common:/opt/intel/compilers_and_libraries_2017.0.098/linux/mpi/man:/usr/local/man:/usr/local/share/man:/usr/share/man
LC_ADDRESS=en_US.UTF-8
XDG_SESSION_ID=c2
XDG_GREETER_DATA_DIR=/var/lib/lightdm-data/harsh
SELINUX_INIT=YES
LC_MONETARY=en_US.UTF-8
CLUTTER_IM_MODULE=xim
SESSION=ubuntu
INTEL_LICENSE_FILE=/opt/intel/compilers_and_libraries_2017.0.098/linux/licenses:/opt/intel/licenses:/home/harsh/intel/licenses
GPG_AGENT_INFO=/run/user/1000/keyring-IcDhu0/gpg:0:1
ACCESS=/opt/moose/seacas
TERM=xterm
VTE_VERSION=3409
XDG_MENU_PREFIX=gnome-
SHELL=/bin/bash
LIBRARY_PATH=/opt/moose/tbb44_20150728/lib
FPATH=/opt/moose/mpich-3.2/gcc-7.2.0/include
WINDOWID=79691787
LC_NUMERIC=en_US.UTF-8
TBB_DIR=/opt/moose/tbb44_20150728
UPSTART_SESSION=unix:abstract=/com/ubuntu/upstart-session/1000/4891
GNOME_KEYRING_CONTROL=/run/user/1000/keyring-IcDhu0
MIC_LD_LIBRARY_PATH=/opt/intel/compilers_and_libraries_2017.0.098/linux/mpi/mic/lib:/opt/intel/compilers_and_libraries_2017.0.098/linux/compiler/lib/mic
GTK_MODULES=overlay-scrollbar:unity-gtk-module
USER=harsh
MOOSE_JOBS=8
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:
LD_LIBRARY_PATH=/opt/moose/seacas/lib:/opt/moose/tbb44_20150728/lib:/opt/moose/gcc-7.2.0/lib64:/opt/moose/gcc-7.2.0/lib:/opt/moose/gcc-7.2.0/lib/i386:/opt/intel/compilers_and_libraries_2017.0.098/linux/compiler/lib/intel64:/opt/intel/compilers_and_libraries_2017.0.098/linux/compiler/lib/intel64_lin:/opt/intel/compilers_and_libraries_2017.0.098/linux/mpi/intel64/lib:/opt/intel/compilers_and_libraries_2017.0.098/linux/mpi/mic/lib
LC_TELEPHONE=en_US.UTF-8
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0
MIC_LIBRARY_PATH=/opt/intel/compilers_and_libraries_2017.0.098/linux/mpi/mic/lib:/opt/intel/compilers_and_libraries_2017.0.098/linux/compiler/lib/mic
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
CPATH=/opt/moose/tbb44_20150728/include
SSH_AUTH_SOCK=/run/user/1000/keyring-IcDhu0/ssh
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
SESSION_MANAGER=local/ramanujan:@/tmp/.ICE-unix/5024,unix/ramanujan:/tmp/.ICE-unix/5024
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/usr/share/upstart/xdg:/etc/xdg
NLSPATH=/opt/intel/compilers_and_libraries_2017.0.098/linux/compiler/lib/intel64/locale/%l_%t/%N
MODULE_VERSION=3.2.10
DESKTOP_SESSION=ubuntu
PATH=/home/harsh/projects/moose/python/peacock:/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:/seacas/etc:/opt/moose/cppunit-1.12.1/gcc-7.2.0/bin:/opt/moose/mpich-3.2/gcc-7.2.0/bin:/opt/moose/llvm-5.0.0/bin:/opt/moose/gcc-7.2.0/bin:/opt/intel/compilers_and_libraries_2017.0.098/linux/bin/intel64:/opt/intel/compilers_and_libraries_2017.0.098/linux/mpi/intel64/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
GCC_BIN=/opt/moose/gcc-7.2.0/bin
QT_QPA_PLATFORMTHEME=appmenu-qt5
TBBROOT=/opt/moose/tbb44_20150728
C_INCLUDE_PATH=/opt/moose/mpich-3.2/gcc-7.2.0/include
LC_IDENTIFICATION=en_US.UTF-8
F90=mpif90
PWD=/home/harsh
JOB=dbus
_LMFILES_=/opt/moose/Modules/3.2.10/modulefiles/moose/.gcc-7.2.0:/opt/moose/Modules/3.2.10/modulefiles/moose/.mpich-3.2_gcc-7.2.0:/opt/moose/Modules/3.2.10/modulefiles/moose/.petsc-3.7.6_mpich-3.2_gcc-7.2.0-opt:/opt/moose/Modules/3.2.10/modulefiles/moose/.tbb44_20150728:/opt/moose/Modules/3.2.10/modulefiles/moose/.cppunit-1.12.1_gcc-7.2.0:/opt/moose/Modules/3.2.10/modulefiles/moose-dev-gcc:/opt/moose/Modules/3.2.10/modulefiles/miniconda:/opt/moose/Modules/3.2.10/modulefiles/moose-tools
XMODIFIERS=@im=none
MPLBACKEND=qt5Agg
GNOME_KEYRING_PID=4889
LANG=en_US.UTF-8
MODULEPATH=/opt/moose/Modules/versions:/opt/moose/Modules/$MODULE_VERSION/modulefiles:/opt/moose/Modules/modulefiles
GDM_LANG=en_US
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
LOADEDMODULES=moose/.gcc-7.2.0:moose/.mpich-3.2_gcc-7.2.0:moose/.petsc-3.7.6_mpich-3.2_gcc-7.2.0-opt:moose/.tbb44_20150728:moose/.cppunit-1.12.1_gcc-7.2.0:moose-dev-gcc:miniconda:moose-tools
LC_MEASUREMENT=en_US.UTF-8
COMPIZ_CONFIG_PROFILE=ubuntu
IM_CONFIG_PHASE=1
F77=mpif77
PAPERSIZE=letter
GDMSESSION=ubuntu
CXX=mpicxx
SESSIONTYPE=gnome-session
SHLVL=1
HOME=/home/harsh
XDG_SEAT=seat0
LANGUAGE=en_US:en
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
GCC_LIB=/opt/moose/gcc-7.2.0/lib:/opt/moose/gcc-7.2.0/lib/i386
FC=mpif90
CPPUNIT_DIR=/opt/moose/cppunit-1.12.1/gcc-7.2.0
MATHEMATICA_HOME=/usr/local/Wolfram/Mathematica/10.0
LOGNAME=harsh
COMPIZ_BIN_PATH=/usr/bin/
CLASSPATH=/opt/intel/compilers_and_libraries_2017.0.098/linux/mpi/intel64/lib/mpi.jar
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-arvVWzFKzv
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/share/gnome:/usr/local/share/:/usr/share/
QT4_IM_MODULE=xim
MPI_HOME=/opt/moose/mpich-3.2/gcc-7.2.0
MODULESHOME=/opt/moose/Modules/3.2.10
LESSOPEN=| /usr/bin/lesspipe %s
INSTANCE=
TEXTDOMAIN=im-config
CC=mpicc
XDG_RUNTIME_DIR=/run/user/1000
DISPLAY=:0
INCLUDE=/opt/moose/cppunit-1.12.1/gcc-7.2.0/include
MOOSE_PPS_WIDTH=180
XDG_CURRENT_DESKTOP=Unity
GTK_IM_MODULE=xim
PETSC_DIR=/opt/moose/petsc-3.7.6/mpich-3.2_gcc-7.2.0-opt
LESSCLOSE=/usr/bin/lesspipe %s %s
LC_TIME=en_US.UTF-8
TEXTDOMAINDIR=/usr/share/locale/
I_MPI_ROOT=/opt/intel/compilers_and_libraries_2017.0.098/linux/mpi
LC_NAME=en_US.UTF-8
XAUTHORITY=/home/harsh/.Xauthority
COLORTERM=gnome-terminal
BASH_FUNC_module%%=() {  eval `/opt/moose/Modules/$MODULE_VERSION/bin/modulecmd bash $*`
}
_=/usr/bin/env



Thanks and best regards
Harsh Soni

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Alger, Brian K

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Jan 30, 2018, 9:59:32 AM1/30/18
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The peacock check for matplotlib does the following:

from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg

Can you try that in a python shell? Just run the "python" command and enter that line, then report what error you get.


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harsh soni

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Jan 30, 2018, 10:13:19 AM1/30/18
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I did run this command and didn't get any error.

Thanks and best regards
Harsh Soni

Miller, Jason M

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Jan 30, 2018, 10:28:07 AM1/30/18
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This is getting odd...  With matplotlib loaded, can you perform the following... perhaps matplotlib is being referenced from some place other than /opt/moose?

$python

import matplotlib
matplotlib.__file__





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harsh soni

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Jan 30, 2018, 10:33:23 AM1/30/18
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This is what I get after running these commands in Python:

>>> import matplotlib
>>> matplotlib.__file__
'/opt/moose/miniconda/lib/python2.7/site-packages/matplotlib/__init__.pyc'
>>> 


With best regards
Harsh Soni

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Miller, Jason M

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Jan 30, 2018, 10:40:49 AM1/30/18
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Well... thats what it should say. Honestly, try to run peacock again. Directly without using the PATH.

cd moose/python/peacock
./peacock

Because, I have no idea why it would complain that it can't import matplotlib, when we have been able to do it correctly.






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harsh soni

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Jan 30, 2018, 11:02:49 AM1/30/18
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getting same error:

$ cd /home/harsh/projects/moose/python/peacock/
harsh@ramanujan:~/projects/moose/python/peacock$ ./peacock 

Error starting peacock: Could not import matplotlib

You need to use the miniconda module. Run:
module load miniconda


With best regards
Harsh Soni

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Miller, Jason M

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Jan 30, 2018, 12:50:34 PM1/30/18
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Harsh,

I created an Ubuntu 14.04 VM, and I can confirm I run into the same issue.

We're looking into this now... Its a little early to start stating solutions, but it looks to be the order in which we are importing modules. The underlying issue is minconda's version of libpng is attempting to load zlib. But its hitting the system's version first, which is of an older version than the one sitting in minconda... Not 100% thats the issue. Feels like it may be the case.

Hopefully we can come up with a solution.

Just thought you would want to know, that we are not ignoring you!

Jason



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harsh soni

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Jan 30, 2018, 1:04:19 PM1/30/18
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Thanks!

With best regards
Harsh Soni

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harsh soni

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Jan 31, 2018, 3:15:47 PM1/31/18
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Hi Jason,
Somehow I am able to open peacock and following is the screenshot of the window of the peacock. I don't understand, how to proceed after this. Do you think that the peacock is working properly?
Thanks!

Derek Gaston

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Jan 31, 2018, 4:37:20 PM1/31/18
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In the menu click "Input File -> Open" to open an input file.

You can also run peacock like:

peacock myinputfile.i

To open an input file as you open Peacock.

Derek

Thanks!
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Dvora Keda

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Oct 9, 2019, 9:07:06 AM10/9/19
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Hi,

I am encountering the same problem (Could not import matplotlib) when now I am trying to install MOOSE on a Linux cluster.
I do use the right path of conda for installed the needed packages (conda install -c idaholab python=2.7 coverage reportlab mako numpy scipy scikit-learn h5py hdf5 scikit-image requests vtk=7.1.0 pyyaml matplotlib pip lxml pyflakes pandas conda-build mock yaml pyqt --yes).

When entering into the python (miniconda's), I can import matplotlib without problem.
However, when execute the "peacock" command or "python ..path..to../peacock", there is always the following error.

Error starting peacock: Could not import matplotlib
You need to use the miniconda module. 
Run: module load miniconda

Though I have struggled this for two days, I cannot pass the problem through. 

Any solution?

Thank you!

Dvora

Dvora Keda

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Oct 9, 2019, 9:35:08 AM10/9/19
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The error comes from "from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg" in "CheckRequirements.py".
How can I avoid this?

Andrew Slaughter

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Oct 9, 2019, 10:40:24 AM10/9/19
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First, peacock is not designed to work on remote cluster machines, so that probably will not work. The error you are seeing is because you don't have a display. 

On your local machine, you should be able to use peacock without trouble. If you have the miniconda module loaded you can install any missing package using "conda install" or "pip install". That being said, our miniconda module should have everything you need. Can you provide the results from running the command "conda list"?

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Dvora Keda

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Oct 9, 2019, 8:18:47 PM10/9/19
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Hi Andrew, 

I am sorry. After your remind I have found the problem was due to I forgot to load llvm when X-forwarding the remote side visualization.
Now after load the llvm environment, peacock now can successfully work .

Thank you.

Dvora
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