Peacock install on Linux from source

[dealmeidavf]

Hello,
Is there a list of packages needed for peacock when installing from source in Linux?
I currently have vtk installed but running peacock gives me:

-> ./peacock

Error starting peacock: Could not import vtk

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

I do not have miniconda. Is it possible to get peacock working without it?

Thanks,

--
Valmor

[milljm]

pyqt, vtk, matplotlib (with qt backends), pandas. Those are the top-level requirements. They have quite a few of their own (like PyQt requiring Qt for starters).

Here is the final list created by Conda, as it attempts to solve the above dependencies. It is extensive, and no doubt your system will already have much of this installed already:

conda create -n testing install pyqt vtk matplotlib pandas

  bzip2              conda-forge/osx-64::bzip2-1.0.8-hc929b4f_4
  c-ares             conda-forge/osx-64::c-ares-1.17.1-hc929b4f_0
  ca-certificates    conda-forge/osx-64::ca-certificates-2020.12.5-h033912b_0
  certifi            conda-forge/osx-64::certifi-2020.12.5-py37hf985489_0
  curl               conda-forge/osx-64::curl-7.71.1-hcb81553_8
  cycler             conda-forge/noarch::cycler-0.10.0-py_2
  dbus               conda-forge/osx-64::dbus-1.13.6-h0c50699_1
  double-conversion  conda-forge/osx-64::double-conversion-3.1.5-h4a8c4bd_2
  eigen              conda-forge/osx-64::eigen-3.3.9-h926bf3e_1
  expat              conda-forge/osx-64::expat-2.2.9-hb1e8313_2
  ffmpeg             conda-forge/osx-64::ffmpeg-4.3.1-he496704_1
  freetype           conda-forge/osx-64::freetype-2.10.4-h3f75d11_0
  gettext            conda-forge/osx-64::gettext-0.19.8.1-h7937167_1005
  gl2ps              conda-forge/osx-64::gl2ps-1.4.2-h4cff582_0
  glew               conda-forge/osx-64::glew-2.1.0-h046ec9c_2
  glib               conda-forge/osx-64::glib-2.66.3-h519c658_1
  gmp                conda-forge/osx-64::gmp-6.2.1-h2e338ed_0
  gnutls             conda-forge/osx-64::gnutls-3.6.13-h756fd2b_1
  hdf4               conda-forge/osx-64::hdf4-4.2.13-h71d84a9_1004
  hdf5               conda-forge/osx-64::hdf5-1.10.6-nompi_h0f9794f_1112
  icu                conda-forge/osx-64::icu-64.2-h6de7cb9_1
  jpeg               conda-forge/osx-64::jpeg-9d-hbcb3906_0
  jsoncpp            conda-forge/osx-64::jsoncpp-1.8.4-ha1b3eb9_1002
  kiwisolver         conda-forge/osx-64::kiwisolver-1.3.1-py37h8ec247f_0
  krb5               conda-forge/osx-64::krb5-1.17.2-h60d9502_0
  lame               conda-forge/osx-64::lame-3.100-h1de35cc_1001
  lcms2              conda-forge/osx-64::lcms2-2.11-h11f7e16_1
  libblas            conda-forge/osx-64::libblas-3.9.0-3_openblas
  libcblas           conda-forge/osx-64::libcblas-3.9.0-3_openblas
  libcurl            conda-forge/osx-64::libcurl-7.71.1-h9bf37e3_8
  libcxx             conda-forge/osx-64::libcxx-11.0.0-h4c3b8ed_1
  libedit            conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2
  libev              conda-forge/osx-64::libev-4.33-haf1e3a3_1
  libffi             conda-forge/osx-64::libffi-3.3-h046ec9c_2
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-h7cc5361_13
  libgfortran5       conda-forge/osx-64::libgfortran5-9.3.0-h7cc5361_13
  libglib            conda-forge/osx-64::libglib-2.66.3-h60154bc_1
  libiconv           conda-forge/osx-64::libiconv-1.16-haf1e3a3_0
  liblapack          conda-forge/osx-64::liblapack-3.9.0-3_openblas
  libnetcdf          conda-forge/osx-64::libnetcdf-4.7.4-nompi_h9d8a93f_107
  libnghttp2         conda-forge/osx-64::libnghttp2-1.41.0-h7580e61_2
  libogg             conda-forge/osx-64::libogg-1.3.4-hc929b4f_0
  libopenblas        conda-forge/osx-64::libopenblas-0.3.12-openmp_h54245bb_1
  libpng             conda-forge/osx-64::libpng-1.6.37-h7cec526_2
  libssh2            conda-forge/osx-64::libssh2-1.9.0-h8a08a2b_5
  libtheora          conda-forge/osx-64::libtheora-1.1.1-haf1e3a3_1004
  libtiff            conda-forge/osx-64::libtiff-4.1.0-hca7d577_6
  libvorbis          conda-forge/osx-64::libvorbis-1.3.7-h4a8c4bd_0
  libwebp-base       conda-forge/osx-64::libwebp-base-1.1.0-hbcb3906_3
  libxml2            conda-forge/osx-64::libxml2-2.9.10-h53d96d6_0
  llvm-openmp        conda-forge/osx-64::llvm-openmp-11.0.0-h73239a0_1
  loguru             conda-forge/osx-64::loguru-0.5.3-py37hc8dfbb8_2
  lz4-c              conda-forge/osx-64::lz4-c-1.9.2-hb1e8313_3
  matplotlib         conda-forge/osx-64::matplotlib-3.3.3-py37hf985489_0
  matplotlib-base    conda-forge/osx-64::matplotlib-base-3.3.3-py37hdacc966_0
  ncurses            conda-forge/osx-64::ncurses-6.2-h2e338ed_4
  nettle             conda-forge/osx-64::nettle-3.6-hedd7734_0
  numpy              conda-forge/osx-64::numpy-1.19.4-py37hec87de9_2
  olefile            conda-forge/noarch::olefile-0.46-pyh9f0ad1d_1
  openh264           conda-forge/osx-64::openh264-2.1.1-hd174df1_0
  openssl            conda-forge/osx-64::openssl-1.1.1i-h35c211d_0
  pandas             conda-forge/osx-64::pandas-1.1.5-py37h010c265_0
  pcre               conda-forge/osx-64::pcre-8.44-hb1e8313_0
  pillow             conda-forge/osx-64::pillow-8.0.1-py37h09f51b7_0
  pip                conda-forge/noarch::pip-20.3.3-pyhd8ed1ab_0
  proj               conda-forge/osx-64::proj-7.1.1-h45baca5_3
  pugixml            conda-forge/osx-64::pugixml-1.10-hb1e8313_1
  pyparsing          conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
  pyqt               conda-forge/osx-64::pyqt-5.9.2-py37h2a560b1_4
  python             conda-forge/osx-64::python-3.7.9-h6c3b2c9_0_cpython
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  python_abi         conda-forge/osx-64::python_abi-3.7-1_cp37m
  pytz               conda-forge/noarch::pytz-2020.4-pyhd8ed1ab_0
  qt                 conda-forge/osx-64::qt-5.9.7-h8cf7e54_3
  readline           conda-forge/osx-64::readline-8.0-h0678c8f_2
  setuptools         conda-forge/osx-64::setuptools-49.6.0-py37h2987424_2
  sip                pkgs/main/osx-64::sip-4.19.8-py37h0a44026_0
  six                conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
  sqlite             conda-forge/osx-64::sqlite-3.34.0-h17101e1_0
  tbb                conda-forge/osx-64::tbb-2020.2-h926bf3e_1
  tbb-devel          conda-forge/osx-64::tbb-devel-2020.2-h926bf3e_1
  tk                 conda-forge/osx-64::tk-8.6.10-h0419947_1
  tornado            conda-forge/osx-64::tornado-6.1-py37h4b544eb_0
  utfcpp             conda-forge/osx-64::utfcpp-3.1.2-0
  vtk                conda-forge/osx-64::vtk-9.0.1-no_osmesa_py37hc0470e1_102
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  x264               conda-forge/osx-64::x264-1!152.20180806-h1de35cc_0
  xz                 conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
  zlib               conda-forge/osx-64::zlib-1.2.11-h7795811_1010
  zstd               conda-forge/osx-64::zstd-1.4.5-h289c70a_2

I respect your attempt at building from source! I used to do this for our older moose-environment package we once distributed (before using Conda).

[dealmeidavf]

I may have all dependencies there. At the moment I run peacock, then open the input file and run. This is the output on my terminal screen:

-> peacock
QCssParser::parseColorValue: Specified color without alpha value but alpha given: 'r1, 111, 111, 255'
[snip]
QCssParser::parseColorValue: Specified color without alpha value but alpha given: 'r1, 111, 111, 255'
Found executable: [snip]
QCssParser::parseColorValue: Specified color without alpha value but alpha given: 'r1, 111, 111, 255'
[snip]
Numeric mode unsupported in the posix collation implementation
Exodus filenames: ['peacock_run_exe_tmp_my-input_out.e']
Postprocessor filenames: ['peacock_run_exe_tmp_my-input_out.csv']
Running command: [snip]/diffusion-opt Outputs/csv=true -i peacock_run_exe_tmp_my-input.i
Working directory: [snip]/diffusion
Finished: Exit code: 0

Files are created etc. in the directory of the input file.
Next, in peacock I click on ExodusViewer tab and peacock crashes

Segmentation fault

I had to install vtk from PyPI on my system because the vtk package from my distribution does not seem to allow for python bindings (?). peacock gives me an error of package not found unless I use vtk from PyPI. I am assuming this is what conda does. However I think my system will be inconsistent since PyQt is from my linux distro and not PyPI. Again I am assuming conda will use everything from PyPI.

Yes these are the troubleshooting headaches when building from source :)

At the moment I get what I need from peacock which is inspection of the input file. I typically run a moose app from the command line; not from peacock. However it would be nice to be able to take a quick view of the exodus output file while in peacock. Otherwise I use VisIt which is another matter for getting it installed...

Thanks for inputs.