unable to plot with xmgrace/cdat8
puneet336 opened this issue · comments
Hi,
I am trying to test xmgrace module (cdat8) on sles 12 machine (logged in using ssh -Y) . On running python script the xmgrace GUI shows up , but it seems that the xmgrace's python module is unable to communicate with GUI.
The expected plot is not showing up.
i have tried running python script with xmgrace - 5.99.
(cdat8) user@machine01:~/TESTING_XMGRACE> xmgrace -version
Grace-5.99.0 preview
GUI toolkit: @(#)Motif Version 2.3.4
Xbae version: 4007
T1lib: 5.0.2p1-grace
FFT: built-in
NetCDF support: off
Built: Tue Mar 27 04:54:25 2018 on Linux 4.4.59-92.24-default x86_64
Compiler flags: gcc -O2 -fno-common -Wall -pedantic -Wpointer-arith -Wnested-externs -I../include -I../cephes -I. -I../T1lib/t1lib -I../Xbae -L/usr/lib64 ../Xbae/Xbae/libXbae.a -lXm -lXpm -lXp -lXmu -lXt -lXext -lX11 -lSM -lICE ../cephes/libcephes.a -lexpat ../lib/core/libgrace-core.a ../lib/canvas/libgrace-canvas.a ../T1lib/libt1.a -ljpeg -lpng -lz ../lib/base/libgrace-base.a -lm -ldl
Registered devices:
X11 PostScript EPS MIF SVG Metafile
(C) Copyright 1991-1995 Paul J Turner
(C) Copyright 1996-2004 Grace Development Team
All Rights Reserved
here is the conda environment -
(cdat8) user@machine01:~/TESTING_XMGRACE> conda list
# packages in environment at /home/apps/SiteSoftwares/gnu/ANACONDA2/5.1.0/envs/cdat8:
#
# Name Version Build Channel
alabaster 0.7.10 py27_1 conda-forge
asn1crypto 0.24.0 py27_0 conda-forge
astroid 1.6.3 py27_0 conda-forge
autopep8 1.3.4 py_0 conda-forge
babel 2.5.3 py27_0 conda-forge
backports 1.0 py27_1 conda-forge
backports.functools_lru_cache 1.5 py27_0 conda-forge
backports.shutil_get_terminal_size 1.0.0 py_3 conda-forge
backports_abc 0.5 py27_0 conda-forge
basemap 1.1.0 py27_4 conda-forge
biggus 0.15.0 py27_0 conda-forge
bleach 2.1.3 py_0 conda-forge
bokeh 0.12.15 py27_0 conda-forge
bzip2 1.0.6 1 conda-forge
ca-certificates 2018.4.16 0 conda-forge
cartopy 0.16.0 py27_0 conda-forge
cdat 8.0 0 cdat
cdat_info 8.0 py27_0 conda-forge
cdms2 3.0 py27_6 conda-forge
cdp 1.3.3 py27_0 cdat
cdtime 3.0 py27_0 conda-forge
cdutil 8.0 py27_1 conda-forge
certifi 2018.4.16 py27_0 conda-forge
cf_units 1.2.0 py27_0 conda-forge
cffi 1.11.5 py27_0 conda-forge
chardet 3.0.4 py27_0 conda-forge
cibots 0.2 py27_0 conda-forge
clapack 3.2.1 0 conda-forge
click 6.7 py_1 conda-forge
cloudpickle 0.5.2 py_0 conda-forge
configparser 3.5.0 py27_0 conda-forge
cryptography 2.2.1 py27_0 conda-forge
curl 7.59.0 1 conda-forge
cycler 0.10.0 py27_0 conda-forge
cytoolz 0.9.0.1 py27_0 conda-forge
dask 0.17.4 py_0 conda-forge
dask-core 0.17.4 py_0 conda-forge
dbus 1.11.0 0 conda-forge
decorator 4.3.0 py_0 conda-forge
distarray 2.12.2 py27_0 conda-forge
distributed 1.21.8 py27_0 conda-forge
docutils 0.14 py27_0 conda-forge
dv3d 8.0 py27_0 cdat
ecmwf_grib 1.26.0 0 conda-forge
entrypoints 0.2.3 py27_1 conda-forge
enum34 1.1.6 py27_1 conda-forge
eofs 1.3.0 py27_0 conda-forge
esmf 7.1.0r 0 conda-forge
esmpy 7.1.0r py27_1 conda-forge
expat 2.2.5 0 conda-forge
ffmpeg 3.4.2 0 conda-forge
flake8 3.5.0 py27_0 conda-forge
fontconfig 2.12.6 0 conda-forge
freetype 2.8.1 0 conda-forge
functools32 3.2.3.2 py27_2 conda-forge
future 0.16.0 py27_0 conda-forge
futures 3.2.0 py27_0 conda-forge
g2clib 1.6.0 5 conda-forge
genutil 8.0 py27_1 conda-forge
geos 3.6.2 1 conda-forge
gettext 0.19.8.1 0 conda-forge
glib 2.55.0 0 conda-forge
gmp 6.1.2 0 conda-forge
gnutls 3.5.17 0 conda-forge
gst-plugins-base 1.8.0 0 conda-forge
gstreamer 1.8.0 1 conda-forge
hdf4 4.2.13 0 conda-forge
hdf5 1.10.1 2 conda-forge
heapdict 1.0.0 py27_0 conda-forge
html5lib 1.0.1 py_0 conda-forge
icu 58.2 0 conda-forge
idna 2.6 py27_1 conda-forge
imageio 2.3.0 py27_0 conda-forge
imagesize 1.0.0 py27_0 conda-forge
intel-openmp 2018.0.0 8
ipaddress 1.0.22 py_1 conda-forge
ipykernel 4.8.2 py27_0 conda-forge
ipython 5.6.0 py27_0 conda-forge
ipython_genutils 0.2.0 py27_0 conda-forge
ipywidgets 7.2.1 py27_1 conda-forge
iris 1.13.0 py27_1 conda-forge
iris-grib 0.12.0 py27_0 conda-forge
isort 4.3.4 py27_0 conda-forge
jasper 1.900.1 4 conda-forge
jedi 0.12.0 py27_0 conda-forge
jinja2 2.10 py27_0 conda-forge
jpeg 9b 2 conda-forge
jsonschema 2.6.0 py27_1 conda-forge
jupyter 1.0.0 py_1 conda-forge
jupyter_client 5.2.3 py27_0 conda-forge
jupyter_console 5.2.0 py27_0 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
kiwisolver 1.0.1 py27_1 conda-forge
krb5 1.14.6 0 conda-forge
lapack 3.6.1 1 conda-forge
lazy-object-proxy 1.3.1 py27_0 conda-forge
libcdms 3.0.1 0 conda-forge
libcf 1.0.1 py27_1 conda-forge
libdrs 3.0 0 conda-forge
libdrs_f 3.0 0 conda-forge
libffi 3.2.1 3 conda-forge
libgcc 7.2.0 h69d50b8_2
libgcc-ng 7.2.0 hdf63c60_3
libgfortran 3.0.0 1
libgfortran-ng 7.2.0 hdf63c60_3
libiconv 1.15 0 conda-forge
libidn11 1.33 0 conda-forge
libmo_unpack 3.1.2 0 conda-forge
libnetcdf 4.4.1.1 10 conda-forge
libpng 1.6.34 0 conda-forge
libsodium 1.0.16 0 conda-forge
libssh2 1.8.0 2 conda-forge
libstdcxx-ng 7.2.0 hdf63c60_3
libtiff 4.0.9 0 conda-forge
libxcb 1.13 0 conda-forge
libxml2 2.9.8 0 conda-forge
libxslt 1.1.32 0 conda-forge
locket 0.2.0 py27_1 conda-forge
lxml 4.2.1 py27_0 conda-forge
markupsafe 1.0 py27_0 conda-forge
matplotlib 2.2.2 py27_1 conda-forge
mccabe 0.6.1 py27_0 conda-forge
mistune 0.8.3 py27_1 conda-forge
mkl 2018.0.2 1
mkl_fft 1.0.2 py27_0 conda-forge
mkl_random 1.0.1 py27_0 conda-forge
mo_pack 0.2.0 py27_1 conda-forge
mpi 1.0 mpich conda-forge
mpich 3.2.1 0 conda-forge
msgpack-python 0.5.6 py27_1 conda-forge
nb_conda 2.2.1 py27_0 conda-forge
nb_conda_kernels 2.1.0 py27_0 conda-forge
nbconvert 5.3.1 py_1 conda-forge
nbformat 4.4.0 py27_0 conda-forge
nc_time_axis 1.0.2 py27_0 conda-forge
ncurses 5.9 10 conda-forge
netcdf-fortran 4.4.4 6 conda-forge
netcdf4 1.3.1 py27_1 conda-forge
nettle 3.3 0 conda-forge
networkx 2.1 py27_0 conda-forge
notebook 5.4.1 py27_0 conda-forge
numpy 1.14.2 py27hdbf6ddf_1
numpydoc 0.8.0 py27_0 conda-forge
olefile 0.45.1 py27_0 conda-forge
openssl 1.0.2o 0 conda-forge
ossuuid 1.6.2 0 conda-forge
output_viewer 1.2.5 py27_0 cdat
owslib 0.16.0 py_0 conda-forge
packaging 17.1 py_0 conda-forge
pandas 0.22.0 py27_1 conda-forge
pandoc 2.2 0 conda-forge
pandocfilters 1.4.2 py27_0 conda-forge
parso 0.2.0 py_0 conda-forge
partd 0.3.8 py27_0 conda-forge
pathlib2 2.3.2 py27_0 conda-forge
pcre 8.41 1 conda-forge
pexpect 4.5.0 py27_0 conda-forge
pickleshare 0.7.4 py27_0 conda-forge
pillow 5.1.0 py27_0 conda-forge
pip 9.0.3 py27_0 conda-forge
proj4 4.9.3 5 conda-forge
prompt_toolkit 1.0.15 py27_0 conda-forge
psutil 5.4.5 py27_0 conda-forge
ptyprocess 0.5.2 py27_0 conda-forge
pycodestyle 2.3.1 py27_0 conda-forge
pycparser 2.18 py27_0 conda-forge
pyepsg 0.3.2 py27_0 conda-forge
pyflakes 1.6.0 py27_0 conda-forge
pygments 2.2.0 py27_0 conda-forge
pyke 1.1.1 py27_0 conda-forge
pylint 1.8.4 py27_0 conda-forge
pyopenssl 17.5.0 py27_1 conda-forge
pyparsing 2.2.0 py27_0 conda-forge
pyproj 1.9.5.1 py27_0 conda-forge
pyqt 5.6.0 py27_5 conda-forge
pyshp 1.2.12 py_0 conda-forge
pysocks 1.6.8 py27_1 conda-forge
pyspharm 1.0.9 py27_3 conda-forge
python 2.7.14 5 conda-forge
python-dateutil 2.7.2 py_0 conda-forge
python-ecmwf_grib 1.26.0 py27_0 conda-forge
pytz 2018.4 py_0 conda-forge
pywavelets 0.5.2 py27_1 conda-forge
pyyaml 3.12 py27_1 conda-forge
pyzmq 17.0.0 py27_4 conda-forge
qt 5.6.2 7 conda-forge
qtawesome 0.4.4 py27_0 conda-forge
qtconsole 4.3.1 py27_0 conda-forge
qtpy 1.4.2 py27h8a2030e_0 conda-forge
readline 7.0 0 conda-forge
requests 2.18.4 py27_1 conda-forge
rope 0.10.7 py27_0 conda-forge
scandir 1.7 py27_0 conda-forge
scikit-image 0.13.1 py27_0 conda-forge
scipy 1.0.1 py27hfc37229_0
send2trash 1.5.0 py_0 conda-forge
setuptools 39.1.0 py27_0 conda-forge
shapely 1.6.4 py27_0 conda-forge
simplegeneric 0.8.1 py27_0 conda-forge
singledispatch 3.4.0.3 py27_0 conda-forge
sip 4.18 py27_1 conda-forge
six 1.11.0 py27_1 conda-forge
snowballstemmer 1.2.1 py27_0 conda-forge
sortedcontainers 1.5.10 py27_0 conda-forge
sphinx 1.7.4 py27_0 conda-forge
sphinxcontrib-websupport 1.0.1 py27_0 conda-forge
spyder 3.2.8 py27_0 conda-forge
sqlite 3.20.1 2 conda-forge
subprocess32 3.2.7 py27_0 conda-forge
tblib 1.3.2 py27_0 conda-forge
terminado 0.8.1 py27_0 conda-forge
testpath 0.3.1 py27_0 conda-forge
thermo 8.0 py27_0 cdat
tk 8.6.7 0 conda-forge
toolz 0.9.0 py_0 conda-forge
tornado 5.0.2 py27_0 conda-forge
traitlets 4.3.2 py27_0 conda-forge
typing 3.6.4 py27_0 conda-forge
udunits2 2.2.26 0 conda-forge
urllib3 1.22 py27_0 conda-forge
vcs 8.0 py27_0 cdat
vcsaddons 8.0 py27_0 cdat
vtk-cdat 8.0.1.8.0 py27_1 cdat
wcwidth 0.1.7 py27_0 conda-forge
webencodings 0.5 py27_0 conda-forge
wheel 0.31.0 py27_0 conda-forge
widgetsnbextension 3.2.1 py27_0 conda-forge
windspharm 1.5.1 py27_0 conda-forge
wk 8.0 py27_0 cdat
wrapt 1.10.11 py27_0 conda-forge
x264 20131218 0 conda-forge
xmgrace 8.0 py27_0 cdat
xorg-libxau 1.0.8 3 conda-forge
xorg-libxdmcp 1.1.2 3 conda-forge
xz 5.2.3 0 conda-forge
yaml 0.1.7 0 conda-forge
zeromq 4.2.5 1 conda-forge
zict 0.1.3 py_0 conda-forge
zlib 1.2.11 0 conda-forge
python potting script is attached - testing_xmgrace.py.txt
Terminal output while running the script is attached herewith - terminal.png
Please let me know if i can provide you with any further information on this issue.
I tried testing a VCS plot at - https://cdat.llnl.gov/getting_started.html. It worked,
seems we are having issues when xmgrace is involved.
@charlesdoutriaux We do not have any problem in IBM machine, but we are facing the above problem in CRAY machine. Is there any system compatibility with Xmgrace-Python-API ? System xmgrace is working in cray machine, but cdat xmgrace-python module is unable to plot any figure. Any clue will help us to solve this problem.
Thanks.
@puneet336 Now I cross-checked the grace version 5.1.25, it seems working after I reinstalled cdat8 as follows "conda create -n cdat8_grace -c conda-forge -c cdat python=2.7 cdat xmgrace".
@charlesdoutriaux So xmgrace version 5.99 is not compatible with cdat8. Could you please confirm it ? Thanks.
@arulalant , thanks for the information. xmgrace-5.1.25 seems to be working fine as of now under cdat8 ( /home/apps/SiteSoftwares/gnu/ANACONDA2/5.1.0/envs/cdat8 ) env.
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Marking this issue as closed. Let me know if i can provide further information wrt. 5.99 compatibility issue.
@arulalant @puneet336 the interface between xmgrace and python is made via pipes. I will check and see if anything changed in 5.99.