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Enabling virtual_packet_logging causes error #1764

Closed
1 of 2 tasks
atharva-2001 opened this issue Jul 30, 2021 · 2 comments · Fixed by #1846
Closed
1 of 2 tasks

Enabling virtual_packet_logging causes error #1764

atharva-2001 opened this issue Jul 30, 2021 · 2 comments · Fixed by #1846
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bug 🐞 logging virtual packets

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@atharva-2001
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Describe the bug

An error is raised when one tries to enable virtual_packet_logging after run_tardis has been called once with virtual_packet_logging disabled.

To Reproduce

from tardis import run_tardis
sim = run_tardis('tardis_example.yml',log_level="info", show_cplots = False)
sim = run_tardis('tardis_example.yml', log_level="info",  virtual_packet_logging = True,show_cplots = False)

The error is raised in the last iteration of the second run:

[tardis.simulation.base][INFO   ]  Starting iteration 20 of 20 (base.py:359)
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-1-c1d93772a6a1> in <module>
      1 from tardis import run_tardis
      2 sim = run_tardis('tardis_example.yml',log_level="info", show_cplots = False)
----> 3 sim = run_tardis('tardis_example.yml', log_level="info",  virtual_packet_logging = True,show_cplots = False)

~/workspace/gsoc/tardis-fork2/tardis/tardis/base.py in run_tardis(config, atom_data, packet_source, simulation_callbacks, virtual_packet_logging, show_cplots, log_level, specific, **kwargs)
    107         simulation.add_callback(*cb)
    108 
--> 109     simulation.run()
    110 
    111     return simulation

~/workspace/gsoc/tardis-fork2/tardis/tardis/simulation/base.py in run(self)
    429         )
    430         self.iterate(
--> 431             self.last_no_of_packets, self.no_of_virtual_packets, last_run=True
    432         )
    433 

~/workspace/gsoc/tardis-fork2/tardis/tardis/simulation/base.py in iterate(self, no_of_packets, no_of_virtual_packets, last_run)
    366             nthreads=self.nthreads,
    367             last_run=last_run,
--> 368             iteration=self.iterations_executed,
    369         )
    370         output_energy = self.runner.output_energy

~/workspace/gsoc/tardis-fork2/tardis/tardis/montecarlo/base.py in run(self, model, plasma, no_of_packets, no_of_virtual_packets, nthreads, last_run, iteration)
    302 
    303         configuration_initialize(self, no_of_virtual_packets)
--> 304         montecarlo_radial1d(model, plasma, self)
    305         self._integrator = FormalIntegrator(model, plasma, self)
    306         # montecarlo.montecarlo_radial1d(

~/workspace/gsoc/tardis-fork2/tardis/tardis/montecarlo/montecarlo_numba/base.py in montecarlo_radial1d(model, plasma, runner)
     87     if montecarlo_configuration.VPACKET_LOGGING and number_of_vpackets > 0:
     88         runner.virt_packet_nus = np.concatenate(
---> 89             np.array(virt_packet_nus)
     90         ).ravel()
     91         runner.virt_packet_energies = np.concatenate(

<__array_function__ internals> in concatenate(*args, **kwargs)

ValueError: need at least one array to concatenate

One can also raise the error by enabling virtual_packet_logging via the config file instead of the option in the run_tardis function, after the first run, without virtual_packet_logging enabled.

Screenshots

System

  • OS:

    • GNU/Linux
    • macOS

  • Environment (conda list):

# packages in environment at /home/atharva/.conda/envs/tardis:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
alabaster                 0.7.12                     py_0    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
argon2-cffi               20.1.0           py37h5e8e339_2    conda-forge
astropy                   3.2.3            py37h516909a_0    conda-forge
astropy-sphinx-theme      1.1                        py_0    conda-forge
async_generator           1.10                       py_0    conda-forge
atk-1.0                   2.36.0               h3371d22_4    conda-forge
attrs                     21.2.0             pyhd8ed1ab_0    conda-forge
babel                     2.9.1              pyh44b312d_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
black                     21.5b2             pyhd8ed1ab_0    conda-forge
bleach                    3.3.0              pyh44b312d_0    conda-forge
blosc                     1.21.0               h9c3ff4c_0    conda-forge
brotlipy                  0.7.0           py37h5e8e339_1001    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.1               h7f98852_1    conda-forge
ca-certificates           2021.5.30            ha878542_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cairo                     1.16.0            h6cf1ce9_1008    conda-forge
certifi                   2021.5.30        py37h89c1867_0    conda-forge
cffi                      1.14.5           py37hc58025e_0    conda-forge
chardet                   4.0.0            py37h89c1867_1    conda-forge
click                     8.0.1            py37h89c1867_0    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
commonmark                0.9.1                      py_0    conda-forge
coverage                  5.5              py37h5e8e339_0    conda-forge
cryptography              3.4.7            py37h5d9358c_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
dataclasses               0.8                pyhc8e2a94_1    conda-forge
dbus                      1.13.6               h48d8840_2    conda-forge
decorator                 4.4.2                      py_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
docutils                  0.16             py37h89c1867_3    conda-forge
dokuwiki                  1.2.1                    pypi_0    pypi
dot2tex                   2.11.3                   pypi_0    pypi
entrypoints               0.3             pyhd8ed1ab_1003    conda-forge
expat                     2.4.1                h9c3ff4c_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.13.1            hba837de_1005    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
future                    0.18.2           py37h89c1867_3    conda-forge
gdk-pixbuf                2.42.6               h04a7f16_0    conda-forge
gettext                   0.19.8.1          h0b5b191_1005    conda-forge
giflib                    5.2.1                h36c2ea0_2    conda-forge
git-lfs                   2.13.3               ha770c72_0    conda-forge
glib                      2.68.3               h9c3ff4c_0    conda-forge
glib-tools                2.68.3               h9c3ff4c_0    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
graphviz                  2.47.2               h85b4f2f_0    conda-forge
gst-plugins-base          1.18.4               hf529b03_2    conda-forge
gstreamer                 1.18.4               h76c114f_2    conda-forge
gtk2                      2.24.33              h539f30e_1    conda-forge
gts                       0.7.6                h64030ff_2    conda-forge
h5py                      3.2.1           nompi_py37ha3df211_100    conda-forge
harfbuzz                  2.8.1                h83ec7ef_0    conda-forge
hdf5                      1.10.6          nompi_h6a2412b_1114    conda-forge
hypothesis                6.14.0             pyhd8ed1ab_0    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
idna                      2.10               pyh9f0ad1d_0    conda-forge
imagesize                 1.2.0                      py_0    conda-forge
importlib-metadata        4.5.0            py37h89c1867_0    conda-forge
importlib_metadata        4.5.0                hd8ed1ab_0    conda-forge
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
ipykernel                 5.5.5            py37h085eea5_0    conda-forge
ipython                   7.24.1           py37h085eea5_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.6.3              pyhd3deb0d_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jedi                      0.18.0           py37h89c1867_2    conda-forge
jinja2                    3.0.1              pyhd8ed1ab_0    conda-forge
jpeg                      9d                   h36c2ea0_0    conda-forge
jsonpointer               2.0                        py_0    conda-forge
jsonschema                3.2.0              pyhd8ed1ab_3    conda-forge
jupyter                   1.0.0            py37h89c1867_6    conda-forge
jupyter_client            6.1.12             pyhd8ed1ab_0    conda-forge
jupyter_console           6.4.0              pyhd8ed1ab_0    conda-forge
jupyter_core              4.7.1            py37h89c1867_0    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_widgets        1.0.0              pyhd8ed1ab_1    conda-forge
kaleido-core              0.2.1                h3644ca4_0    conda-forge
kiwisolver                1.3.1            py37h2527ec5_1    conda-forge
krb5                      1.19.1               hcc1bbae_0    conda-forge
latexcodec                2.0.1              pyh9f0ad1d_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.35.1               hea4e1c9_2    conda-forge
lerc                      2.2.1                h9c3ff4c_0    conda-forge
libblas                   3.9.0                9_openblas    conda-forge
libcblas                  3.9.0                9_openblas    conda-forge
libclang                  11.1.0          default_ha53f305_1    conda-forge
libcurl                   7.77.0               h2574ce0_0    conda-forge
libdeflate                1.7                  h7f98852_5    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               hcdb4288_3    conda-forge
libffi                    3.3                  h58526e2_2    conda-forge
libgcc-ng                 9.3.0               h2828fa1_19    conda-forge
libgd                     2.3.2                h78a0170_0    conda-forge
libgfortran-ng            9.3.0               hff62375_19    conda-forge
libgfortran5              9.3.0               hff62375_19    conda-forge
libglib                   2.68.3               h3e27bee_0    conda-forge
libgomp                   9.3.0               h2828fa1_19    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0                9_openblas    conda-forge
libllvm10                 10.0.1               he513fc3_3    conda-forge
libllvm11                 11.1.0               hf817b99_2    conda-forge
libnghttp2                1.43.0               h812cca2_0    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.15          pthreads_h8fe5266_1    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libpq                     13.3                 hd57d9b9_0    conda-forge
librsvg                   2.50.7               hc3c00ef_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libssh2                   1.9.0                ha56f1ee_6    conda-forge
libstdcxx-ng              9.3.0               h6de172a_19    conda-forge
libtiff                   4.3.0                hf544144_1    conda-forge
libtool                   2.4.6             h58526e2_1007    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp                   1.2.0                h3452ae3_0    conda-forge
libwebp-base              1.2.0                h7f98852_2    conda-forge
libxcb                    1.13              h7f98852_1003    conda-forge
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.12               h72842e0_0    conda-forge
libxslt                   1.1.33               h15afd5d_2    conda-forge
llvmlite                  0.36.0           py37h9d7f4d0_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
markupsafe                2.0.1            py37h5e8e339_0    conda-forge
mathjax                   2.7.7                         0    conda-forge
matplotlib                3.4.2            py37h89c1867_0    conda-forge
matplotlib-base           3.4.2            py37hdd32ed1_0    conda-forge
matplotlib-inline         0.1.2              pyhd8ed1ab_2    conda-forge
mistune                   0.8.4           py37h5e8e339_1003    conda-forge
mock                      4.0.3            py37h89c1867_1    conda-forge
more-itertools            8.8.0              pyhd8ed1ab_0    conda-forge
mypy                      0.901              pyhd3eb1b0_0  
mypy_extensions           0.4.3            py37h89c1867_3    conda-forge
mysql-common              8.0.25               ha770c72_2    conda-forge
mysql-libs                8.0.25               hfa10184_2    conda-forge
nbclient                  0.5.3              pyhd8ed1ab_0    conda-forge
nbconvert                 6.0.7            py37h89c1867_3    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
nbsphinx                  0.8.6              pyhd8ed1ab_1    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
nest-asyncio              1.5.1              pyhd8ed1ab_0    conda-forge
networkx                  2.5.1              pyhd8ed1ab_0    conda-forge
notebook                  6.4.0              pyha770c72_0    conda-forge
nspr                      4.30                 h9c3ff4c_0    conda-forge
nss                       3.67                 hb5efdd6_0    conda-forge
numba                     0.53.1           py37hb11d6e1_1    conda-forge
numexpr                   2.7.3            py37hdc94413_0    conda-forge
numpy                     1.19.5           py37haa41c4c_1    conda-forge
numpydoc                  1.1.0                      py_1    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openssl                   1.1.1k               h7f98852_0    conda-forge
packaging                 20.9               pyh44b312d_0    conda-forge
pandas                    1.0.5            py37h0da4684_0    conda-forge
pandoc                    2.14.0.1             h7f98852_0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
pango                     1.48.5               hb8ff022_0    conda-forge
parso                     0.8.2              pyhd8ed1ab_0    conda-forge
pathspec                  0.8.1              pyhd3deb0d_0    conda-forge
pbr                       5.6.0              pyhd8ed1ab_0    conda-forge
pcre                      8.44                 he1b5a44_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickle5                   0.0.11           py37h5e8e339_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    8.2.0            py37h4600e1f_1    conda-forge
pip                       21.1.2             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
plotly                    4.14.3             pyh44b312d_0    conda-forge
pluggy                    0.13.1           py37h89c1867_4    conda-forge
prometheus_client         0.11.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.18             pyha770c72_0    conda-forge
prompt_toolkit            3.0.18               hd8ed1ab_0    conda-forge
psutil                    5.8.0            py37h5e8e339_1    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
py                        1.10.0             pyhd3deb0d_0    conda-forge
pybtex                    0.24.0           py37h89c1867_0    conda-forge
pybtex-docutils           1.0.0            py37h89c1867_0    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pydocstyle                6.1.1              pyhd3eb1b0_0  
pygments                  2.9.0              pyhd8ed1ab_0    conda-forge
pygraphviz                1.7              py37h0b1d2a2_0    conda-forge
pyne                      0.7.3           nomoab_noopenmcpy37h879b29b_1    conda-forge
pyopenssl                 20.0.1             pyhd8ed1ab_0    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pyqt                      5.12.3           py37h89c1867_7    conda-forge
pyqt-impl                 5.12.3           py37he336c9b_7    conda-forge
pyqt5-sip                 4.19.18          py37hcd2ae1e_7    conda-forge
pyqtchart                 5.12             py37he336c9b_7    conda-forge
pyqtwebengine             5.12.1           py37he336c9b_7    conda-forge
pyrsistent                0.17.3           py37h5e8e339_2    conda-forge
pyside2                   5.13.2           py37hfa98aef_4    conda-forge
pysocks                   1.7.1            py37h89c1867_3    conda-forge
pytables                  3.6.1            py37h0c4f3e0_3    conda-forge
pytest                    6.2.4            py37h89c1867_0    conda-forge
pytest-arraydiff          0.3                        py_0    conda-forge
pytest-astropy            0.8.0              pyhd8ed1ab_0    conda-forge
pytest-astropy-header     0.1.2                      py_0    conda-forge
pytest-cov                2.12.1             pyhd8ed1ab_0    conda-forge
pytest-doctestplus        0.9.0              pyhd8ed1ab_0    conda-forge
pytest-filter-subpackage  0.1.1                      py_0    conda-forge
pytest-html               3.1.1              pyhd8ed1ab_0    conda-forge
pytest-metadata           1.11.0             pyhd3deb0d_0    conda-forge
pytest-mock               3.6.1              pyhd8ed1ab_0    conda-forge
pytest-openfiles          0.5.0                      py_0    conda-forge
pytest-remotedata         0.3.2              pyh9f0ad1d_0    conda-forge
python                    3.7.10          hffdb5ce_100_cpython    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python-kaleido            0.2.1              pyhd8ed1ab_0    conda-forge
python_abi                3.7                     1_cp37m    conda-forge
pytz                      2021.1             pyhd8ed1ab_0    conda-forge
pyyaml                    5.4.1            py37h5e8e339_0    conda-forge
pyzmq                     22.1.0           py37h336d617_0    conda-forge
qgrid                     1.3.1              pyhd8ed1ab_3    conda-forge
qt                        5.12.9               hda022c4_4    conda-forge
qtconsole                 5.1.0              pyhd8ed1ab_0    conda-forge
qtpy                      1.9.0                      py_0    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
recommonmark              0.7.1              pyhd8ed1ab_0    conda-forge
regex                     2021.4.4         py37h5e8e339_0    conda-forge
requests                  2.25.1             pyhd3deb0d_0    conda-forge
retrying                  1.3.3                      py_2    conda-forge
scipy                     1.5.3            py37h14a347d_0    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                49.6.0           py37h89c1867_3    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snowballstemmer           2.1.0              pyhd8ed1ab_0    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
sphinx                    4.0.2              pyh6c4a22f_1    conda-forge
sphinx-astropy            1.3                pyh9f0ad1d_0    conda-forge
sphinx-automodapi         0.13                       py_0    conda-forge
sphinx-gallery            0.9.0              pyhd8ed1ab_0    conda-forge
sphinx-jsonschema         1.16.8             pyhd8ed1ab_0    conda-forge
sphinx_bootstrap_theme    0.8.0                      py_0    conda-forge
sphinx_rtd_theme          0.5.2              pyhd8ed1ab_1    conda-forge
sphinxcontrib-apidoc      0.3.0                      py_1    conda-forge
sphinxcontrib-applehelp   1.0.2                      py_0    conda-forge
sphinxcontrib-bibtex      2.3.0              pyhd8ed1ab_0    conda-forge
sphinxcontrib-devhelp     1.0.2                      py_0    conda-forge
sphinxcontrib-htmlhelp    2.0.0              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1                      py_0    conda-forge
sphinxcontrib-qthelp      1.0.3                      py_0    conda-forge
sphinxcontrib-serializinghtml 1.1.5              pyhd8ed1ab_0    conda-forge
sphinxcontrib-tikz        0.4.13                   pypi_0    pypi
sqlite                    3.35.5               h74cdb3f_0    conda-forge
tardis-sn                 3.0.dev3992               dev_0    <develop>
terminado                 0.10.1           py37h89c1867_0    conda-forge
testpath                  0.5.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.10               h21135ba_1    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tornado                   6.1              py37h5e8e339_1    conda-forge
tqdm                      4.61.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.0.5                      py_0    conda-forge
typed-ast                 1.4.3            py37h5e8e339_0    conda-forge
typing_extensions         3.10.0.0           pyha770c72_0    conda-forge
urllib3                   1.26.5             pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.36.2             pyhd3deb0d_0    conda-forge
widgetsnbextension        3.5.1            py37h89c1867_4    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h516909a_0    conda-forge
zeromq                    4.3.4                h9c3ff4c_0    conda-forge
zipp                      3.4.1              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstd                      1.5.0                ha95c52a_0    conda-forge
​

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@yuyizheng1112
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Same error

@AstronoMoore
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Same error

@atharva-2001 atharva-2001 mentioned this issue Nov 20, 2021
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@atharva-2001 atharva-2001 mentioned this issue Dec 19, 2021
Merged
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bug 🐞 logging virtual packets
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Fix Virtual Packet Logging Bug atharva-2001/tardis
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@andrewfullard @atharva-2001 @yuyizheng1112 @AstronoMoore