Error: Segmentation fault (core dumped)
mariokreutzfeldt opened this issue · comments
Hi,
I am trying to train on my own data. But I get the error:
Segmentation fault (core dumped)
The build graph contains 43946 genes with 41 labels supported.
data.gz -> Nonzero Ratio: 19.50%
Added 17267 nodes and 148004641 edges.
#Nodes in Graph: 61213, #Edges: 296009282.
Segmentation fault (core dumped)
Any idea what could cause this error?
Best regards,
Mario
# packages in environment at /home/mario/miniconda3/envs/egervari:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
ca-certificates 2020.12.5 ha878542_0 conda-forge
certifi 2020.12.5 py36h5fab9bb_0 conda-forge
cpuonly 1.0 0 pytorch
decorator 4.4.2 py_0 conda-forge
dgl 0.4.3post2 py36_0 dglteam
freetype 2.10.4 h7ca028e_0 conda-forge
intel-openmp 2020.2 254
joblib 0.17.0 py_0 conda-forge
jpeg 9d h36c2ea0_0 conda-forge
lcms2 2.11 hcbb858e_1 conda-forge
ld_impl_linux-64 2.35.1 hed1e6ac_0 conda-forge
libblas 3.9.0 3_openblas conda-forge
libcblas 3.9.0 3_openblas conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc-ng 9.3.0 h5dbcf3e_17 conda-forge
libgfortran-ng 7.5.0 hae1eefd_17 conda-forge
libgfortran4 7.5.0 hae1eefd_17 conda-forge
libgomp 9.3.0 h5dbcf3e_17 conda-forge
liblapack 3.9.0 3_openblas conda-forge
libopenblas 0.3.12 pthreads_hb3c22a3_1 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libstdcxx-ng 9.3.0 h2ae2ef3_17 conda-forge
libtiff 4.1.0 h4f3a223_6 conda-forge
libwebp-base 1.1.0 h36c2ea0_3 conda-forge
lz4-c 1.9.2 he1b5a44_3 conda-forge
mkl 2020.2 256
ncurses 6.2 h58526e2_4 conda-forge
networkx 2.5 py_0 conda-forge
ninja 1.10.2 h4bd325d_0 conda-forge
numpy 1.17.2 py36h95a1406_0 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openssl 1.1.1h h516909a_0 conda-forge
pandas 0.25.1 py36hb3f55d8_0 conda-forge
pillow 8.0.1 py36h10ecd5c_0 conda-forge
pip 20.3.1 pyhd8ed1ab_0 conda-forge
python 3.6.11 hffdb5ce_3_cpython conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python_abi 3.6 1_cp36m conda-forge
pytorch 1.4.0 py3.6_cpu_0 [cpuonly] pytorch
pytz 2020.4 pyhd8ed1ab_0 conda-forge
readline 8.0 he28a2e2_2 conda-forge
scikit-learn 0.22.2.post1 py36hcdab131_0 conda-forge
scipy 1.3.1 py36h921218d_2 conda-forge
setuptools 49.6.0 py36h9880bd3_2 conda-forge
six 1.15.0 pyh9f0ad1d_0 conda-forge
sqlite 3.34.0 h74cdb3f_0 conda-forge
tk 8.6.10 hed695b0_1 conda-forge
torchvision 0.5.0 py36_cpu [cpuonly] pytorch
wheel 0.36.1 pyhd3deb0d_0 conda-forge
xlrd 1.2.0 pyh9f0ad1d_1 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zlib 1.2.11 h516909a_1010 conda-forge
zstd 1.4.5 h6597ccf_2 conda-forge
Maybe you can try python3.7 as I succeed in training on my own data using train.py. (Ubuntu 18.04, 64G)
Hi,
thank you for your comment. I managed now to start the training. It turned out that my training data was too big. When I reduce the classes or number of genes, I can run it without problems.
Best regards,
Mario