Error running python script after conda and gcc update

Hi, I switched over to the new Conda version (4.12.0) after the new gcc compiler install (11.3.0) and now my python script is giving me the following error:

prune_ngsLD.py --input AipResult20_noclones_ngsLD --max_dist 50000 --min_weight 0.1 --out AipResult20_noclones_unlinked.pos
OpenBLAS blas_thread_init: pthread_create failed for thread 61 of 64: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 4096 current, 767406 max
OpenBLAS blas_thread_init: pthread_create failed for thread 62 of 64: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 4096 current, 767406 max
OpenBLAS blas_thread_init: pthread_create failed for thread 63 of 64: Resource temporarily unavailable
OpenBLAS blas_thread_init: RLIMIT_NPROC 4096 current, 767406 max
Traceback (most recent call last):
File “/project/ckenkel_26/software/ngsLD/scripts/prune_ngsLD.py”, line 49, in
import pandas as pd
File “/home1/mruggeri/.conda/envs/gt/lib/python3.11/site-packages/pandas/init.py”, line 11, in
import(_dependency)
File “/home1/mruggeri/.conda/envs/gt/lib/python3.11/site-packages/numpy/init.py”, line 141, in
from . import core
File “/home1/mruggeri/.conda/envs/gt/lib/python3.11/site-packages/numpy/core/init.py”, line 23, in
from . import multiarray
File “/home1/mruggeri/.conda/envs/gt/lib/python3.11/site-packages/numpy/core/multiarray.py”, line 10, in
from . import overrides
File “/home1/mruggeri/.conda/envs/gt/lib/python3.11/site-packages/numpy/core/overrides.py”, line 6, in
from numpy.core._multiarray_umath import (
KeyboardInterrupt

I am running this script in a conda environment with the following package versions:

packages in environment at /home1/mruggeri/.conda/envs/gt:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
at-spi2-atk 2.38.0 h0630a04_3 conda-forge
at-spi2-core 2.40.3 h0630a04_0 conda-forge
atk-1.0 2.38.0 hd4edc92_1 conda-forge
boost 1.78.0 py311h59ea3da_4 conda-forge
boost-cpp 1.78.0 h75c5d50_1 conda-forge
brotli 1.0.9 h166bdaf_8 conda-forge
brotli-bin 1.0.9 h166bdaf_8 conda-forge
brotlipy 0.7.0 py311hd4cff14_1005 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2023.01.10 h06a4308_0
cairo 1.16.0 ha61ee94_1014 conda-forge
cairomm-1.0 1.14.4 h09cb3b9_0 conda-forge
certifi 2020.6.20 pyhd3eb1b0_3
cffi 1.15.1 py311h409f033_3 conda-forge
charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge
contourpy 1.0.7 py311ha3edf6b_0 conda-forge
cryptography 39.0.0 py311h9b4c7bb_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
epoxy 1.5.10 h166bdaf_1 conda-forge
expat 2.5.0 h27087fc_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 2.14.1 hc2a2eb6_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.38.0 py311hd4cff14_1 conda-forge
freetype 2.12.1 hca18f0e_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gdk-pixbuf 2.42.10 h05c8ddd_0 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
glib-tools 2.74.1 h6239696_1 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
graph-tool 2.45 py311h35b2f40_4 conda-forge
graph-tool-base 2.45 py311h0ef9027_4 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
gtk3 3.24.36 h1e7d460_0 conda-forge
harfbuzz 6.0.0 h8e241bc_0 conda-forge
hicolor-icon-theme 0.17 ha770c72_2 conda-forge
icu 70.1 h27087fc_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
jpeg 9e h166bdaf_2 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.4 py311h4dd048b_1 conda-forge
krb5 1.20.1 h81ceb04_0 conda-forge
lcms2 2.14 hfd0df8a_1 conda-forge
ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libblas 3.9.0 16_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_8 conda-forge
libbrotlidec 1.0.9 h166bdaf_8 conda-forge
libbrotlienc 1.0.9 h166bdaf_8 conda-forge
libcblas 3.9.0 16_linux64_openblas conda-forge
libcups 2.3.3 h36d4200_3 conda-forge
libdeflate 1.17 h0b41bf4_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgfortran-ng 12.2.0 h69a702a_19 conda-forge
libgfortran5 12.2.0 h337968e_19 conda-forge
libgirepository 1.74.0 ha2a38d2_1 conda-forge
libglib 2.74.1 h606061b_1 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
libjpeg-turbo 2.1.4 h166bdaf_0 conda-forge
liblapack 3.9.0 16_linux64_openblas conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
librsvg 2.54.4 h7abd40a_0 conda-forge
libsqlite 3.40.0 h753d276_0 conda-forge
libstdcxx-ng 12.2.0 h46fd767_19 conda-forge
libtiff 4.5.0 h6adf6a1_2 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp-base 1.2.4 h166bdaf_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxml2 2.10.3 h7463322_0 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
matplotlib-base 3.6.3 py311h8597a09_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
numpy 1.24.1 py311hbde0eaa_0 conda-forge
openjpeg 2.5.0 hfec8fc6_2 conda-forge
openssl 3.0.7 h0b41bf4_1 conda-forge
packaging 23.0 pyhd8ed1ab_0 conda-forge
pandas 1.5.3 py311h2872171_0 conda-forge
pango 1.50.12 hd33c08f_1 conda-forge
pcre2 10.40 hc3806b6_0 conda-forge
pillow 9.4.0 py311h104bd61_0 conda-forge
pip 22.3.1 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
pooch 1.6.0 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pycairo 1.23.0 py311hdece40b_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygobject 3.42.2 py311h7271657_1 conda-forge
pyopenssl 23.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.11.0 he550d4f_1_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.11 3_cp311 conda-forge
pytz 2021.3 pyhd3eb1b0_0
readline 8.1.2 h0f457ee_0 conda-forge
requests 2.28.2 pyhd8ed1ab_0 conda-forge
scipy 1.10.0 py311h8e6699e_0 conda-forge
setuptools 66.1.1 pyhd8ed1ab_0 conda-forge
sigcpp-2.0 2.10.8 h27087fc_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sparsehash 2.0.4 h9c3ff4c_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tzdata 2022g h191b570_0 conda-forge
urllib3 1.26.14 pyhd8ed1ab_0 conda-forge
wheel 0.38.4 pyhd8ed1ab_0 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-inputproto 2.3.2 h7f98852_1002 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-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxtst 1.2.3 h7f98852_1002 conda-forge
xorg-recordproto 1.14.2 h7f98852_1002 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 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.13 h166bdaf_4 conda-forge
zstandard 0.19.0 py311hbe0fcd7_1 conda-forge
zstd 1.5.2 h3eb15da_6 conda-forge

This script was running fine prior to the new installs. Please advise how I can fix this error.

Are you running this script on a login node? There’s a process limit on the login nodes that would generate this error. If so, log on to a compute node instead via salloc or restrict the threads with export OPENBLAS_NUM_THREADS=1.

1 Like