Hello, I understand there are a few similar questions being asked and I also understand the reasons behind that is rather complicated as it depends on the platform we are running. But here is my situation:
[1] I really want to my code to use faster implementation
[2] I followed the exact same installation instructions using mamba
[3] I didn’t have this issue when tested on my Mac, but now it pops up on our HPC cluster (Linux)
My mamba environment and my OS are like below, I am just hoping to know, which package I need to update. Or how I can change the environment variable to make it work? Much appreciated!
# packages in environment at /data/salomonis2/LabFiles/Frank-Li/neoantigen/revision/ts/bayesian/pymc5_mamba_env:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_kmp_llvm conda-forge
alsa-lib 1.2.8 h166bdaf_0 conda-forge
anndata 0.8.0 pyhd8ed1ab_1 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
arviz 0.14.0 pyhd8ed1ab_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
binutils 2.39 hdd6e379_1 conda-forge
binutils_impl_linux-64 2.39 he00db2b_1 conda-forge
binutils_linux-64 2.39 h5fc0e48_11 conda-forge
blas 2.116 openblas conda-forge
blas-devel 3.9.0 16_linux64_openblas 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
c-ares 1.18.1 h7f98852_0 conda-forge
c-compiler 1.5.2 h0b41bf4_0 conda-forge
ca-certificates 2022.12.7 ha878542_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.2.1 pyhd8ed1ab_0 conda-forge
certifi 2022.12.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py311h409f033_3 conda-forge
cftime 1.6.2 py311h4c7f6c3_1 conda-forge
charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge
cloudpickle 2.2.1 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
cons 0.4.5 pyhd8ed1ab_0 conda-forge
contourpy 1.0.7 py311ha3edf6b_0 conda-forge
cryptography 39.0.0 py311h9b4c7bb_0 conda-forge
curl 7.87.0 hdc1c0ab_0 conda-forge
cxx-compiler 1.5.2 hf52228f_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
etuples 0.3.8 pyhd8ed1ab_0 conda-forge
expat 2.5.0 h27087fc_0 conda-forge
fastprogress 1.0.3 pyhd8ed1ab_0 conda-forge
fftw 3.3.10 nompi_hf0379b8_106 conda-forge
filelock 3.9.0 pyhd8ed1ab_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
gcc 11.3.0 h02d0930_11 conda-forge
gcc_impl_linux-64 11.3.0 hab1b70f_19 conda-forge
gcc_linux-64 11.3.0 he6f903b_11 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
glib 2.74.1 h6239696_1 conda-forge
glib-tools 2.74.1 h6239696_1 conda-forge
gst-plugins-base 1.21.3 h4243ec0_1 conda-forge
gstreamer 1.21.3 h25f0c4b_1 conda-forge
gstreamer-orc 0.4.33 h166bdaf_0 conda-forge
gxx 11.3.0 h02d0930_11 conda-forge
gxx_impl_linux-64 11.3.0 hab1b70f_19 conda-forge
gxx_linux-64 11.3.0 hc203a17_11 conda-forge
h5py 3.7.0 nompi_py311hbe7f6d8_102 conda-forge
hdf4 4.2.15 h9772cbc_5 conda-forge
hdf5 1.12.2 nompi_h4df4325_101 conda-forge
icu 70.1 h27087fc_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
importlib-metadata 6.0.0 pyha770c72_0 conda-forge
importlib_metadata 6.0.0 hd8ed1ab_0 conda-forge
jack 1.9.21 h583fa2b_2 conda-forge
jpeg 9e h166bdaf_2 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 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
lame 3.100 h166bdaf_1003 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
libaec 1.0.6 hcb278e6_1 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
libcap 2.66 ha37c62d_0 conda-forge
libcblas 3.9.0 16_linux64_openblas conda-forge
libclang 15.0.7 default_had23c3d_0 conda-forge
libclang13 15.0.7 default_h3e3d535_0 conda-forge
libcups 2.3.3 h36d4200_3 conda-forge
libcurl 7.87.0 hdc1c0ab_0 conda-forge
libdb 6.2.32 h9c3ff4c_0 conda-forge
libdeflate 1.17 h0b41bf4_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.10 h28343ad_4 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.2 h27087fc_0 conda-forge
libgcc-devel_linux-64 11.3.0 h210ce93_19 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgcrypt 1.10.1 h166bdaf_0 conda-forge
libgfortran-ng 12.2.0 h69a702a_19 conda-forge
libgfortran5 12.2.0 h337968e_19 conda-forge
libglib 2.74.1 h606061b_1 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
libgpg-error 1.46 h620e276_0 conda-forge
libhwloc 2.8.0 h32351e8_1 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
liblapacke 3.9.0 16_linux64_openblas conda-forge
libllvm15 15.0.7 hadd5161_0 conda-forge
libnetcdf 4.8.1 nompi_h261ec11_106 conda-forge
libnghttp2 1.51.0 hff17c54_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libpq 15.1 hb675445_3 conda-forge
libsanitizer 11.3.0 h239ccf8_19 conda-forge
libsndfile 1.2.0 hb75c966_0 conda-forge
libsqlite 3.40.0 h753d276_0 conda-forge
libssh2 1.10.0 hf14f497_3 conda-forge
libstdcxx-devel_linux-64 11.3.0 h210ce93_19 conda-forge
libstdcxx-ng 12.2.0 h46fd767_19 conda-forge
libsystemd0 252 h2a991cd_0 conda-forge
libtiff 4.5.0 h6adf6a1_2 conda-forge
libtool 2.4.7 h27087fc_0 conda-forge
libudev1 252 h166bdaf_0 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.2.4 h166bdaf_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.10.3 h7463322_0 conda-forge
libzip 1.9.2 hc929e4a_1 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
llvm-openmp 15.0.7 h0cdce71_0 conda-forge
logical-unification 0.4.5 pyhd8ed1ab_0 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
matplotlib 3.6.3 py311h38be061_0 conda-forge
matplotlib-base 3.6.3 py311h8597a09_0 conda-forge
minikanren 1.0.3 pyhd8ed1ab_0 conda-forge
mkl 2022.2.1 h84fe81f_16997 conda-forge
mkl-service 2.4.0 py311hb711fc7_0 conda-forge
mpg123 1.31.2 hcb278e6_0 conda-forge
multipledispatch 0.6.0 py_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.32 ha901b37_0 conda-forge
mysql-libs 8.0.32 hd7da12d_0 conda-forge
natsort 8.2.0 pyhd8ed1ab_0 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
netcdf4 1.6.2 nompi_py311hc6fcf29_100 conda-forge
nspr 4.35 h27087fc_0 conda-forge
nss 3.82 he02c5a1_0 conda-forge
numpy 1.24.1 py311hbde0eaa_0 conda-forge
openblas 0.3.21 pthreads_h320a7e8_3 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
patsy 0.5.3 pyhd8ed1ab_0 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
ply 3.11 py_1 conda-forge
pooch 1.6.0 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pulseaudio 16.1 ha8d29e2_1 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pymc 5.0.2 hd8ed1ab_0 conda-forge
pymc-base 5.0.2 pyhd8ed1ab_0 conda-forge
pyopenssl 23.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pyqt 5.15.7 py311h3408d8f_2 conda-forge
pyqt5-sip 12.11.0 py311ha362b79_2 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pytensor 2.9.1 py311hcafe171_0 conda-forge
pytensor-base 2.9.1 py311hcafe171_0 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 2022.7.1 pyhd8ed1ab_0 conda-forge
qt-main 5.15.6 hf6cd601_5 conda-forge
readline 8.1.2 h0f457ee_0 conda-forge
requests 2.28.2 pyhd8ed1ab_0 conda-forge
scipy 1.10.0 py311h8e6699e_0 conda-forge
seaborn 0.12.2 hd8ed1ab_0 conda-forge
seaborn-base 0.12.2 pyhd8ed1ab_0 conda-forge
setuptools 66.0.0 pyhd8ed1ab_0 conda-forge
sip 6.7.5 py311ha362b79_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
statsmodels 0.13.5 py311h4c7f6c3_2 conda-forge
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tbb 2021.7.0 h924138e_1 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
tornado 6.2 py311hd4cff14_1 conda-forge
tqdm 4.64.1 pyhd8ed1ab_0 conda-forge
typing-extensions 4.4.0 hd8ed1ab_0 conda-forge
typing_extensions 4.4.0 pyha770c72_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
xarray 2023.1.0 pyhd8ed1ab_0 conda-forge
xarray-einstats 0.5.0 pyhd8ed1ab_0 conda-forge
xcb-util 0.4.0 h516909a_0 conda-forge
xcb-util-image 0.4.0 h166bdaf_0 conda-forge
xcb-util-keysyms 0.4.0 h516909a_0 conda-forge
xcb-util-renderutil 0.3.9 h166bdaf_0 conda-forge
xcb-util-wm 0.4.1 h516909a_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zipp 3.11.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h166bdaf_4 conda-forge
zstd 1.5.2 h3eb15da_5 conda-forge
And my OS system:
NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"
CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"