The following issue seems to touch R, conda installation issues and possibly memory mapping.
Here is a minimal example that already results in the problem:
Running mamba create -n R_test r-base -c r seems to work just fine. But when trying to run R from within this env I get the following error (important part):
When looking up this error message online, it often popped up in relation to distinct packages with library mismatches (e.g. caught segfault - 'memory not mapped' error in R) which seem to be examinable from within R ... unless it happens directly at startup like it does for me.
Running R in another, already existing, R 4.1.2 env worked. Also scpecifying that version for a new env resulted in the same problem. So it seems, rather than the version, the issue is with whatever happens when I icreate a new envirmonment.
I tried removing potentially problematic unused packages with conda clean --all and the follwing packages seem to require reboot to remove file handle, e.g.removing conda-env-2.6.0-1 WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(143): Could not remove or rename /opt/anaconda/anaconda3/pkgs/conda-env-2.6.0-1/info/recipe/meta.yaml. Please remove this file manually (you may need to reboot to free file handles):
blas-1.0-mkl 15 KB
conda-env-2.6.0-1 6 KB
_libgcc_mutex-0.1-main 7 KB
path.py-12.5.0-0 8 KB
get_terminal_size-1.0.0-haa9412d_0 7 KB
importlib_metadata-3.10.0-hd3eb1b0_0 37 KB
prompt_toolkit-3.0.17-hd3eb1b0_0 39 KB
numpy-1.20.1-py38h93e21f0_0 70 KB
matplotlib-3.3.4-py38h06a4308_0 92 KB
anaconda-2021.05-py38_0 81 KB
dask-2021.4.0-pyhd3eb1b0_0 12 KB
_openmp_mutex-4.5-1_gnu 93 KB
openssl-1.1.1k-h7f98852_0 6.0 MB
conda-4.10.1-py38h06a4308_1 11.7 MB
python_abi-3.9-2_cp39 11 KB
_libgcc_mutex-0.1-conda_forge 6 KB
python_abi-3.8-2_cp38 11 KB
libgfortran-ng-7.5.0-ha8ba4b0_17 92 KB
numpy-1.21.5-py38he7a7128_2 26 KB
The minimal example works for someone else on our computing cluster, so I'd exclude some "global" reasons as the culprit. Btw: I cannot reboot the cluster myself, so I am hoing there might be something I can do on my own to resolve the issue.
Does anyone have an idea what could be the problem here or (since I am not an IT expert) how to further investigate what's going on? Thanks a lot for your suggestions!
---------------------------------EDIT--------------------------------------
Some edits and additions based on comments by @merv :
New environment creation command: mamba create -c conda-forge r-base -n R_test_cf
Here's all packages installed for the new conda env:
_libgcc_mutex 0.1 conda_forge conda-forge/linux-64 Cached
_openmp_mutex 4.5 2_gnu conda-forge/linux-64 Cached
_r-mutex 1.0.1 anacondar_1 conda-forge/noarch Cached
binutils_impl_linux-64 2.40 hf600244_0 conda-forge/linux-64 Cached
blas 1.1 openblas conda-forge/linux-64 Cached
bwidget 1.9.14 ha770c72_1 conda-forge/linux-64 Cached
bzip2 1.0.8 h7f98852_4 conda-forge/linux-64 Cached
c-ares 1.19.0 h5eee18b_0 pkgs/main/linux-64 Cached
ca-certificates 2023.01.10 h06a4308_0 pkgs/main/linux-64 Cached
cairo 1.16.0 h35add3b_1015 conda-forge/linux-64 Cached
curl 7.88.1 hdc1c0ab_1 conda-forge/linux-64 Cached
expat 2.5.0 hcb278e6_1 conda-forge/linux-64 Cached
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge/noarch Cached
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge/noarch Cached
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge/noarch Cached
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge/noarch Cached
fontconfig 2.14.2 h14ed4e7_0 conda-forge/linux-64 Cached
fonts-conda-ecosystem 1 0 conda-forge/noarch Cached
fonts-conda-forge 1 0 conda-forge/noarch Cached
freetype 2.12.1 hca18f0e_1 conda-forge/linux-64 Cached
fribidi 1.0.10 h516909a_0 conda-forge/linux-64 Cached
gcc_impl_linux-64 12.2.0 hcc96c02_19 conda-forge/linux-64 Cached
gettext 0.21.1 h27087fc_0 conda-forge/linux-64 Cached
gfortran_impl_linux-64 12.2.0 h55be85b_19 conda-forge/linux-64 Cached
graphite2 1.3.14 h295c915_1 pkgs/main/linux-64 Cached
gsl 2.7.1 h917eeb2_1 pkgs/main/linux-64 Cached
gxx_impl_linux-64 12.2.0 hcc96c02_19 conda-forge/linux-64 Cached
harfbuzz 6.0.0 h3ff4399_1 conda-forge/linux-64 Cached
icu 72.1 hcb278e6_0 conda-forge/linux-64 Cached
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge/noarch Cached
keyutils 1.6.1 h166bdaf_0 conda-forge/linux-64 Cached
krb5 1.20.1 h81ceb04_0 conda-forge/linux-64 Cached
ld_impl_linux-64 2.40 h41732ed_0 conda-forge/linux-64 Cached
lerc 4.0.0 h27087fc_0 conda-forge/linux-64 Cached
libblas 3.9.0 16_linux64_openblas conda-forge/linux-64 Cached
libcurl 7.88.1 hdc1c0ab_1 conda-forge/linux-64 Cached
libdeflate 1.18 h0b41bf4_0 conda-forge/linux-64 Cached
libedit 3.1.20221030 h5eee18b_0 pkgs/main/linux-64 Cached
libev 4.33 h516909a_1 conda-forge/linux-64 Cached
libexpat 2.5.0 hcb278e6_1 conda-forge/linux-64 Cached
libffi 3.4.2 h7f98852_5 conda-forge/linux-64 Cached
libgcc-devel_linux-64 12.2.0 h3b97bd3_19 conda-forge/linux-64 Cached
libgcc-ng 12.2.0 h65d4601_19 conda-forge/linux-64 Cached
libgfortran-ng 12.2.0 h69a702a_19 conda-forge/linux-64 Cached
libgfortran5 12.2.0 h337968e_19 conda-forge/linux-64 Cached
libglib 2.74.1 h606061b_1 conda-forge/linux-64 Cached
libgomp 12.2.0 h65d4601_19 conda-forge/linux-64 Cached
libiconv 1.17 h166bdaf_0 conda-forge/linux-64 Cached
libjpeg-turbo 2.1.5.1 h0b41bf4_0 conda-forge/linux-64 Cached
liblapack 3.9.0 16_linux64_openblas conda-forge/linux-64 Cached
libnghttp2 1.52.0 h61bc06f_0 conda-forge/linux-64 Cached
libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge/linux-64 Cached
libpng 1.6.39 h753d276_0 conda-forge/linux-64 Cached
libsanitizer 12.2.0 h46fd767_19 conda-forge/linux-64 Cached
libssh2 1.10.0 hf14f497_3 conda-forge/linux-64 Cached
libstdcxx-devel_linux-64 12.2.0 h3b97bd3_19 conda-forge/linux-64 Cached
libstdcxx-ng 12.2.0 h46fd767_19 conda-forge/linux-64 Cached
libtiff 4.5.0 ha587672_6 conda-forge/linux-64 Cached
libuuid 2.38.1 h0b41bf4_0 conda-forge/linux-64 Cached
libwebp-base 1.3.0 h0b41bf4_0 conda-forge/linux-64 Cached
libxcb 1.13 h7f98852_1004 conda-forge/linux-64 Cached
libxml2 2.10.3 hfdac1af_6 conda-forge/linux-64 Cached
libzlib 1.2.13 h166bdaf_4 conda-forge/linux-64 Cached
lz4-c 1.9.4 hcb278e6_0 conda-forge/linux-64 Cached
make 4.3 hd18ef5c_1 conda-forge/linux-64 Cached
ncurses 6.4 h6a678d5_0 pkgs/main/linux-64 Cached
openblas 0.3.21 pthreads_h320a7e8_3 conda-forge/linux-64 Cached
openssl 3.1.0 h0b41bf4_0 conda-forge/linux-64 Cached
pango 1.50.14 hd33c08f_0 conda-forge/linux-64 Cached
pcre2 10.40 hc3806b6_0 conda-forge/linux-64 Cached
pixman 0.40.0 h36c2ea0_0 conda-forge/linux-64 Cached
pthread-stubs 0.4 h36c2ea0_1001 conda-forge/linux-64 Cached
r-base 4.2.3 h4a03800_2 conda-forge/linux-64 Cached
readline 8.2 h8228510_1 conda-forge/linux-64 Cached
sed 4.8 he412f7d_0 conda-forge/linux-64 Cached
sysroot_linux-64 2.12 he073ed8_15 conda-forge/noarch Cached
tk 8.6.12 h27826a3_0 conda-forge/linux-64 Cached
tktable 2.10 hb7b940f_3 conda-forge/linux-64 Cached
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge/linux-64 Cached
xorg-libice 1.0.10 h516909a_0 conda-forge/linux-64 Cached
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge/linux-64 Cached
xorg-libx11 1.8.4 h0b41bf4_0 conda-forge/linux-64 Cached
xorg-libxau 1.0.9 h14c3975_0 conda-forge/linux-64 Cached
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge/linux-64 Cached
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge/linux-64 Cached
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge/linux-64 Cached
xorg-libxt 1.2.1 h7f98852_2 conda-forge/linux-64 Cached
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge/linux-64 Cached
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge/linux-64 Cached
xorg-xproto 7.0.31 h14c3975_1007 conda-forge/linux-64 Cached
xz 5.2.10 h5eee18b_1 pkgs/main/linux-64 Cached
zlib 1.2.13 h166bdaf_4 conda-forge/linux-64 Cached
zstd 1.5.4 hc292b87_0 pkgs/main/linux-64 Cached
Summary:
Install: 93 packages
Total download: 0 B
Here's the output of mamba env export:
name: R_test_cf
channels:
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- _r-mutex=1.0.1=anacondar_1
- binutils_impl_linux-64=2.40=hf600244_0
- blas=1.1=openblas
- bwidget=1.9.14=ha770c72_1
- bzip2=1.0.8=h7f98852_4
- c-ares=1.19.0=h5eee18b_0
- ca-certificates=2023.01.10=h06a4308_0
- cairo=1.16.0=h35add3b_1015
- curl=7.88.1=hdc1c0ab_1
- expat=2.5.0=hcb278e6_1
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=hab24e00_0
- fontconfig=2.14.2=h14ed4e7_0
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- freetype=2.12.1=hca18f0e_1
- fribidi=1.0.10=h516909a_0
- gcc_impl_linux-64=12.2.0=hcc96c02_19
- gettext=0.21.1=h27087fc_0
- gfortran_impl_linux-64=12.2.0=h55be85b_19
- graphite2=1.3.14=h295c915_1
- gsl=2.7.1=h917eeb2_1
- gxx_impl_linux-64=12.2.0=hcc96c02_19
- harfbuzz=6.0.0=h3ff4399_1
- icu=72.1=hcb278e6_0
- kernel-headers_linux-64=2.6.32=he073ed8_15
- keyutils=1.6.1=h166bdaf_0
- krb5=1.20.1=h81ceb04_0
- ld_impl_linux-64=2.40=h41732ed_0
- lerc=4.0.0=h27087fc_0
- libblas=3.9.0=16_linux64_openblas
- libcurl=7.88.1=hdc1c0ab_1
- libdeflate=1.18=h0b41bf4_0
- libedit=3.1.20221030=h5eee18b_0
- libev=4.33=h516909a_1
- libexpat=2.5.0=hcb278e6_1
- libffi=3.4.2=h7f98852_5
- libgcc-devel_linux-64=12.2.0=h3b97bd3_19
- libgcc-ng=12.2.0=h65d4601_19
- libgfortran-ng=12.2.0=h69a702a_19
- libgfortran5=12.2.0=h337968e_19
- libglib=2.74.1=h606061b_1
- libgomp=12.2.0=h65d4601_19
- libiconv=1.17=h166bdaf_0
- libjpeg-turbo=2.1.5.1=h0b41bf4_0
- liblapack=3.9.0=16_linux64_openblas
- libnghttp2=1.52.0=h61bc06f_0
- libopenblas=0.3.21=pthreads_h78a6416_3
- libpng=1.6.39=h753d276_0
- libsanitizer=12.2.0=h46fd767_19
- libssh2=1.10.0=hf14f497_3
- libstdcxx-devel_linux-64=12.2.0=h3b97bd3_19
- libstdcxx-ng=12.2.0=h46fd767_19
- libtiff=4.5.0=ha587672_6
- libuuid=2.38.1=h0b41bf4_0
- libwebp-base=1.3.0=h0b41bf4_0
- libxcb=1.13=h7f98852_1004
- libxml2=2.10.3=hfdac1af_6
- libzlib=1.2.13=h166bdaf_4
- lz4-c=1.9.4=hcb278e6_0
- make=4.3=hd18ef5c_1
- ncurses=6.4=h6a678d5_0
- openblas=0.3.21=pthreads_h320a7e8_3
- openssl=3.1.0=h0b41bf4_0
- pango=1.50.14=hd33c08f_0
- pcre2=10.40=hc3806b6_0
- pixman=0.40.0=h36c2ea0_0
- pthread-stubs=0.4=h36c2ea0_1001
- r-base=4.2.3=h4a03800_2
- readline=8.2=h8228510_1
- sed=4.8=he412f7d_0
- sysroot_linux-64=2.12=he073ed8_15
- tk=8.6.12=h27826a3_0
- tktable=2.10=hb7b940f_3
- xorg-kbproto=1.0.7=h14c3975_1002
- xorg-libice=1.0.10=h516909a_0
- xorg-libsm=1.2.3=hd9c2040_1000
- xorg-libx11=1.8.4=h0b41bf4_0
- xorg-libxau=1.0.9=h14c3975_0
- xorg-libxdmcp=1.1.3=h516909a_0
- xorg-libxext=1.3.4=h0b41bf4_2
- xorg-libxrender=0.9.10=h7f98852_1003
- xorg-libxt=1.2.1=h7f98852_2
- xorg-renderproto=0.11.1=h14c3975_1002
- xorg-xextproto=7.3.0=h0b41bf4_1003
- xorg-xproto=7.0.31=h14c3975_1007
- xz=5.2.10=h5eee18b_1
- zlib=1.2.13=h166bdaf_4
- zstd=1.5.4=hc292b87_0
The conda info details:
active environment : R_test_cf
active env location : /home/rstrasser/.conda/envs/R_test_cf
shell level : 1
user config file : /home/rstrasser/.condarc
populated config files : /home/rstrasser/.condarc
conda version : 4.12.0
conda-build version : 3.21.4
python version : 3.8.8.final.0
virtual packages : __linux=3.10.0=0
__glibc=2.17=0
__unix=0=0
__archspec=1=x86_64
base environment : /opt/anaconda/anaconda3 (read only)
conda av data dir : /opt/anaconda/anaconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /opt/anaconda/anaconda3/pkgs
/home/rstrasser/.conda/pkgs
envs directories : /home/rstrasser/.conda/envs
/opt/anaconda/anaconda3/envs
platform : linux-64
user-agent : conda/4.12.0 requests/2.25.1 CPython/3.8.8 Linux/3.10.0-1160.53.1.el7.x86_64 centos/7.9.2009 glibc/2.17
UID:GID : 1003:1004
netrc file : None
offline mode : False
LD_LIBRARY_PATH does not have a value
ldd ~/.conda/envs/R_test_cf/bin/R returns not a dynamic executable
-------------------EDIT 2-----------------------------------------
Another user on the cluster seems to be able to simply run R from my environment... --> Maybe the issue is not how things are installed, but how the env is activated or that I accidentally installed something globally that is being accessed now.
