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Error 132 #1702

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jobstdavid opened this issue Dec 8, 2024 · 10 comments
Open

Error 132 #1702

jobstdavid opened this issue Dec 8, 2024 · 10 comments

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@jobstdavid
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I am running the following code:

library(reticulate)
use_python("/home/jobst/.virtualenvs/r-reticulate/bin/python3.10")

yielding to the error

Error in python_config_impl(python) : 
  Error 132 occurred running /home/jobst/.virtualenvs/r-reticulate/bin/python: 
In addition: Warning message:
In system2(command = python, args = shQuote(script), stdout = TRUE,  :
  running command ''/home/jobst/.virtualenvs/r-reticulate/bin/python' '/home/jobst/miniconda3/envs/R-4.3.3/lib/R/library/reticulate/config/config.py' 2>/dev/null' had status 132
Error: Installation of Python not found, Python bindings not loaded.
Please create a default virtual environment with `reticulate::virtualenv_create('r-reticulate')`.
Execution halted
sh: 1: rm: not found
srun: error: node-200: task 0: Exited with exit code 1

Actually, the r-reticulate env. has been created via reticulate::virtualenv_create('r-reticulate').

Session Info:

R version 4.3.3 (2024-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS/LAPACK: /home/jobst/miniconda3/envs/R-4.3.3/lib/libopenblasp-r0.3.28.so;  LAPACK version 3.12.0

locale:
[1] C

time zone: Europe/Berlin
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] reticulate_1.40.0

loaded via a namespace (and not attached):
[1] compiler_4.3.3 Matrix_1.6-5   cli_3.6.3      Rcpp_1.0.13-1  grid_4.3.3    
[6] jsonlite_1.8.9 rlang_1.1.4    png_0.1-8      lattice_0.22-6 

Any ideas? Thank you very much in advance!

@t-kalinowski
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Error 132

This might be due to the OS sending a SIGILL due to an attempt to load DLL symbols that can't be loaded.

Does this error occur outside of Conda? Switching from a Conda environment to a virtual environment is often the simplest way to side-step binary incompatibility issues like this.

Would you be able to provide a docker file that reproduces the error with a virtual env?

@jobstdavid
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I run this code on a cluster and start it via a slurm script.
What do you mean by: does this error also occur outside of conda? When I run the code local and do not start it via a slurm script to send it to the cluster, I do not get any error message.

Unfortunately, I do not know how to generate such a docker file and I am also not sure if it is possible, when I sent the slurm script to generate such a file.

Do you have any ideas how to solve this issue? :)

@t-kalinowski
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How is the conda environment created?

Is it something like reticulate::conda_create(...)?

If you replace that with reticulate::virtualenv_create(...), does it solve the issue?

@jobstdavid
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jobstdavid commented Dec 9, 2024

The R environment R-4.3.3 was directly created via conda using
conda create -n R-4.3.3 r-base=4.3.3
The r-reticulate environment was created via
reticulate::virtualenv_create('r-reticulate')

@t-kalinowski
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Can you post the full output from virtualenv_create('r-reticulate')?

@jobstdavid
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jobstdavid commented Dec 10, 2024

Sure, here is the output:

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(reticulate)
> virtualenv_create('r-reticulate')
Using Python: /home/jobst/.pyenv/versions/3.10.16/bin/python3.10
Creating virtual environment 'r-reticulate' ... 
+ /home/jobst/.pyenv/versions/3.10.16/bin/python3.10 -m venv /home/jobst/.virtualenvs/r-reticulate
Done!
Installing packages: pip, wheel, setuptools
+ /home/jobst/.virtualenvs/r-reticulate/bin/python -m pip install --upgrade pip wheel setuptools
Requirement already satisfied: pip in /home/jobst/.virtualenvs/r-reticulate/lib/python3.10/site-packages (23.0.1)
Collecting pip
  Using cached pip-24.3.1-py3-none-any.whl (1.8 MB)
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Requirement already satisfied: setuptools in /home/jobst/.virtualenvs/r-reticulate/lib/python3.10/site-packages (65.5.0)
Collecting setuptools
  Using cached setuptools-75.6.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 65.5.0
    Uninstalling setuptools-65.5.0:
      Successfully uninstalled setuptools-65.5.0
  Attempting uninstall: pip
    Found existing installation: pip 23.0.1
    Uninstalling pip-23.0.1:
      Successfully uninstalled pip-23.0.1
Successfully installed pip-24.3.1 setuptools-75.6.0 wheel-0.45.1
Installing packages: numpy
+ /home/jobst/.virtualenvs/r-reticulate/bin/python -m pip install --upgrade --no-user numpy
Collecting numpy
  Using cached numpy-2.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
Using cached numpy-2.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.4 MB)
Installing collected packages: numpy
Successfully installed numpy-2.2.0
Virtual environment 'r-reticulate' successfully created.

If I run the code from above again and send it to the cluster, it yields again to error 132. Otherwise, i.e. if I run the code from above locally, it does not generate this error.

@t-kalinowski
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If the same code runs fine locally but errors when sent to the cluster, then the task is to figure out what's different on the cluster. It might be best to speak to your cluster administrator.

It's possible the system binaries found on the cluster runners are different from those found locally. For example, perhaps the python binary used to seed the virtual env might not have been built with the --enable-shared flag on the cluster.

Diffing str(reticulate:::python_config("/usr/bin/python3")) and/or python -m sysconfig might be helpful while investigating.

@jobstdavid
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For both of your suggestions I get the following:

str(reticulate:::python_config("/usr/bin/python3"))
List of 22
 $ python              : chr "/usr/bin/python3"
 $ libpython           : chr "/usr/lib/python3.8/config-3.8-x86_64-linux-gnu/libpython3.8.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/usr/lib/python38.zip:/usr/lib/python3.8:/usr/lib/python3.8/lib-dynload:/usr/local/lib/python3.8/dist-packages:"| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ executable          : chr "/usr/bin/python3"
 $ base_executable     : chr "/usr/bin/python3"
 $ version_string      : chr "3.8.10 (default, Nov 26 2021, 20:14:08)  [GCC 9.3.0]"
 $ version             :Classes 'package_version', 'numeric_version'  hidden list of 1
  ..$ : int [1:2] 3 8
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : chr "False"
 $ numpy               : NULL
 $ required_module     : NULL
 $ required_module_path: NULL
 $ available           : logi FALSE
 $ python_versions     : chr "/usr/bin/python3"
 $ forced              : NULL
 - attr(*, "class")= chr "py_config"

and

Platform: "linux-x86_64"
Python version: "3.9"
Current installation scheme: "posix_prefix"

Paths: 
	data = "/home/jobst/miniconda3"
	include = "/home/jobst/miniconda3/include/python3.9"
	platinclude = "/home/jobst/miniconda3/include/python3.9"
	platlib = "/home/jobst/miniconda3/lib/python3.9/site-packages"
	platstdlib = "/home/jobst/miniconda3/lib/python3.9"
	purelib = "/home/jobst/miniconda3/lib/python3.9/site-packages"
	scripts = "/home/jobst/miniconda3/bin"
	stdlib = "/home/jobst/miniconda3/lib/python3.9"

Variables: 
	ABIFLAGS = ""
	AC_APPLE_UNIVERSAL_BUILD = "0"
	AIX_BUILDDATE = "0"
	AIX_GENUINE_CPLUSPLUS = "0"
	ALT_SOABI = "0"
	ANDROID_API_LEVEL = "0"
	AR = "ar"
	ARFLAGS = "rcs"
	BASECFLAGS = "-Wno-unused-result -Wsign-compare"
	BASECPPFLAGS = "-IObjects -IInclude -IPython"
	BASEMODLIBS = ""
	BINDIR = "/home/jobst/miniconda3/bin"
	BINLIBDEST = "/home/jobst/miniconda3/lib/python3.9"
	BLDLIBRARY = "libpython3.9.a"
	BLDSHARED = "gcc -pthread -B /home/jobst/miniconda3/compiler_compat -shared  -Wl,-rpath,/home/jobst/miniconda3/lib -Wl,-rpath-link,/home/jobst/miniconda3/lib -L/home/jobst/miniconda3/lib -Wl,-rpath,/home/jobst/miniconda3/lib -Wl,-rpath-link,/home/jobst/miniconda3/lib -L/home/jobst/miniconda3/lib"
	BUILDEXE = ""
	BUILDPYTHON = "python"
	BUILD_GNU_TYPE = "x86_64-conda_cos6-linux-gnu"
	BYTESTR_DEPS = "\"
	CC = "gcc -pthread -B /home/jobst/miniconda3/compiler_compat"
	CCSHARED = "-fPIC"
	CFLAGS = "-Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2   -isystem /home/jobst/miniconda3/include -fPIC -O2   -isystem /home/jobst/miniconda3/include "
	CFLAGSFORSHARED = ""
	CFLAGS_ALIASING = ""
	CONFIGFILES = "configure configure.ac acconfig.h pyconfig.h.in Makefile.pre.in"
	CONFIGURE_CFLAGS = "-fPIC -O2 -isystem /home/jobst/miniconda3/include "
	CONFIGURE_CFLAGS_NODIST = "-g -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -Werror=implicit-function-declaration -fvisibility=hidden"
	CONFIGURE_CPPFLAGS = "-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jobst/miniconda3/include -I/home/jobst/miniconda3/include"
	CONFIGURE_LDFLAGS = "-Wl,-rpath,/home/jobst/miniconda3/lib -Wl,-rpath-link,/home/jobst/miniconda3/lib -L/home/jobst/miniconda3/lib"
	CONFIGURE_LDFLAGS_NODIST = "-g"
	CONFIG_ARGS = "'--prefix=/home/jobst/miniconda3''--build=x86_64-conda_cos6-linux-gnu''--host=x86_64-conda_cos6-linux-gnu''--enable-ipv6''--with-ensurepip=no''--with-tzpath=/home/jobst/miniconda3/share/zoneinfo:/home/jobst/miniconda3/share/tzinfo''--with-computed-gotos''--with-system-ffi''--enable-loadable-sqlite-extensions''--with-tcltk-includes=-I/home/jobst/miniconda3/include''--with-tcltk-libs=-L/home/jobst/miniconda3/lib -ltcl8.6 -ltk8.6''--with-platlibdir=lib''--with-lto''--enable-optimizations''-oldincludedir=/home/conda/feedstock_root/build_artifacts/python-split_1643749964416/_build_env/x86_64-conda_cos6-linux-gnu/sysroot/usr/include''--disable-shared''PROFILE_TASK=-m test --pgo''build_alias=x86_64-conda_cos6-linux-gnu''host_alias=x86_64-conda_cos6-linux-gnu''MACHDEP=linux''CC=gcc''CFLAGS= -fPIC -O2  -isystem /home/jobst/miniconda3/include ''LDFLAGS=   -Wl,-rpath,/home/jobst/miniconda3/lib -Wl,-rpath-link,/home/jobst/miniconda3/lib -L/home/jobst/miniconda3/lib''CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jobst/miniconda3/include -I/home/jobst/miniconda3/include''CPP=/home/conda/feedstock_root/build_artifacts/python-split_1643749964416/_build_env/bin/cpp''PKG_CONFIG_PATH=/home/jobst/miniconda3/lib/pkgconfig'"
	CONFINCLUDEDIR = "/home/jobst/miniconda3/include"
	CONFINCLUDEPY = "/home/jobst/miniconda3/include/python3.9"
	COREPYTHONPATH = ""
	COVERAGE_INFO = "/home/conda/feedstock_root/build_artifacts/python-split_1643749964416/work/build-static/coverage.info"
	COVERAGE_REPORT = "/home/conda/feedstock_root/build_artifacts/python-split_1643749964416/work/build-static/lcov-report"
	COVERAGE_REPORT_OPTIONS = "--no-branch-coverage --title "CPython lcov report""
	CPPFLAGS = "-IObjects -IInclude -IPython -I. -I/home/conda/feedstock_root/build_artifacts/python-split_1643749964416/work/Include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jobst/miniconda3/include -I/home/jobst/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jobst/miniconda3/include -I/home/jobst/miniconda3/include"
	CXX = "g++ -pthread -B /home/jobst/miniconda3/compiler_compat"
	DESTDIRS = "/home/jobst/miniconda3 /home/jobst/miniconda3/lib /home/jobst/miniconda3/lib/python3.9 /home/jobst/miniconda3/lib/python3.9/lib-dynload"
	DESTLIB = "/home/jobst/miniconda3/lib/python3.9"
	DESTPATH = ""
	DESTSHARED = "/home/jobst/miniconda3/lib/python3.9/lib-dynload"
	DFLAGS = ""
	DIRMODE = "755"
	DIST = "README.rst ChangeLog configure configure.ac acconfig.h pyconfig.h.in Makefile.pre.in Include Lib Misc Ext-dummy"
	DISTDIRS = "Include Lib Misc Ext-dummy"
	DISTFILES = "README.rst ChangeLog configure configure.ac acconfig.h pyconfig.h.in Makefile.pre.in"
	DLINCLDIR = "."
	DLLLIBRARY = ""
	DOUBLE_IS_ARM_MIXED_ENDIAN_IEEE754 = "0"
	DOUBLE_IS_BIG_ENDIAN_IEEE754 = "0"
	DOUBLE_IS_LITTLE_ENDIAN_IEEE754 = "1"
	DTRACE = ""
	DTRACE_DEPS = "\"
	DTRACE_HEADERS = ""
	DTRACE_OBJS = ""
	DYNLOADFILE = "dynload_shlib.o"
	ENABLE_IPV6 = "1"
	ENSUREPIP = "no"
	EXE = ""
	EXEMODE = "755"
	EXPORTSFROM = ""
	EXPORTSYMS = ""
	EXTRATESTOPTS = ""
	EXT_SUFFIX = ".cpython-39-x86_64-linux-gnu.so"
	FILEMODE = "644"
	FLOAT_WORDS_BIGENDIAN = "0"
	FLOCK_NEEDS_LIBBSD = "0"
	GETPGRP_HAVE_ARG = "0"
	GITBRANCH = ""
	GITTAG = ""
	GITVERSION = ""
	GNULD = "no"
	HAVE_ACCEPT4 = "1"
	HAVE_ACOSH = "1"
	HAVE_ADDRINFO = "1"
	HAVE_ALARM = "1"
	HAVE_ALIGNED_REQUIRED = "0"
	HAVE_ALLOCA_H = "1"
	HAVE_ALTZONE = "0"
	HAVE_ASINH = "1"
	HAVE_ASM_TYPES_H = "1"
	HAVE_ATANH = "1"
	HAVE_BIND_TEXTDOMAIN_CODESET = "1"
	HAVE_BLUETOOTH_BLUETOOTH_H = "0"
	HAVE_BLUETOOTH_H = "0"
	HAVE_BROKEN_MBSTOWCS = "0"
	HAVE_BROKEN_NICE = "0"
	HAVE_BROKEN_PIPE_BUF = "0"
	HAVE_BROKEN_POLL = "0"
	HAVE_BROKEN_POSIX_SEMAPHORES = "0"
	HAVE_BROKEN_PTHREAD_SIGMASK = "0"
	HAVE_BROKEN_SEM_GETVALUE = "0"
	HAVE_BROKEN_UNSETENV = "0"
	HAVE_BUILTIN_ATOMIC = "1"
	HAVE_CHFLAGS = "0"
	HAVE_CHOWN = "1"
	HAVE_CHROOT = "1"
	HAVE_CLOCK = "1"
	HAVE_CLOCK_GETRES = "1"
	HAVE_CLOCK_GETTIME = "1"
	HAVE_CLOCK_SETTIME = "1"
	HAVE_COMPUTED_GOTOS = "1"
	HAVE_CONFSTR = "1"
	HAVE_CONIO_H = "0"
	HAVE_COPYSIGN = "1"
	HAVE_COPY_FILE_RANGE = "0"
	HAVE_CRYPT_H = "1"
	HAVE_CRYPT_R = "1"
	HAVE_CTERMID = "1"
	HAVE_CTERMID_R = "0"
	HAVE_CURSES_FILTER = "1"
	HAVE_CURSES_H = "1"
	HAVE_CURSES_HAS_KEY = "1"
	HAVE_CURSES_IMMEDOK = "1"
	HAVE_CURSES_IS_PAD = "1"
	HAVE_CURSES_IS_TERM_RESIZED = "1"
	HAVE_CURSES_RESIZETERM = "1"
	HAVE_CURSES_RESIZE_TERM = "1"
	HAVE_CURSES_SYNCOK = "1"
	HAVE_CURSES_TYPEAHEAD = "1"
	HAVE_CURSES_USE_ENV = "1"
	HAVE_CURSES_WCHGAT = "1"
	HAVE_DECL_ISFINITE = "1"
	HAVE_DECL_ISINF = "1"
	HAVE_DECL_ISNAN = "1"
	HAVE_DECL_RTLD_DEEPBIND = "1"
	HAVE_DECL_RTLD_GLOBAL = "1"
	HAVE_DECL_RTLD_LAZY = "1"
	HAVE_DECL_RTLD_LOCAL = "1"
	HAVE_DECL_RTLD_MEMBER = "0"
	HAVE_DECL_RTLD_NODELETE = "1"
	HAVE_DECL_RTLD_NOLOAD = "1"
	HAVE_DECL_RTLD_NOW = "1"
	HAVE_DECL_TZNAME = "0"
	HAVE_DEVICE_MACROS = "1"
	HAVE_DEV_PTC = "0"
	HAVE_DEV_PTMX = "1"
	HAVE_DIRECT_H = "0"
	HAVE_DIRENT_D_TYPE = "1"
	HAVE_DIRENT_H = "1"
	HAVE_DIRFD = "1"
	HAVE_DLFCN_H = "1"
	HAVE_DLOPEN = "1"
	HAVE_DUP2 = "1"
	HAVE_DUP3 = "1"
	HAVE_DYLD_SHARED_CACHE_CONTAINS_PATH = "0"
	HAVE_DYNAMIC_LOADING = "1"
	HAVE_ENDIAN_H = "1"
	HAVE_EPOLL = "1"
	HAVE_EPOLL_CREATE1 = "1"
	HAVE_ERF = "1"
	HAVE_ERFC = "1"
	HAVE_ERRNO_H = "1"
	HAVE_EXECV = "1"
	HAVE_EXPLICIT_BZERO = "0"
	HAVE_EXPLICIT_MEMSET = "0"
	HAVE_EXPM1 = "1"
	HAVE_FACCESSAT = "1"
	HAVE_FCHDIR = "1"
	HAVE_FCHMOD = "1"
	HAVE_FCHMODAT = "1"
	HAVE_FCHOWN = "1"
	HAVE_FCHOWNAT = "1"
	HAVE_FCNTL_H = "1"
	HAVE_FDATASYNC = "1"
	HAVE_FDOPENDIR = "1"
	HAVE_FDWALK = "0"
	HAVE_FEXECVE = "1"
	HAVE_FINITE = "1"
	HAVE_FLOCK = "1"
	HAVE_FORK = "1"
	HAVE_FORKPTY = "1"
	HAVE_FPATHCONF = "1"
	HAVE_FSEEK64 = "0"
	HAVE_FSEEKO = "1"
	HAVE_FSTATAT = "1"
	HAVE_FSTATVFS = "1"
	HAVE_FSYNC = "1"
	HAVE_FTELL64 = "0"
	HAVE_FTELLO = "1"
	HAVE_FTIME = "1"
	HAVE_FTRUNCATE = "1"
	HAVE_FUTIMENS = "1"
	HAVE_FUTIMES = "1"
	HAVE_FUTIMESAT = "1"
	HAVE_GAI_STRERROR = "1"
	HAVE_GAMMA = "1"
	HAVE_GCC_ASM_FOR_MC68881 = "0"
	HAVE_GCC_ASM_FOR_X64 = "1"
	HAVE_GCC_ASM_FOR_X87 = "1"
	HAVE_GCC_UINT128_T = "1"
	HAVE_GETADDRINFO = "1"
	HAVE_GETC_UNLOCKED = "1"
	HAVE_GETENTROPY = "0"
	HAVE_GETGRGID_R = "1"
	HAVE_GETGRNAM_R = "1"
	HAVE_GETGROUPLIST = "1"
	HAVE_GETGROUPS = "1"
	HAVE_GETHOSTBYNAME = "0"
	HAVE_GETHOSTBYNAME_R = "1"
	HAVE_GETHOSTBYNAME_R_3_ARG = "0"
	HAVE_GETHOSTBYNAME_R_5_ARG = "0"
	HAVE_GETHOSTBYNAME_R_6_ARG = "1"
	HAVE_GETITIMER = "1"
	HAVE_GETLOADAVG = "1"
	HAVE_GETLOGIN = "1"
	HAVE_GETNAMEINFO = "1"
	HAVE_GETPAGESIZE = "1"
	HAVE_GETPEERNAME = "1"
	HAVE_GETPGID = "1"
	HAVE_GETPGRP = "1"
	HAVE_GETPID = "1"
	HAVE_GETPRIORITY = "1"
	HAVE_GETPWENT = "1"
	HAVE_GETPWNAM_R = "1"
	HAVE_GETPWUID_R = "1"
	HAVE_GETRANDOM = "0"
	HAVE_GETRANDOM_SYSCALL = "0"
	HAVE_GETRESGID = "1"
	HAVE_GETRESUID = "1"
	HAVE_GETSID = "1"
	HAVE_GETSPENT = "1"
	HAVE_GETSPNAM = "1"
	HAVE_GETWD = "1"
	HAVE_GLIBC_MEMMOVE_BUG = "0"
	HAVE_GRP_H = "1"
	HAVE_HSTRERROR = "1"
	HAVE_HTOLE64 = "1"
	HAVE_HYPOT = "1"
	HAVE_IEEEFP_H = "0"
	HAVE_IF_NAMEINDEX = "1"
	HAVE_INET_ATON = "1"
	HAVE_INET_PTON = "1"
	HAVE_INITGROUPS = "1"
	HAVE_INTTYPES_H = "1"
	HAVE_IO_H = "0"
	HAVE_IPA_PURE_CONST_BUG = "0"
	HAVE_KILL = "1"
	HAVE_KILLPG = "1"
	HAVE_KQUEUE = "0"
	HAVE_LANGINFO_H = "1"
	HAVE_LARGEFILE_SUPPORT = "0"
	HAVE_LCHFLAGS = "0"
	HAVE_LCHMOD = "0"
	HAVE_LCHOWN = "1"
	HAVE_LGAMMA = "1"
	HAVE_LIBDL = "1"
	HAVE_LIBDLD = "0"
	HAVE_LIBIEEE = "0"
	HAVE_LIBINTL_H = "1"
	HAVE_LIBREADLINE = "1"
	HAVE_LIBRESOLV = "0"
	HAVE_LIBSENDFILE = "0"
	HAVE_LIBUTIL_H = "0"
	HAVE_LIBUUID = "1"
	HAVE_LINK = "1"
	HAVE_LINKAT = "1"
	HAVE_LINUX_CAN_BCM_H = "0"
	HAVE_LINUX_CAN_H = "1"
	HAVE_LINUX_CAN_J1939_H = "0"
	HAVE_LINUX_CAN_RAW_FD_FRAMES = "0"
	HAVE_LINUX_CAN_RAW_H = "1"
	HAVE_LINUX_CAN_RAW_JOIN_FILTERS = "0"
	HAVE_LINUX_MEMFD_H = "0"
	HAVE_LINUX_NETLINK_H = "1"
	HAVE_LINUX_QRTR_H = "0"
	HAVE_LINUX_RANDOM_H = "1"
	HAVE_LINUX_TIPC_H = "1"
	HAVE_LINUX_VM_SOCKETS_H = "0"
	HAVE_LINUX_WAIT_H = "1"
	HAVE_LOCKF = "1"
	HAVE_LOG1P = "1"
	HAVE_LOG2 = "1"
	HAVE_LONG_DOUBLE = "1"
	HAVE_LSTAT = "1"
	HAVE_LUTIMES = "1"
	HAVE_MADVISE = "1"
	HAVE_MAKEDEV = "1"
	HAVE_MBRTOWC = "1"
	HAVE_MEMFD_CREATE = "0"
	HAVE_MEMORY_H = "1"
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	abs_srcdir = "/home/conda/feedstock_root/build_artifacts/python-split_1643749964416/work"
	base = "/home/jobst/miniconda3"
	datarootdir = "/home/jobst/miniconda3/share"
	exec_prefix = "/home/jobst/miniconda3"
	installed_base = "/home/jobst/miniconda3"
	installed_platbase = "/home/jobst/miniconda3"
	platbase = "/home/jobst/miniconda3"
	platlibdir = "lib"
	prefix = "/home/jobst/miniconda3"
	projectbase = "/home/jobst/miniconda3/bin"
	py_version = "3.9.10"
	py_version_nodot = "39"
	py_version_short = "3.9"
	srcdir = "/home/jobst/miniconda3/lib/python3.9/config-3.9-x86_64-linux-gnu"
	userbase = "/home/jobst/.local"

Do you detect anything what should be changed? Help would be really appreciated, cause I do not know how to make it run ... :(

@t-kalinowski
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t-kalinowski commented Dec 10, 2024

One thing that immediately jumps out is that the two configs are for different pythons, which just means that /usr/bin/python is not the first python on your PATH.

But it's not important so much what the config is on your local machine; what's important is the config on the cluster where you see the error, and the diff between the config on the cluster and the config on the local machine.

Let me re-suggest, please reach out to your cluster administrator. In my experience, anytime there is a computing cluster, there is usually a helpful and kind person who's job it is to help people use the cluster. I cannot debug this remotely as I do not have access to the cluster, and do not know the details of how it was setup.

@jobstdavid
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Ok, thanks :)

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