Compilers broken with undefined references to GLIBC_2.2.5 when installed on Rocky 9 OS #130
Description
Solution to issue cannot be found in the documentation.
- I checked the documentation.
Issue
Installing OpenMPI and wrappers with Miniconda3 on a Rocky 9 system results in compilers having GLIBC issues. Performing the exact same sequence of installation commands on an old CentOS 7 system works fine. A Spack installation of OpenMPI on the same Rocky 9 system also works just fine.
The environment installed:
name: chiltepin-env
channels:
- conda-forge
dependencies:
- openmpi
- openmpi-mpicc
- openmpi-mpicxx
- openmpi-mpifort
Attempts to use mpif90 result in the following:
(chiltepin) [src]$ mpif90 mpi_hello.f90
$HOME/miniconda3/envs/chiltepin/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: $HOME/miniconda3/envs/chiltepin/lib/./libopen-pal.so.40: undefined reference to `openpty@GLIBC_2.2.5'
$HOME/miniconda3/envs/chiltepin/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: $HOME/miniconda3/envs/chiltepin/lib/./libopen-pal.so.40: undefined reference to `dlopen@GLIBC_2.2.5'
$HOME/miniconda3/envs/chiltepin/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: $HOME/miniconda3/envs/chiltepin/lib/./libopen-pal.so.40: undefined reference to `dlerror@GLIBC_2.2.5'
$HOME/miniconda3/envs/chiltepin/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libz.so.1: undefined reference to `memcpy@GLIBC_2.14'
$HOME/miniconda3/envs/chiltepin/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: $HOME/miniconda3/envs/chiltepin/lib/./libopen-pal.so.40: undefined reference to `dlclose@GLIBC_2.2.5'
$HOME/miniconda3/envs/chiltepin/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: $HOME/miniconda3/envs/chiltepin/lib/./libopen-pal.so.40: undefined reference to `dlsym@GLIBC_2.2.5'
Attempts to use mpicc results in the same output, with a few additional undefined references:
$HOME/miniconda3/envs/chiltepin/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libm.so.6: undefined reference to `__strtold_nan@GLIBC_PRIVATE'
$HOME/miniconda3/envs/chiltepin/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libm.so.6: undefined reference to `__strtod_nan@GLIBC_PRIVATE'
$HOME/miniconda3/envs/chiltepin/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libm.so.6: undefined reference to `__strtof_nan@GLIBC_PRIVATE'
$HOME/miniconda3/envs/chiltepin/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib64/libm.so.6: undefined reference to `__strtof128_nan@GLIBC_PRIVATE'
I tried export OMPI_FC=$FC, but it did not change the output.
Installed packages
# packages in environment at $HOME/miniconda3/envs/chiltepin:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
binutils_impl_linux-64 2.40 hf600244_0 conda-forge
binutils_linux-64 2.40 hbdbef99_2 conda-forge
gcc_impl_linux-64 12.3.0 he2b93b0_3 conda-forge
gcc_linux-64 12.3.0 h76fc315_2 conda-forge
gfortran_impl_linux-64 12.3.0 hfcedea8_3 conda-forge
gfortran_linux-64 12.3.0 h7fe76b4_2 conda-forge
gxx_impl_linux-64 12.3.0 he2b93b0_3 conda-forge
gxx_linux-64 12.3.0 h8a814eb_2 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_16 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libgcc-devel_linux-64 12.3.0 h8bca6fd_103 conda-forge
libgcc-ng 13.2.0 h807b86a_3 conda-forge
libgfortran-ng 13.2.0 h69a702a_3 conda-forge
libgfortran5 13.2.0 ha4646dd_3 conda-forge
libgomp 13.2.0 h807b86a_3 conda-forge
libsanitizer 12.3.0 h0f45ef3_3 conda-forge
libstdcxx-devel_linux-64 12.3.0 h8bca6fd_103 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
mpi 1.0 openmpi conda-forge
openmpi 4.1.6 hc5af2df_101 conda-forge
openmpi-mpicc 4.1.6 hd590300_101 conda-forge
openmpi-mpicxx 4.1.6 h00ab1b0_101 conda-forge
openmpi-mpifort 4.1.6 heb67821_101 conda-forge
sysroot_linux-64 2.12 he073ed8_16 conda-forge
zlib 1.2.13 hd590300_5 conda-forgeEnvironment info
active environment : chiltepin
active env location : $HOME/miniconda3/envs/chiltepin
shell level : 2
user config file : $HOME/.condarc
populated config files :
conda version : 23.10.0
conda-build version : not installed
python version : 3.11.5.final.0
virtual packages : __archspec=1=icelake
__glibc=2.34=0
__linux=5.14.0=0
__unix=0=0
base environment : $HOME/miniconda3 (writable)
conda av data dir : $HOME/miniconda3/etc/conda
conda av metadata url : None
channel URLs : 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 : $HOME/miniconda3/pkgs
$HOME/.conda/pkgs
envs directories : $HOME/miniconda3/envs
$HOME/.conda/envs
platform : linux-64
user-agent : conda/23.10.0 requests/2.31.0 CPython/3.11.5 Linux/5.14.0-162.12.1.el9_1.0.2.x86_64 rocky/9.1 glibc/2.34 solver/libmamba conda-libmamba-solver/23.11.1 libmambapy/1.5.3
UID:GID : 7966:17000
netrc file : None
offline mode : False