Error When Building

[Novascone]

Hello, I am trying to build SALAMANDER for the first time on my system. I installed moose through conda and I have activated the moose environment. I followed the installation guide and installed all dependencies. I set the location of the cross sections with export. When I build it seems to fail when linking. I get the following output

Output when linking executable

Linking Executable /home/warren_novascone/INL/projects/SALAMANDER/salamander-opt...
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libresolv.so.2: undefined reference to `__libc_res_queriesmatch@GLIBC_PRIVATE'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libldap.so.2: undefined reference to `pthread_rwlock_trywrlock@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libldap.so.2: undefined reference to `pthread_kill@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libkrb5.so.3: undefined reference to `ns_name_uncompress@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libldap.so.2: undefined reference to `pthread_mutexattr_init@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/liblzma.so.5: undefined reference to `pthread_condattr_setclock@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libresolv.so.2: undefined reference to `__res_context_hostalias@GLIBC_PRIVATE'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libresolv.so.2: undefined reference to `__libc_ns_samename@GLIBC_PRIVATE'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2: undefined reference to `lstat@GLIBC_2.33'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libresolv.so.2: undefined reference to `__res_get_nsaddr@GLIBC_PRIVATE'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libunistring.so.5: undefined reference to `pthread_rwlockattr_setkind_np@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libldap.so.2: undefined reference to `pthread_rwlock_tryrdlock@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libresolv.so.2: undefined reference to `__res_context_query@GLIBC_PRIVATE'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `dlclose@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcurl.so.4: undefined reference to `pthread_detach@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `pthread_key_delete@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `pthread_rwlock_unlock@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libresolv.so.2: undefined reference to `__libc_ns_makecanon@GLIBC_PRIVATE'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `pthread_setspecific@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `dlopen@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `pthread_rwlock_init@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libldap.so.2: undefined reference to `fstat64@GLIBC_2.33'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `dlerror@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `__isoc23_strtol@GLIBC_2.38'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libresolv.so.2: undefined reference to `__res_context_search@GLIBC_PRIVATE'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `pthread_getspecific@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libunistring.so.5: undefined reference to `pthread_rwlockattr_init@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/warren_novascone/miniforge/envs/moose/lib/libmpi.so: undefined reference to `aio_suspend@GLIBC_2.2.5'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libldap.so.2: undefined reference to `dn_expand@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/warren_novascone/miniforge/envs/moose/lib/libmpi.so: undefined reference to `aio_error@GLIBC_2.2.5'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libldap.so.2: undefined reference to `pthread_mutexattr_destroy@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/warren_novascone/miniforge/envs/moose/lib/libmpi.so: undefined reference to `aio_read@GLIBC_2.2.5'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/liblzma.so.5: undefined reference to `pthread_join@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libldap.so.2: undefined reference to `pthread_attr_setguardsize@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `stat@GLIBC_2.33'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `pthread_rwlock_destroy@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/warren_novascone/miniforge/envs/moose/lib/libmpi.so: undefined reference to `shm_open@GLIBC_2.2.5'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libkrb5.so.3: undefined reference to `res_nsearch@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libkrb5.so.3: undefined reference to `strlcpy@GLIBC_2.38'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `pthread_rwlock_wrlock@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libresolv.so.2: undefined reference to `dn_skipname@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/librt.so.1: undefined reference to `__libc_unwind_link_get@GLIBC_PRIVATE'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/liblzma.so.5: undefined reference to `pthread_create@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libldap.so.2: undefined reference to `__isoc23_strtoul@GLIBC_2.38'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libunistring.so.5: undefined reference to `__libc_single_threaded@GLIBC_2.32'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libresolv.so.2: undefined reference to `__libc_dn_expand@GLIBC_PRIVATE'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/warren_novascone/miniforge/envs/moose/lib/libmpi.so: undefined reference to `aio_write@GLIBC_2.2.5'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libresolv.so.2: undefined reference to `__libc_res_nameinquery@GLIBC_PRIVATE'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libpng16.so.16: undefined reference to `pow@GLIBC_2.29'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `dlsym@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libunistring.so.5: undefined reference to `pthread_rwlockattr_destroy@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libresolv.so.2: undefined reference to `res_dnok@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libldap.so.2: undefined reference to `pthread_setconcurrency@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/liblzma.so.5: undefined reference to `pthread_sigmask@GLIBC_2.32'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libldap.so.2: undefined reference to `res_query@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libkrb5.so.3: undefined reference to `__strlcpy_chk@GLIBC_2.38'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libresolv.so.2: undefined reference to `res_hnok@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libldap.so.2: undefined reference to `pthread_mutex_trylock@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libldap.so.2: undefined reference to `pthread_attr_setstacksize@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/warren_novascone/miniforge/envs/moose/lib/libmpi.so: undefined reference to `shm_unlink@GLIBC_2.2.5'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libldap.so.2: undefined reference to `pthread_mutexattr_settype@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `pthread_rwlock_rdlock@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `fstat@GLIBC_2.33'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `pthread_once@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libldap.so.2: undefined reference to `pthread_getconcurrency@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `pthread_key_create@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: undefined reference to `dladdr@GLIBC_2.34'
/home/warren_novascone/miniforge/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/warren_novascone/miniforge/envs/moose/lib/libmpi.so: undefined reference to `aio_return@GLIBC_2.2.5'
collect2: error: ld returned 1 exit status
make: *** [/home/warren_novascone/INL/projects/SALAMANDER/moose/framework/app.mk:466: /home/warren_novascone/INL/projects/SALAMANDER/salamander-opt] Error 1

I'm not sure where to go from here. It's possible that I made a mistake during installation, but I went though the instructions twice and I don't see were I missed anything. I'm new to using moose so perhaps I messed something up there.

If anybody has an idea where I went wrong and how it can be fixed I would greatly appreciate it.

Thanks!

Warren

OS: Pop!_os 24.04 LTS

g++: g++ (conda-forge gcc 12.3.0-13) 12.3.0

[cticenhour]

Hi Warren! Could you please post the output of moose/scripts/diagnostics.sh? This will give me more information regarding your environment and setup. Given your output, it almost appears that you have multiple versions of GLIBC available to the compiler, which could cause the issue you are seeing.

[cticenhour]

For SALAMANDER CI testing, we use a Rocky Linux 8.9 container to perform regular testing, but MOOSE also tests the conda environment against Rocky and Ubuntu 20.04 (I would guess to allow for those running older environments). We regularly have users on Ubuntu and Fedora releases, but I haven't seen too many mention PopOS (though I know historically it was on an Ubuntu base). Ubuntu would likely be your best bet to get started on if you are thinking of changing distros to get this workflow installed.

[Novascone]

Thanks for the info! I'm going to try a container on my system first and then I may switch over to Ubuntu.

[loganharbour]

If you're using linux, you can install apptainer and download our base container directly (it contains petsc, libmesh, etc all built). You can simply enter a shell into the container and build salamander without dealing with the dependencies:

apptainer shell oras://ghcr.io/idaholab/apptainer/moose-dev-openmpi-x86_64:2025.12.08
cd /path/to/salamander
make -j 4

[Novascone]

I was able to successfully build and test MOOSE with a Podman container (Rocky 9). @loganharbour I will look into this! Thank you guys for the replies. I appreciate your time and advice.