some errors when installing moose

[Hejie-Guo]

Hello, my computer encounter a installing problem, could anybody help?

I notice that you guys update the method of installing moose by "conda -n moose ..", but this method does not work in my computer. I installed the moose by the old way successfully in my another computer, so I installed the software by the old way through mamba command "mamba create -n moose moose-tools moose-libmesh"，this way works.

And I git clone the moose from github through command:

"mkdir -p ~/projects
cd ~/projects
git clone https://github.com/idaholab/moose.git
cd moose
git checkout master"

These are ok.

But when i make and test the software:"cd ~/projects/moose/test, make -j 4"，the terminal shows error:

"Make sure to either run scripts/update_and_rebuild_wasp.sh in your MOOSE directory,
or set WASP_DIR to a valid WASP install
make: *** [/home/guohejie/projects/moose/framework/moose.mk:371: wasp_submodule_status] Error 1"

and then I run the command:"scripts/update_and_rebuild_wasp.sh" this seems also work.
but when I make the test:"make -j 4"
some errors occur:

"Creating Unity /home/guohejie/projects/moose/test/build/unity_src/actions_Unity.C
Compiling C++ (in opt mode) /home/guohejie/projects/moose/test/build/unity_src/auxkernels_Unity.C...
Compiling C++ (in opt mode) /home/guohejie/projects/moose/test/build/unity_src/bcs_Unity.C...
/home/guohejie/mambaforge3/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/guohejie/mambaforge3/envs                                    /moose/lib/libsuperlu_dist.so: undefined reference to `GOMP_loop_nonmonotonic_guided_start@GOMP_4.5'
/home/guohejie/mambaforge3/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/guohejie/mambaforge3/envs                                    /moose/libmesh/lib/libmesh_opt.so: undefined reference to `GOMP_loop_nonmonotonic_dynamic_start@GOMP_4.5'
/home/guohejie/mambaforge3/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/guohejie/mambaforge3/envs                                    /moose/lib/libstrumpack.so: undefined reference to `GOMP_taskloop_ull@GOMP_4.5'
/home/guohejie/mambaforge3/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/guohejie/mambaforge3/envs                                    /moose/lib/libstrumpack.so: undefined reference to `GOMP_loop_ull_nonmonotonic_dynamic_next@GOMP_4.5'
/home/guohejie/mambaforge3/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/guohejie/mambaforge3/envs                                    /moose/libmesh/lib/libmesh_opt.so: undefined reference to `GOMP_loop_nonmonotonic_dynamic_next@GOMP_4.5'
/home/guohejie/mambaforge3/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/guohejie/mambaforge3/envs                                    /moose/lib/libsuperlu_dist.so: undefined reference to `GOMP_loop_nonmonotonic_guided_next@GOMP_4.5'
/home/guohejie/mambaforge3/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/guohejie/mambaforge3/envs                                    /moose/lib/libstrumpack.so: undefined reference to `GOMP_taskloop@GOMP_4.5'
/home/guohejie/mambaforge3/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/guohejie/mambaforge3/envs                                    /moose/lib/libstrumpack.so: undefined reference to `GOMP_loop_ull_nonmonotonic_dynamic_start@GOMP_4.5'
collect2: error: ld returned 1 exit status"

[lindsayad]

It seems like you have a problem in your environment related to the threading library. What is the output of mamba list?

[Hejie-Guo]

I use the following command:

"echo $LD_LIBRARY_PATH
/usr/local/lib64:"

and in the directory /usr/local/lib64:
"gcj-5.4.0-16         libgcc_s.so             libgomp.a                            libobjc.so.4                libsupc++.la
libasan.a            libgcc_s.so.1           libgomp.la                           libobjc.so.4.0.0            libtsan.a
libasan.la           libgcj_bc.so            libgomp-plugin-host_nonshm.la        libquadmath.a               libtsan.la
libasan_preinit.o    libgcj_bc.so.1          libgomp-plugin-host_nonshm.so        libquadmath.la              libtsan_preinit.o
libasan.so           libgcj_bc.so.1.0.0      libgomp-plugin-host_nonshm.so.1      libquadmath.so              libtsan.so
libasan.so.2         libgcj.la               libgomp-plugin-host_nonshm.so.1.0.0  libquadmath.so.0            libtsan.so.0
libasan.so.2.0.0     libgcj.so               libgomp.so                           libquadmath.so.0.0.0        libtsan.so.0.0.0
libasan.so.5         libgcj.so.16            libgomp.so.1                         libsanitizer.spec           libubsan.a
libasan.so.5.0.0     libgcj.so.16.0.0        libgomp.so.1.0.0                     libssp.a                    libubsan.la
libatomic.a          libgcj-tools.la         libgomp.spec                         libssp.la                   libubsan.so
libatomic.la         libgcj-tools.so         libitm.a                             libssp_nonshared.a          libubsan.so.0
libatomic.so         libgcj-tools.so.16      libitm.la                            libssp_nonshared.la         libubsan.so.0.0.0
libatomic.so.1       libgcj-tools.so.16.0.0  libitm.so                            libssp.so                   libubsan.so.1
libatomic.so.1.1.0   libgfortran.a           libitm.so.1                          libssp.so.0                 libubsan.so.1.0.0
libatomic.so.1.2.0   libgfortran.la          libitm.so.1.0.0                      libssp.so.0.0.0             libvtv.a
libcc1.la            libgfortran.so          libitm.spec                          libstdc++.a                 libvtv.la
libcc1.so            libgfortran.so.3        liblsan.a                            libstdc++fs.a               libvtv.so
libcc1.so.0          libgfortran.so.3.0.0    liblsan.la                           libstdc++fs.la              libvtv.so.0
libcc1.so.0.0.0      libgfortran.so.5        liblsan_preinit.o                    libstdc++.la                libvtv.so.0.0.0
libcilkrts.a         libgfortran.so.5.0.0    liblsan.so                           libstdc++.so                logging.properties
libcilkrts.la        libgfortran.spec        liblsan.so.0                         libstdc++.so.6              pkgconfig
libcilkrts.so        libgij.la               liblsan.so.0.0.0                     libstdc++.so.6.0.21         security
libcilkrts.so.5      libgij.so               libobjc.a                            libstdc++.so.6.0.28
libcilkrts.so.5.0.0  libgij.so.16            libobjc.la                           libstdc++.so.6.0.28-gdb.py
libcilkrts.spec      libgij.so.16.0.0        libobjc.so  "

[GiudGiud]

Nothing obvious to me.

I would remove mamba and install with our new miniforge install.
If the problem is tied to conda the issue it will help. If not we ll know where not to look
https://mooseframework.inl.gov/getting_started/installation/conda.html

[milljm]

You are combining a lot of different libraries here.

I see many non conda-forge packages installed (thats a red flag for me)

sysroot_linux-64          2.17                h4a8ded7_13    conda-forge
tabulate                  0.9.0            py39h06a4308_0
tifffile                  2020.6.3                   py_0    conda-forge
tk                        8.6.12               h1ccaba5_0
tomli                     2.0.1            py39h06a4308_0
tomlkit                   0.11.1           py39h06a4308_0
toolz                     0.12.0           py39h06a4308_0
tornado                   6.3.3            py39h5eee18b_0
typing-extensions         4.7.1            py39h06a4308_0
typing_extensions         4.7.1            py39h06a4308_0
tzdata                    2023c                h04d1e81_0
wheel                     0.41.2           py39h06a4308_0
wrapt                     1.14.1           py39h5eee18b_0
xmltodict                 0.13.0           py39h06a4308_0
xorg-damageproto          1.2.1             h7f98852_1002    conda-forge
xorg-fixesproto           5.0               h7f98852_1002    conda-forge
xorg-glproto              1.4.17            h7f98852_1002    conda-forge

These should all be strictly conda-forge supplied packages, except the few from our channel. While this may not be a 100% requirement, it is odd. This suggests you have multiple channels (conda-forge, anaconda base perhaps, and of course our Idaholab channel).

As well as the /usr/local/ stuff. Which suggests a custom installation of what appears to be a GNU compiler (of perhaps only Fortran).

Our Conda Packages were built explicitly using Fortran available from Conda:

gfortran_impl_linux-64    10.4.0              h7d168d2_19    conda-forge
gfortran_linux-64         10.4.0              h69d5af5_13    conda-forge

Which is why the above is being installed in your Conda environment when you install moose-dev. To have other 'compilers' lying around is what usually causes issues like the ones you are seeing.

Because we have no idea why you have compilers in your /usr/local area, we can't ask you to delete them. Meaning: the only proper solution here, is for you to continue using those compilers in /usr/local, and not use Conda at all. You will need to instead build your compiler stack from scratch (you need to add GCC, and an MPI wrapper to your host of applications already in /usr/local). Basically, you must have only one compiler stack present in your environment (/usr/local is checked by default for binaries and libraries. So by having items in this location, these items will always be present in your environment).

[Hejie-Guo]

Yes, I usually use anaconda to do some python coding work which include some other packages. This should not be the problem in my opinion, because my another computer which is ok for installing moose also installed anaconda. I will try as your suggestions, thank you for your help.

[milljm]

You might benefit from adding strict channel priority: conda config --set channel_priority strict.

Indeed, reading the documentation, this feature looks to be slated to be default set in Conda 5.0 in the future. Ref: https://conda-forge.org/docs/user/introduction.html