Unable to solve environment when installing moose

[sSajjad90]

Dear all,
I already had MOOSE on my system, and when I tried to update it, I got a chain of errors. So I decided to uninstall and re-install again. But I got stuck in the below trouble. It was in this state for more than 2 hours without a change. I interrupted it and try again, and the same problem.

Does anyone know what the problem is?

PS: My system memory is 32 Gb

(base) sajjad@sajjad-PC:~$ conda create --name moose moose-libmesh moose-tools
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment:\

[milljm]

I've seen lengthy solves among our continuous integration environment, but not on personal workstations. Can you try the following, and then attempt the install:

conda clean --all --yes

If the above fails, perhaps one module at a time:

conda create -n moose moose-libmesh
conda activate moose
conda install moose-tools

It is moose-tools which contains the most 'dependencies' Conda must solve for. And sometimes I see handing it one-package-at-a-time speeds things up. Let us know if none of these options work! I have more 'ideas'. Conda clean doesn't get everything.

[purepuremilk-zz]

I am having this similar issue, and I am installing moose on my personal laptop: solving the environment takes forever with "conda create --name moose moose-libmesh moose-tools". I tried to use the suggested approach by creating an empty environment first, activate it, and install moose-libmesh and moose-tools separately. I found the order of installing packages matters. Here are my commands:

conda create -n moose
conda install -c idaholab moose-tools
conda install -c idaholab moose-libmesh

Here were what I found: If we installed moose-libmesh first and then moose-tool, solving enviroment for moose-tool would take a very long time since it was a large package.

However, if we installed moose-tools first, which basically took no time, and then went to moose-libmesh, it still took a while to solve moose-libmesh, but in a much shorter time.

[milljm]

Conda solves can be a pain. moose-tools adds a lot of variety to the equation that Conda needs to solve for.

In the world of Conda, I try to be as non-explicit as possible to avoid potential shortcomings of our packages in the event another developer decides to pull a specific version from the Anaconda cloud. A version we might explicitly state as a requirement. Thus, things work... most of the time. But that does come at a cost of solve time.

I am being very explicit with moose-libmesh. Because that package requires that we use the same compiler stack to build MOOSE (and allows you to build your Application). Hence, installing moose-libmesh is quick. Or rather, quicker than moose-tools.

[milljm]

@purepuremilk-zz thank you for this advice!

I have (will be) implementing this change into our Continuous Integration recipes on https://civet.inl.gov. To facilitate installing Conda packages separately. Specifically moose-tools first. As I too see a substantial speed increase doing so.

I will also modify our instructions to reflect this optimization: #17934

[milljm]

@purepuremilk-zz

There also exists an interesting downgrading routine (explicit dependency somewhere?) for the following packages when installing moose-tools first, and then moose-libmesh (this being the only two packages requesting to be installed in a fresh environment on a Darwin machine):

The following packages will be REMOVED:

  glib-tools-2.68.2-he49afe7_0
  libgfortran5-9.3.0-h6c81a4c_22
  libglib-2.68.2-hd556434_0
  libnghttp2-1.43.0-h07e645a_0

The following packages will be SUPERSEDED by a higher-priority channel:

  glib                  conda-forge::glib-2.68.2-he49afe7_0 --> pkgs/main::glib-2.68.0-hdf23fa2_0

The following packages will be DOWNGRADED:

  curl                                    7.76.1-hb861fe1_2 --> 7.71.1-hbdca1c0_1
  dbus                                    1.13.6-ha13b53f_2 --> 1.13.6-h2f22bb5_0
  expat                                    2.4.1-he49afe7_0 --> 2.2.9-hb1e8313_2
  hdf4                                    4.2.15-hefd3b78_3 --> 4.2.13-h71d84a9_1004
  hdf5                           1.10.6-nompi_hc5d9132_1114 --> 1.10.6-nompi_h34ad4e8_1111
  krb5                                    1.19.1-hcfbf3a7_0 --> 1.17.2-h60d9502_0
  libblas                                  3.9.0-9_openblas --> 3.8.0-15_openblas
  libcblas                                 3.9.0-9_openblas --> 3.8.0-15_openblas
  libcurl                                 7.76.1-hf45b732_2 --> 7.71.1-he6690cf_1
  libcxx                                  11.1.0-habf9029_0 --> 11.0.0-h4c3b8ed_1
  libgfortran                       5.0.0-9_3_0_h6c81a4c_22 --> 4.0.0-7_5_0_h1a10cd1_22
  liblapack                                3.9.0-9_openblas --> 3.8.0-15_openblas
  libopenblas                      0.3.15-openmp_h5e1b9a4_1 --> 0.3.8-h3d69b6c_0
  libpng                                  1.6.37-h7cec526_2 --> 1.6.37-h2573ce8_0
  llvm-openmp                             11.1.0-hda6cdc1_1 --> 11.0.0-h73239a0_1
  matplotlib                           3.4.2-py37hf985489_0 --> 3.3.3-py37hf985489_0
  matplotlib-base                      3.4.2-py37hb018525_0 --> 3.3.3-py37hef07623_0
  openjpeg                                 2.4.0-h6e7aa92_1 --> 2.4.0-h6cbf5cd_0
  pandas                               1.2.4-py37hb23ed4d_0 --> 1.2.1-py37h010c265_0
  python                        3.7.10-h7728216_100_cpython --> 3.7.9-h6c3b2c9_0_cpython
  scipy                                1.6.3-py37h866764c_0 --> 1.5.3-py37h04d6967_0
  tbb                                     2020.2-h940c156_4 --> 2020.2-h926bf3e_3

So it stands to reason that perhaps moose-tools and moose-libmesh are at odds with one another. I'll continue investigating. But again, thank you for bringing this to my attention.

[milljm]

For reference. On Linux, the following seems to be inconsistent following a moose-tools installation:

The following packages will be SUPERSEDED by a higher-priority channel:

  libtiff               pkgs/main::libtiff-4.2.0-h85742a9_0 --> conda-forge::libtiff-4.1.0-hc3755c2_3
  zstd                     pkgs/main::zstd-1.4.5-h9ceee32_0 --> conda-forge::zstd-1.4.4-h3b9ef0a_2

The following packages will be DOWNGRADED:

  hdf5                           1.10.6-nompi_h6a2412b_1114 --> 1.10.5-nompi_h5b725eb_1114
  lcms2                                     2.12-hddcbb42_0 --> 2.11-hcbb858e_1
  libnetcdf                        4.7.4-nompi_h56d31a8_107 --> 4.6.2-h303dfb8_1003
  libpng                                  1.6.37-h21135ba_2 --> 1.6.37-hed695b0_0
  lz4-c                                    1.9.2-he1b5a44_3 --> 1.8.3-he1b5a44_1001
  openjpeg                                 2.4.0-hb52868f_1 --> 2.4.0-hf7af979_0
  pillow                               8.2.0-py37h4600e1f_1 --> 8.1.0-py37he6b4880_1
  vtk                                8.2.0-py37h2bd422c_218 --> 8.2.0-py37hfdee58b_203

[sSajjad90]

Many thanks for your response. it works, but I got another problem. when I make the application (make -j4) There is the below error:

In file included from /home/sajjad/projects/moose/framework/build/unity_src/meshgenerators_Unity.C:25:0:
/home/sajjad/projects/moose/framework/src/meshgenerators/MeshGenerator.C: In member function 'std::unique_ptrlibMesh::MeshBase MeshGenerator::generateInternal()':
/home/sajjad/projects/moose/framework/src/meshgenerators/MeshGenerator.C:92:62: error: no matching function for call to 'libMesh::MeshBase::get_info(int)'
const auto mesh_info = mesh->get_info(/* verbosity = */ 2);
^
In file included from /home/sajjad/projects/moose/framework/build/header_symlinks/MooseApp.h:26:0,
from /home/sajjad/projects/moose/framework/build/header_symlinks/MeshGenerator.h:14,
from /home/sajjad/projects/moose/framework/build/header_symlinks/SideSetsGeneratorBase.h:12,
from /home/sajjad/projects/moose/framework/build/header_symlinks/AllSideSetsByNormalsGenerator.h:12,
from /home/sajjad/projects/moose/framework/src/meshgenerators/AllSideSetsByNormalsGenerator.C:10,
from /home/sajjad/projects/moose/framework/build/unity_src/meshgenerators_Unity.C:2:
/home/sajjad/miniconda3/envs/moose/libmesh/include/libmesh/mesh_base.h:1194:15: note: candidate: std::__cxx11::string libMesh::MeshBase::get_info() const
std::string get_info () const;
^~~~~~~~
/home/sajjad/miniconda3/envs/moose/libmesh/include/libmesh/mesh_base.h:1194:15: note: candidate expects 0 arguments, 1 provided
Compiling C++ (in opt mode) /home/sajjad/projects/moose/framework/build/unity_src/executioners_Unity.C...
/home/sajjad/projects/moose/framework/build.mk:118: recipe for target '/home/sajjad/projects/moose/framework/build/unity_src/meshgenerators_Unity.x86_64-pc-linux-gnu.opt.lo' failed
make: *** [/home/sajjad/projects/moose/framework/build/unity_src/meshgenerators_Unity.x86_64-pc-linux-gnu.opt.lo] Error 1
make: *** Waiting for unfinished jobs....

I should mention that I updated conda and moose but I receive this error. would you please let me know how could I fix it?

[milljm]

Performing conda update, or conda install commands should be followed by rebuilding your application after a cleaning. This is due to the library stack possibly getting updated (moose-libmesh was updated, as well as the compiler versions). There a few ways to 'clean' your application:

1. perform a make clobber all while in your application. Make sure to save (git commit) any changes you may have before doing so. Or:
2. perform a git clean -xfd while in the root of your application, and then again while inside the root of the moose directory. Again, making sure to save any changes you may have before doing so.

Once the above is complete, proceed to building your application.