MooseServer moose_server(*this) error when make cardinal-opt #798

Wang-Yihu · 2023-10-12T16:08:37Z

Wang-Yihu
Oct 12, 2023

When I try to make cardinal-opt in the MOOSE conda environment, the error will return:

(moose) sjtu@sjtu:~/cardinal$ make -j8
Cardinal is using HDF5 from /home/sjtu/mambaforge3
Linking libpng: -L/home/sjtu/mambaforge3/envs/moose/lib -lpng16
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/actions_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/auxkernels_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/bcs_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/constraints_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/controls_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/dampers_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/dgkernels_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/dirackernels_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/distributions_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/executioners_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/executors_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/functions_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/functormaterials_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/fvbcs_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/fviks_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/fvkernels_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/geomsearch_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/ics_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/indicators_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/interfacekernels_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/interfaces_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/kernels_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/limiters_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/linesearches_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/loops_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/markers_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/materials_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/mesh_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/meshgenerators_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/multiapps_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/nodalkernels_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/outputs_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/outputs_formatters_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/parser_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/partitioner_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/positions_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/postprocessors_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/preconditioners_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/predictors_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/problems_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/relationshipmanagers_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/reporters_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/restart_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/samplers_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/scalarkernels_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/splits_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/systems_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/timeintegrators_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/times_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/timesteppers_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/transfers_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/userobjects_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/variables_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/build/unity_src/vectorpostprocessors_Unity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/Adaptivity.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/AppFactory.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/Assembly.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/Attributes.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/ExecFlagRegistry.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/Factory.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/MaxVarNDofsPerElem.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/MaxVarNDofsPerNode.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/MeshGeneratorSystem.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/Moose.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/MooseApp.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/MooseError.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/MooseInit.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/MooseObject.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/MooseServer.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/NeighborResidualObject.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/Registry.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/ResidualObject.C...
/home/sjtu/cardinal/contrib/moose/framework/src/base/MooseApp.C: In member function 'virtual void MooseApp::setupOptions()':
/home/sjtu/cardinal/contrib/moose/framework/src/base/MooseApp.C:1033:17: error: cannot declare variable 'moose_server' to be of abstract type 'MooseServer'
 1033 |     MooseServer moose_server(*this);
      |                 ^~~~~~~~~~~~
In file included from /home/sjtu/cardinal/contrib/moose/framework/src/base/MooseApp.C:54:
/home/sjtu/cardinal/contrib/moose/framework/build/header_symlinks/MooseServer.h:28:7: note:   because the following virtual functions are pure within 'MooseServer':
   28 | class MooseServer : public wasp::lsp::ServerImpl
      |       ^~~~~~~~~~~
In file included from /home/sjtu/cardinal/contrib/moose/framework/build/header_symlinks/MooseServer.h:16,
                 from /home/sjtu/cardinal/contrib/moose/framework/src/base/MooseApp.C:54:
/home/sjtu/mambaforge3/envs/moose/wasp/include/wasplsp/ServerImpl.h:219:18: note:     'virtual bool wasp::lsp::ServerImpl::gatherDocumentFormattingTextEdits(wasp::DataArray&, int, bool)'
  219 |     virtual bool gatherDocumentFormattingTextEdits(
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/SolverParams.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/base/TheWarehouse.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/utils/ADFParser.C...
Compiling C++ (in opt mode) /home/sjtu/cardinal/contrib/moose/framework/src/utils/ADUtils.C...
make: *** [/home/sjtu/cardinal/contrib/moose/framework/build.mk:144: /home/sjtu/cardinal/contrib/moose/framework/src/base/MooseApp.x86_64-conda-linux-gnu.opt.lo] Error 1
make: *** Waiting for unfinished jobs....

So how to deal with it
I have also searched this discussion in MOOSE
idaholab/moose#25358

Answered by Wang-Yihu

Oct 17, 2023

Jesus! It worrrrrrrks! cardinal-opt is successfully generated!!!!!! The whole terminal is

(base) sjtu@sjtu:~$ cd $HOME
(base) sjtu@sjtu:~$ conda activate moose
(moose) sjtu@sjtu:~$ git clone https://github.com/neams-th-coe/cardinal.git
(moose) sjtu@sjtu:~$ cd cardinal
(moose) sjtu@sjtu:~/cardinal$ git remote add april https://github.com/aprilnovak/cardinal
(moose) sjtu@sjtu:~/cardinal$ git fetch april
(moose) sjtu@sjtu:~/cardinal$ git checkout -b update-moose april/update-moose
(moose) sjtu@sjtu:~/cardinal$ ./scripts/get-dependencies.sh
(moose) sjtu@sjtu:~/cardinal$ cd contrib/moose
(moose) sjtu@sjtu:~/cardinal/contrib/moose$ git clean -xfd
(moose) sjtu@sjtu:~/cardinal/contrib/moose$ expor…

View full answer

aprilnovak · 2023-10-13T00:06:11Z

aprilnovak
Oct 13, 2023
Maintainer

Can you tell me a little more about your configuration? Did you recently pull in a new version of Cardinal? If so, did you do ./scripts/get-dependencies.sh to fetch the most up-to-date submodules?

25 replies

aprilnovak Oct 16, 2023
Maintainer

The full steps, if Cardinal was deleted, will need to include pointing to my fork of Cardinal (which we named april) and fetching it. I think this should work:

cd cardinal
git remote add april https://github.com/aprilnovak/cardinal
git fetch april
git checkout -b update-moose april/update-moose

./scripts/get-dependencies.sh
cd contrib/moose
git clean -xfd

cd ../../
make -j4

Wang-Yihu Oct 17, 2023
Author

If I

git clone https://github.com/neams-th-coe/cardinal.git
cd cardinal
git remote add april https://github.com/aprilnovak/cardinal
git fetch april
git checkout -b update-moose april/update-moose
./scripts/get-dependencies.sh
cd contrib/moose
git clean -xfd
export ENABLE_NEK=false
export HDF5_ROOT=$CONDA_PREFIX
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
cd ../../
conda activate moose
make -j8

It throws errors like before:

CMake Error at /home/sjtu/mambaforge3/envs/moose/share/cmake-3.25/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
  Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS
  HDF5_HL_LIBRARIES C HL) (found version "")
Call Stack (most recent call first):
  /home/sjtu/mambaforge3/envs/moose/share/cmake-3.25/Modules/FindPackageHandleStandardArgs.cmake:600 (_FPHSA_FAILURE_MESSAGE)
  /home/sjtu/mambaforge3/envs/moose/share/cmake-3.25/Modules/FindHDF5.cmake:1007 (find_package_handle_standard_args)
  CMakeLists.txt:156 (find_package)

And if I make it again

rm -rf build
make -j8

It throws the same error about Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS
I do not know the reason... I have set export HDF5_ROOT=$CONDA_PREFIX.... in the terminal. em....

aprilnovak Oct 17, 2023
Maintainer

You need to have run conda activate moose BEFORE doing any of those export statements. This is indicated in the online instructions. Otherwise those environment variables like CONDA_PREFIX do not exist yet.

Wang-Yihu Oct 17, 2023
Author

Jesus! It worrrrrrrks! cardinal-opt is successfully generated!!!!!! The whole terminal is

(base) sjtu@sjtu:~$ cd $HOME
(base) sjtu@sjtu:~$ conda activate moose
(moose) sjtu@sjtu:~$ git clone https://github.com/neams-th-coe/cardinal.git
(moose) sjtu@sjtu:~$ cd cardinal
(moose) sjtu@sjtu:~/cardinal$ git remote add april https://github.com/aprilnovak/cardinal
(moose) sjtu@sjtu:~/cardinal$ git fetch april
(moose) sjtu@sjtu:~/cardinal$ git checkout -b update-moose april/update-moose
(moose) sjtu@sjtu:~/cardinal$ ./scripts/get-dependencies.sh
(moose) sjtu@sjtu:~/cardinal$ cd contrib/moose
(moose) sjtu@sjtu:~/cardinal/contrib/moose$ git clean -xfd
(moose) sjtu@sjtu:~/cardinal/contrib/moose$ export ENABLE_NEK=false
export HDF5_ROOT=$CONDA_PREFIX
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
(moose) sjtu@sjtu:~/cardinal/contrib/moose$ cd ../../
(moose) sjtu@sjtu:~/cardinal$ make -j8

And the terminal output is following in the file

CardinalInstallOutput.txt

Answer selected by Wang-Yihu

aprilnovak Oct 17, 2023
Maintainer

Nice! Thanks for sticking with it.

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MooseServer moose_server(*this) error when make cardinal-opt #798

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