Error in Moose Installation

[npaloskey]

I keep getting the following errors when attempting to run tests after compiling libmesh

misc/check_error.steady_no_converge: Working Directory: /storage/home/n/ngp11/projects/moose/test/tests/misc/check_error
misc/check_error.steady_no_converge: Running command: /storage/home/n/ngp11/projects/moose/test/moose_test-opt -i steady_no_converge.i --error --error-unused --error-override --no-gdb-backtrace
misc/check_error.steady_no_converge: 
misc/check_error.steady_no_converge: Framework Information:
misc/check_error.steady_no_converge: MOOSE Version:           git commit 16505c7 on 2022-03-28
misc/check_error.steady_no_converge: LibMesh Version:         7315cdb99555e4d774fc149b8c659f1e56955053
misc/check_error.steady_no_converge: PETSc Version:           3.16.5
misc/check_error.steady_no_converge: SLEPc Version:           3.16.2
misc/check_error.steady_no_converge: Current Time:            Wed Mar 30 11:56:42 2022
misc/check_error.steady_no_converge: Executable Timestamp:    Wed Mar 30 03:40:32 2022
misc/check_error.steady_no_converge: 
misc/check_error.steady_no_converge: Parallelism:
misc/check_error.steady_no_converge:   Num Processors:          1
misc/check_error.steady_no_converge:   Num Threads:             1
misc/check_error.steady_no_converge: 
misc/check_error.steady_no_converge: Mesh: 
misc/check_error.steady_no_converge:   Parallel Type:           replicated
misc/check_error.steady_no_converge:   Mesh Dimension:          2
misc/check_error.steady_no_converge:   Spatial Dimension:       2
misc/check_error.steady_no_converge:   Nodes:                   121
misc/check_error.steady_no_converge:   Elems:                   100
misc/check_error.steady_no_converge:   Num Subdomains:          1
misc/check_error.steady_no_converge: 
misc/check_error.steady_no_converge: Nonlinear System:
misc/check_error.steady_no_converge:   Num DOFs:                121
misc/check_error.steady_no_converge:   Num Local DOFs:          121
misc/check_error.steady_no_converge:   Variables:               "u" 
misc/check_error.steady_no_converge:   Finite Element Types:    "LAGRANGE" 
misc/check_error.steady_no_converge:   Approximation Orders:    "FIRST" 
misc/check_error.steady_no_converge: 
misc/check_error.steady_no_converge: Execution Information:
misc/check_error.steady_no_converge:   Executioner:             Steady
misc/check_error.steady_no_converge:   Solver Mode:             Preconditioned JFNK
misc/check_error.steady_no_converge:   PETSc Preconditioner:    hypre boomeramg 
misc/check_error.steady_no_converge: 
misc/check_error.steady_no_converge: HDF5-DIAG: Error detected in HDF5 (1.12.1) thread 0:
misc/check_error.steady_no_converge:   #000: H5T.c line 1929 in H5Tcopy(): not a datatype or dataset
misc/check_error.steady_no_converge:     major: Invalid arguments to routine
misc/check_error.steady_no_converge:     minor: Inappropriate type

Not sure what the issue is here but the tests stop after about 176 passing and 50 failed.

[GiudGiud]

Hello

Looks like an hdf5 error.
Can you please paste the output of ldd <your_executable (probably moose_test-opt)> ?

Guillaume

[npaloskey]

Great, I hope so too haha. Ill let you know how it goes. Thanks again

[GiudGiud]

To check the hdf5 in libmesh btw:

cd libmesh/build/.libs
ldd libmesh_opt.so

[npaloskey]

Hey @GiudGiud, I think what we did worked. 3050 tests passed and only 10 failed when doing

cd ~/projects/moose/test
make -j 4
./run_tests -j 4

Thanks for the help!!

[GiudGiud]

I’m glad!
if you please could paste the full error messages for these ten tests, could help us find an issue.
‘./run_tests —failed-tests’ will only run these ten

[npaloskey]

Hey @GiudGiud , I think some of the tests call for the system default version of python, my system defaults to python 2.7 for some reason so I created a virtual environment that would default my system to using python 3.6.8 and now all tests are passing. 0 failed. I think we're all good here.

Thanks again!

[npaloskey]

Set HDF5_DIR env variable to location of HDF5 installation in system

[milljm]

I was unaware of HDF5_DIR as an influential environment variable. Good to know, and I probably should have :) Cheers!

[jessecarterMOOSE]

Thanks all. Had this same problem. Fixed by using system HDF5, which was 1.10.7.