Open
Description
What happened?
First, my system is:
- macOS 13.4
- GCC 12.2
- Open MPI 4.1.5
- HDF5 1.10.10
- python 3.11.3
This is part of my ongoing attempt to make neural-fortran work with pre-compiled libraries (see modern-fortran/neural-fortran#128 and modern-fortran/neural-fortran#129).
Also, I've tried this with both 4.6.3 (the version neural-fortran points to) and 4.10.2 (the current latest release). All errors below are for 4.10.2, but I had failures with 4.6.3 as well
Now, I have to do some weird things due to how we build HDF5 in our library stack (autotools, static, and then weird install paths on that), but if I add:
-DHDF5_ROOT="$(prefix);$(prefix)/include/hdf5;$(prefix)/include/szlib
to the cmake line, everything seems to be found:
-- Looking for H5_HAVE_FILTER_SZIP
-- Looking for H5_HAVE_FILTER_SZIP - found
-- Looking for H5_HAVE_FILTER_DEFLATE
-- Looking for H5_HAVE_FILTER_DEFLATE - found
-- Looking for H5_HAVE_PARALLEL
-- Looking for H5_HAVE_PARALLEL - found
...
-- Looking for H5Pset_fapl_mpio
-- Looking for H5Pset_fapl_mpio - found
-- Performing Test HDF5_C_links
-- Performing Test HDF5_C_links - Success
-- Performing Test HDF5_Fortran_links
-- Performing Test HDF5_Fortran_links - Success
-- Found HDF5: /Users/mathomp4/Baselibs/ESMA-Baselibs-main-with-neural-fortran/aarch64-apple-darwin22.5.0/gfortran/Darwin/lib/libhdf5_hl.a;/Users/mathomp4/Baselibs/ESMA-Baselibs-main-with-neural-fortran/aarch64-apple-darwin22.5.0/gfortran/Darwin/lib/libhdf5.a (found version "1.10.10") found components: Fortran
...
and a make install runs fine as well.
But on ctest:
Test project /Users/mathomp4/Baselibs/ESMA-Baselibs-main-with-neural-fortran/src/h5fortran/build
Start 1: minimal
1/27 Test #1: minimal .......................... Passed 0.70 sec
Start 2: array
2/27 Test #2: array ............................***Failed 0.28 sec
Start 3: attributes
3/27 Test #3: attributes .......................***Failed 0.27 sec
Start 24: PythonAttributes
4/27 Test #24: PythonAttributes ................. Passed 0.13 sec
Start 4: attributes_read
5/27 Test #4: attributes_read .................. Passed 0.27 sec
Start 5: cast
6/27 Test #5: cast .............................***Failed 0.28 sec
Start 6: deflate_write
7/27 Test #6: deflate_write ....................***Failed 0.26 sec
Start 7: deflate_read
Failed test dependencies: deflate_write
8/27 Test #7: deflate_read .....................***Not Run 0.00 sec
Start 8: deflate_props
Failed test dependencies: deflate_write
9/27 Test #8: deflate_props ....................***Not Run 0.00 sec
Start 9: destructor
10/27 Test #9: destructor ....................... Passed 0.26 sec
Start 10: exist
11/27 Test #10: exist ............................***Failed 0.26 sec
Start 11: fill
12/27 Test #11: fill .............................***Failed 0.25 sec
Start 12: groups
13/27 Test #12: groups ...........................***Failed 0.26 sec
Start 20: write
14/27 Test #20: write ............................ Passed 0.25 sec
Start 13: layout
15/27 Test #13: layout ...........................***Failed 0.25 sec
Start 14: lt
16/27 Test #14: lt ...............................***Failed 0.25 sec
Start 15: scalar
17/27 Test #15: scalar ........................... Passed 0.26 sec
Start 16: shape
18/27 Test #16: shape ............................ Passed 0.25 sec
Start 17: string
19/27 Test #17: string ...........................***Failed 0.26 sec
Start 26: PythonString
20/27 Test #26: PythonString ..................... Passed 0.12 sec
Start 18: string_read
21/27 Test #18: string_read ...................... Passed 0.28 sec
Start 19: version
22/27 Test #19: version .......................... Passed 0.25 sec
Start 21: fail_read_size_mismatch
23/27 Test #21: fail_read_size_mismatch .......... Passed 0.26 sec
Start 22: fail_read_rank_mismatch
24/27 Test #22: fail_read_rank_mismatch .......... Passed 0.25 sec
Start 23: fail_nonexist_variable
25/27 Test #23: fail_nonexist_variable ........... Passed 0.25 sec
Start 25: PythonShape
26/27 Test #25: PythonShape ...................... Passed 0.13 sec
Start 27: h5ls
27/27 Test #27: h5ls .............................***Not Run (Disabled) 0.00 sec
54% tests passed, 12 tests failed out of 26
Label Time Summary:
h5fortran = 6.28 sec*proc (27 tests)
python = 0.38 sec*proc (3 tests)
shaky = 0.76 sec*proc (3 tests)
Total Test time (real) = 6.29 sec
The following tests did not run:
27 - h5ls (Disabled)
The following tests FAILED:
2 - array (Failed)
3 - attributes (Failed)
5 - cast (Failed)
6 - deflate_write (Failed)
7 - deflate_read (Not Run)
8 - deflate_props (Not Run)
10 - exist (Failed)
11 - fill (Failed)
12 - groups (Failed)
13 - layout (Failed)
14 - lt (Failed)
17 - string (Failed)
Errors while running CTest
Output from these tests are in: /Users/mathomp4/Baselibs/ESMA-Baselibs-main-with-neural-fortran/src/h5fortran/build/Testing/Temporary/LastTest.log
Use "--rerun-failed --output-on-failure" to re-run the failed cases verbosely.
I'll paste below the --rerun-failed --output-on-failure output.
Any ideas what is happening? The weird thing is, I'm pretty sure I got this working a few weeks back. I had to move on to other projects, but I had time today and...not working. You can see below that there seem to be a lot of:
ERROR STOP ERROR:h5fortran:open: HDF5 library initialize
errors.
Relevant log output
Test project /Users/mathomp4/Baselibs/ESMA-Baselibs-main-with-neural-fortran/src/h5fortran/build
Start 2: array
1/13 Test #2: array ............................***Failed 0.01 sec
1 2 3 4
2 4 6 8
3 6 9 12
4 8 12 16
PASSED: array write
PASSED: slice read
PASSED: create dataset and write slice 1D
PASSED: overwrite slice 1d, stride=1
PASSED: overwrite slice 1d, no stride
h5fortran:TRACE:create: deflate: /int32a-2d
create and write slice 2d, stride=1
PASSED: slice write
ERROR STOP ERROR:h5fortran:open: HDF5 library initialize
Start 3: attributes
2/13 Test #3: attributes .......................***Failed 0.01 sec
ERROR STOP ERROR:h5fortran:open: HDF5 library initialize
Start 5: cast
3/13 Test #5: cast .............................***Failed 0.01 sec
OK: cast write
ERROR STOP ERROR:h5fortran:open: HDF5 library initialize
Start 6: deflate_write
4/13 Test #6: deflate_write ....................***Failed 0.01 sec
ERROR STOP ERROR:h5fortran:open: HDF5 library initialize
Start 7: deflate_read
Failed test dependencies: deflate_write
5/13 Test #7: deflate_read .....................***Not Run 0.00 sec
Start 8: deflate_props
Failed test dependencies: deflate_write
6/13 Test #8: deflate_props ....................***Not Run 0.00 sec
Start 10: exist
7/13 Test #10: exist ............................***Failed 0.01 sec
OK: is_hdf5
ERROR STOP ERROR:h5fortran:open: HDF5 library initialize
Start 11: fill
8/13 Test #11: fill .............................***Failed 0.01 sec
ERROR STOP ERROR:h5fortran:open: HDF5 library initialize
Start 12: groups
9/13 Test #12: groups ...........................***Failed 0.01 sec
OK: HDF5 group
ERROR STOP ERROR:h5fortran:open: HDF5 library initialize
Start 20: write
10/13 Test #20: write ............................ Passed 0.01 sec
Start 13: layout
11/13 Test #13: layout ...........................***Failed 0.01 sec
ERROR STOP ERROR:h5fortran:open: HDF5 library initialize
Start 14: lt
12/13 Test #14: lt ...............................***Failed 0.01 sec
ERROR STOP ERROR:h5fortran:open: HDF5 library initialize
Start 17: string
13/13 Test #17: string ...........................***Failed 0.01 sec
OK: HDF5 string write
OK: HDF5 string read
ERROR STOP ERROR:h5fortran:open: HDF5 library initialize
8% tests passed, 12 tests failed out of 13
Label Time Summary:
h5fortran = 0.13 sec*proc (13 tests)
Total Test time (real) = 0.13 sec
The following tests FAILED:
2 - array (Failed)
3 - attributes (Failed)
5 - cast (Failed)
6 - deflate_write (Failed)
7 - deflate_read (Not Run)
8 - deflate_props (Not Run)
10 - exist (Failed)
11 - fill (Failed)
12 - groups (Failed)
13 - layout (Failed)
14 - lt (Failed)
17 - string (Failed)
Errors while running CTest