[BUG]error in mpi4py setup command: 'python_requires' must be a string containing valid version specifiers; Invalid specifier: '!=3.4.*''

[LemonBoy68]

Hi all~
I have some problems with self-compilation and installation of hdf5:

version:
Python 3.9.16
mpi4py ：3.1.4
certifi 2023.5.7
charset-normalizer 3.1.0
Cython 0.29.34
idna 3.4
mpi4py 3.1.4
numpy 1.24.3
packaging 23.1
Pint 0.21
pip 23.1.2
platformdirs 3.5.1
pooch 1.7.0
PySocks 1.7.1
requests 2.31.0
scipy 1.10.1
setuptools 67.7.2
typing_extensions 4.6.0

Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple
Collecting h5py
Using cached https://pypi.tuna.tsinghua.edu.cn/packages/69/f4/3172bb63d3c57e24aec42bb93fcf1da4102752701ab5ad10b3ded00d0c5b/h5py-3.8.0.tar.gz (400 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Installing backend dependencies ... error
error: subprocess-exited-with-error

× pip subprocess to install backend dependencies did not run successfully.
│ exit code: 1
╰─> [23 lines of output]
Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple
Collecting mpi4py==3.1.0
Using cached https://pypi.tuna.tsinghua.edu.cn/packages/1a/a3/3a33c19379cb08cc1be16d1928a899e5b18151c7e8994d315a66017bc46f/mpi4py-3.1.0.tar.gz (2.4 MB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'error'
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [1 lines of output]
    error in mpi4py setup command: 'python_requires' must be a string containing valid version specifiers; Invalid specifier: '!=3.4.*''
    [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
[end of output]

[derobins]

Is this an HDF5 problem?

[ajelenak]

No, this is not HDF5 problem. It is a known issue and has a known solution. This issue can be closed here because it is duplicated as h5py/h5py#2267.

[LemonBoy68]

Ok，tanks

[LemonBoy68]

No, this is not HDF5 problem. It is a known issue and has a known solution. This issue can be closed here because it is duplicated as h5py/h5py#2267.

see all messages. Rank 0 message is:
Traceback (most recent call last):
File "inputA.py", line 1360, in
dtStep,model_time,step,MeshOutput = update(MeshOutput)
File "inputA.py", line 1332, in update
MeshOutput = SaveData(MeshOutput)
File "inputA.py", line 841, in SaveData
s1Hnd=swarm.save(outputPath+"swarm"+ str(step).zfill(4)+".h5")
File "/share/home/Tninghui/anaconda3/envs/uwgo_oneapi/lib/python3.8/site-packages/underworld/swarm/_swarm.py", line 290, in save
self.particleCoordinates.save(filename, collective, units=units, **kwargs)
File "/share/home/Tninghui/anaconda3/envs/uwgo_oneapi/lib/python3.8/site-packages/underworld/swarm/_swarmvariable.py", line 499, in save
h5f.attrs[str(kwarg)] = str(val)
File "/share/home/Tninghui/anaconda3/envs/uwgo_oneapi/lib/python3.8/site-packages/underworld/utils/_io.py", line 105, in exit
self.h5f.close()
File "/share/home/Tninghui/anaconda3/envs/uwgo_oneapi/lib/python3.8/site-packages/h5py/_hl/files.py", line 586, in close
self.id._close_open_objects(h5f.OBJ_LOCAL | h5f.OBJ_FILE)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5f.pyx", line 360, in h5py.h5f.FileID._close_open_objects
RuntimeError: Can't decrement id ref count (Invalid argument, error stack:
MPI_FILE_SET_SIZE(75): Inconsistent arguments to collective routine )
Abort(1) on node 1 (rank 1 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 1
Abort(1) on node 48 (rank 48 in comm 496): application called MPI_Abort(comm=0x84000003, 1) - process 48
Abort(1) on node 96 (rank 96 in comm 496): application called MPI_Abort(comm=0x84000003, 1) - process 96
Abort(1) on node 9 (rank 9 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 9
Abort(1) on node 49 (rank 49 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 49
Abort(1) on node 142 (rank 142 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 142
Abort(1) on node 144 (rank 144 in comm 496): application called MPI_Abort(comm=0x84000003, 1) - process 144
Abort(1) on node 20 (rank 20 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 20
Abort(1) on node 68 (rank 68 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 68
Abort(1) on node 97 (rank 97 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 97
Abort(1) on node 168 (rank 168 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 168
Abort(1) on node 33 (rank 33 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 33
Abort(1) on node 86 (rank 86 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 86
Abort(1) on node 98 (rank 98 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 98
Abort(1) on node 172 (rank 172 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 172
Abort(1) on node 47 (rank 47 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 47
Abort(1) on node 93 (rank 93 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 93
Abort(1) on node 112 (rank 112 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 112
Abort(1) on node 174 (rank 174 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 174
Abort(1) on node 2 (rank 2 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 2
Abort(1) on node 94 (rank 94 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 94
Abort(1) on node 113 (rank 113 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 113
Abort(1) on node 189 (rank 189 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 189
Abort(1) on node 6 (rank 6 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 6
Abort(1) on node 57 (rank 57 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 57
Abort(1) on node 114 (rank 114 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 114
Abort(1) on node 158 (rank 158 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 158
Abort(1) on node 7 (rank 7 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 7
Abort(1) on node 58 (rank 58 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 58
Abort(1) on node 115 (rank 115 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 115
Abort(1) on node 160 (rank 160 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 160
Abort(1) on node 8 (rank 8 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 8
Abort(1) on node 72 (rank 72 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 72
Abort(1) on node 116 (rank 116 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 116
Abort(1) on node 161 (rank 161 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 161
Abort(1) on node 10 (rank 10 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 10
Abort(1) on node 74 (rank 74 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 74
Abort(1) on node 117 (rank 117 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 117
Abort(1) on node 162 (rank 162 in comm 496): application called MPI_Abort(comm=0x84000002, 1) - process 162

[ajelenak]

The errors you posted above have nothing to do with building h5py with custom MPI-enabled libhdf5. So this issue is not any more appropriate to use. I suggest you consider posting your problem on the HDF Forum and see if someone from the HDF community can help you.