Python binding issues
Created by: JasonRuonanWang
I get the following error when I try to run gray-scott. This was on Mac 10.15.3 with Clang 11.0.0, and Python 3.7.7. Python was installed through homebrew and is the only Python3 installation on the machine.
jason@iMac ~/w/adiosvm/Tutorial/gray-scott master mpirun --oversubscribe -n 4 build/gray-scott simulation/settings-staging.json : -n 1 build/pdf_calc gs.bp pdf.bp 100 : -n 1 python3 plot/pdfplot.py -i pdf.bp
Traceback (most recent call last):
File "plot/pdfplot.py", line 3, in <module>
import adios2
File "/usr/local/lib/python3.7/site-packages/adios2/__init__.py", line 1, in <module>
from .adios2 import *
ImportError: dlopen(/usr/local/lib/python3.7/site-packages/adios2/adios2.so, 2): Symbol not found: __PyThreadState_Current
Referenced from: /usr/local/lib/python3.7/site-packages/adios2/adios2.so
Expected in: flat namespace
in /usr/local/lib/python3.7/site-packages/adios2/adios2.so
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[50203,1],5]
Exit code: 1
--------------------------------------------------------------------------
The following error is a compile error I got from compiling ADIOS2 with python3 on Ubuntu 19.10. It was a brand new VM installation, with everything (gcc 9.2.1 and libpython3-dev) installed through apt. Cmake in this case is not able to find the python3 installation automatically. I had to specify DPython_LIBRARIES and DPython_INCLUDE_DIR, but it still didn't work.
jason@vm ~/build/adios2 cmake ~/d/a2 -DPython_LIBRARIES=/usr/lib/python3.7/config-3.7m-x86_64-linux-gnu/libpython3.7.so -DPython_INCLUDE_DIR=/usr/include/python3.7m
-- Could NOT find Blosc (missing: BLOSC_LIBRARY BLOSC_INCLUDE_DIR) (Required is at least version "1.7")
-- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR)
-- Could NOT find ZFP (missing: ZFP_DIR)
-- Could NOT find SZ (missing: SZ_LIBRARY ZLIB_LIBRARY ZSTD_LIBRARY SZ_INCLUDE_DIR)
-- Could NOT find MGARD (missing: MGARD_LIBRARY ZLIB_LIBRARY BLOSC_LIBRARY MGARD_INCLUDE_DIR)
-- Could NOT find ZLIB (missing: ZLIB_LIBRARY ZLIB_INCLUDE_DIR)
-- Could NOT find PNG (missing: PNG_LIBRARY PNG_PNG_INCLUDE_DIR) (Required is at least version "1.6.0")
-- Found MPI: TRUE (found version "3.1") found components: C Fortran CXX
-- Could NOT find ZeroMQ (missing: ZeroMQ_LIBRARY ZeroMQ_INCLUDE_DIR) (Required is at least version "4.1")
-- Could NOT find DataSpaces (missing: DATASPACES_VERSION DATASPACES_INCLUDE_DIR DATASPACES_LIBRARIES DSPACES_LIBRARY) (Required is at least version "1.8")
-- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (found version "")
CMake Error at cmake/upstream/FindPython/Support.cmake:2068 (if):
if given arguments:
"_Python_INC_VERSION" "VERSION_EQUAL"
Unknown arguments specified
Call Stack (most recent call first):
cmake/upstream/FindPython.cmake:326 (include)
cmake/FindPython.cmake:8 (include)
cmake/DetectOptions.cmake:213 (find_package)
CMakeLists.txt:130 (include)
-- Configuring incomplete, errors occurred!
See also "/home/jason/build/adios2/CMakeFiles/CMakeOutput.log".
See also "/home/jason/build/adios2/CMakeFiles/CMakeError.log".
✘ jason@vm ~/build/adios2