Python on aurora (Lund)
Let’s get it to work! :)
I'll document what happened so far.
After successfully building the code, I simply try a a script like:
build/utils/view_midplane_disk ./out/disk100.h5 -g polar -s log
The error I get is this: ModuleNotFoundError: No module named 'matplotlib'
I did not have that module and module avail matplotlib gives on aurora no compatible version(see original module list below). So I instead added/replaced
Python/3.7.0
Boost/1.68.0-Python-3.7.0
h5py/2.8.0-Python-3.7.0
matplotlib/3.0.0-Python-3.6.6
And then rebuild the code and tried again, but then I get the error
[michiel@aurora-rviz01 elena2Dc]$ /home/michiel/meetfargoca2020/fargOCA/build18c/utils/view_midplane_disk ./disk100.h5 -g polar -s log
/home/michiel/meetfargoca2020/fargOCA/build18c/utils/view_midplane_disk:82: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
if 'polar_grid' in obj[path]: fields.append(path)
Traceback (most recent call last):
File "/home/michiel/meetfargoca2020/fargOCA/build18c/utils/view_midplane_disk", line 92, in <module>
paths = extract_field_paths(disk)
File "/home/michiel/meetfargoca2020/fargOCA/build18c/utils/view_midplane_disk", line 83, in extract_field_paths
obj.visit(collect_fields)
File "/sw/easybuild/software/MPI/intel/2018.3.222-GCC-7.3.0-2.30/impi/2018.3.222/h5py/2.8.0-Python-3.6.6/lib/python3.6/site-packages/h5py-2.8.0-py3.6-linux-x86_64.egg/h5py/_hl/group.py", line 448, in visit
return h5o.visit(self.id, proxy)
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/h5o.pyx", line 355, in h5py.h5o.visit
File "h5py/defs.pyx", line 1560, in h5py.defs.H5Ovisit_by_name
File "h5py/h5o.pyx", line 302, in h5py.h5o.cb_obj_simple
File "/sw/easybuild/software/MPI/intel/2018.3.222-GCC-7.3.0-2.30/impi/2018.3.222/h5py/2.8.0-Python-3.6.6/lib/python3.6/site-packages/h5py-2.8.0-py3.6-linux-x86_64.egg/h5py/_hl/group.py", line 447, in proxy
return func(self._d(name))
File "/home/michiel/meetfargoca2020/fargOCA/build18c/utils/view_midplane_disk", line 82, in collect_fields
if 'polar_grid' in obj[path]: fields.append(path)
File "/sw/easybuild/software/MPI/intel/2018.3.222-GCC-7.3.0-2.30/impi/2018.3.222/h5py/2.8.0-Python-3.6.6/lib/python3.6/site-packages/h5py-2.8.0-py3.6-linux-x86_64.egg/h5py/_hl/dataset.py", line 394, in __iter__
raise TypeError("Can't iterate over a scalar dataset")
TypeError: Can't iterate over a scalar dataset
So my questions are:
1 Do I need to load matplotlib the way I did? (Or anaconda? Scipy? I am lost)
2 what does the error mean?
3 any suggestions on how to proceed? :)
Thanks! Michiel
====
[michiel@aurora-rviz01 build]$ ml list
Currently Loaded Modules:
1) GCCcore/7.3.0 17) CMake/3.12.1
2) binutils/2.30 18) Szip/2.1.1
3) icc/2018.3.222-GCC-7.3.0-2.30 19) HDF5/1.10.2
4) ifort/2018.3.222-GCC-7.3.0-2.30 20) git-lfs/2.7.1
5) impi/2018.3.222 21) pkg-config/0.29.2
6) imkl/2018.3.222 22) pkgconfig/1.3.1-Python-3.7.0
7) intel/2018b 23) h5py/2.8.0-Python-3.7.0
8) bzip2/1.0.6 24) GMP/6.1.2
9) zlib/1.2.11 25) expat/2.2.5
10) ncurses/6.1 26) Perl/5.28.0
11) Tcl/8.6.8 27) libxml2/2.9.8
12) SQLite/3.24.0 28) gettext/0.19.8.1
13) XZ/5.2.4 29) git/2.19.1
14) Python/3.7.0 30) ipp/2019.4.243
15) Boost/1.68.0-Python-3.7.0 31) libffi/3.2.1
16) cURL/7.60.0 32) libreadline/7.0