Reading stiffness matrix from op4 fails with large matrices #661
Comments
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I’m on vacation for another week, but have you tried using the op2
instead? If you search for OUTPUT2 you’ll find an example. Obviously
you’ll need to change your file number to (I believe) 12 (not 2) to send
the data to the op2.
…On Fri, Sep 24, 2021 at 10:12 AM Jrois ***@***.***> wrote:
Hi,
I am having a issues reading in a stiffness matrix from an .op4 file.
Everything worked fine until I started scaling up the number of nodes,
which led me to believe my issue is similar to a previous issue
<#293>. However my error
traceback was different so I decided to make a separate issue.
I have tried two set-ups and they both produce a different error:
Python v3.8 & pyNastran v1.3.1 give the following traceback:
Traceback (most recent call last):
File "test2.py", line 14, in
MAT = model.read_op4("./MSCNpyBenchmarkN10/MSCNpyBenchmarkN10_kelems.op4",
matrix_names=["KAA"])
File "c:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 137, in read_op4
return self.read_op4_binary(op4_filename, matrix_names, precision)
File "c:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 686, in read_op4_binary
(name, form, matrix) = self._read_matrix_binary(op4, precision,
matrix_names)
File "c:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 804, in _read_matrix_binary
A = self._read_real_binary(op4, nrows, ncols, Type, is_sparse, is_big_mat)
File "c:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 895, in _read_real_binary
A = self._read_real_sparse_binary(op4, nrows, ncols, matrix_type,
is_big_mat)
File "c:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 914, in _read_real_sparse_binary
(icol, irow, nwords) = self.get_markers_sparse(op4, is_big_mat)
File "c:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 1354, in get_markers_sparse
unused_a, icol, irow, nwords = self.read_start_marker(op4)
File "c:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 726, in read_start_marker
assert self.n == op4.tell(), 'n=%s tell=%s' % (self.n, op4.tell())
AssertionError: n=5177352 tell=5177344
When debug=True I get a different error:
Traceback (most recent call last):
File
"C:\user\anaconda3\envs\py38\lib\site-packages\IPython\core\interactiveshell.py",
line 3441, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 1, in
runfile('C:/user/WF/python/MSCN-PY/test2.py',
wdir='C:/SpaceLabs/WF/python/MSCN-PY')
File "C:\user\PyCharm Community Edition
2021.2.1\plugins\python-ce\helpers\pydev_pydev_bundle\pydev_umd.py", line
198, in runfile
pydev_imports.execfile(filename, global_vars, local_vars) # execute the
script
File "C:\user\PyCharm Community Edition
2021.2.1\plugins\python-ce\helpers\pydev_pydev_imps_pydev_execfile.py",
line 18, in execfile
exec(compile(contents+"\n", file, 'exec'), glob, loc)
File "C:/user/WF/python/MSCN-PY/test2.py", line 14, in
MAT = model.read_op4("./MSCNpyBenchmarkN10/MSCNpyBenchmarkN10_kelems.op4",
matrix_names=["KAA"])
File "C:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 137, in read_op4
return self.read_op4_binary(op4_filename, matrix_names, precision)
File "C:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 686, in read_op4_binary
(name, form, matrix) = self._read_matrix_binary(op4, precision,
matrix_names)
File "C:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 804, in _read_matrix_binary
A = self._read_real_binary(op4, nrows, ncols, Type, is_sparse, is_big_mat)
File "C:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 895, in _read_real_binary
A = self._read_real_sparse_binary(op4, nrows, ncols, matrix_type,
is_big_mat)
File "C:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 938, in _read_real_sparse_binary
self._show(op4, 100, types='qd')
File "C:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 1015, in _show
strings, ints, floats = self._show_data(data, types=types, endian=endian)
File "C:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 1044, in _show_data
return self._write_data(sys.stdout, data, types=types, endian=endian)
File "C:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 1092, in _write_data
doubles = unpack(b'%s%id' % (endian, ndoubles), data[:ndoubles*8])
TypeError: %b requires a bytes-like object, or an object that implements
*bytes*, not 'str'
Python v3.6 & pyNastran v1.2.1 gives this traceback:
Traceback (most recent call last):
File "test2.py", line 5, in
MAT = model.read_op4("K.op4")
File "c:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 137, in read_op4
return self.read_op4_binary(op4_filename, matrix_names, precision)
File "c:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 686, in read_op4_binary
(name, form, matrix) = self._read_matrix_binary(op4, precision,
matrix_names)
File "c:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 804, in _read_matrix_binary
A = self._read_real_binary(op4, nrows, ncols, Type, is_sparse, is_big_mat)
File "c:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 895, in _read_real_binary
A = self._read_real_sparse_binary(op4, nrows, ncols, matrix_type,
is_big_mat)
File "c:\user\anaconda3\envs\py38\lib\site-packages\pyNastran\op4\op4.py",
line 974, in _read_real_sparse_binary
value_list = unpack(str_values, data[0:nvalues * nbytes_per_value])
struct.error: bad char in struct format
Moreover, for some attempts I have gotten the same traceback as the first
above (ending in AssertionError).
Below you can find a .zip containing the model and a code snippet to
reproduce the error. I also added the op4 file produced since it can take
some time to run the model.
Thanks in advance!
Kind regards,
Joris
test.zip <https://github.com/SteveDoyle2/pyNastran/files/7227107/test.zip>
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Hi Steve, Thanks for the suggestion. I had not tried that yet. Unfortunately, I couldn't get that working either. PARAM,EXTOUT,DMIGOP2 After adding matrices to read using the method model.set_additional_matrices_to_read (as suggested by arising errors) I get an message saying there was a FATAL ERROR in the f06: pyNastran.f06.errors.FatalError: There was a Nastran FATAL Error. Check the F06. However, upon inspecting the f06, I could not find any fatal errors or other signs of errors. I also tried to output using EXTSEOUT(STIF, EXTID=30, DMIGOP2=13) But that lead to the same results. Moreover, both small and large problems yield the same error. I understand that you don't have time to look at the problem now. So when you do, please send me an update. Enjoy you holiday! |
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Oh I didn’t realize you were trying to do superelements. Those get weird.
Try:
PARAM,EXTSEOUT,DMIGPCH
you should be able to read it with the BDF reader and punch=True. Nastran
is weird with their definition of a punch file. Sometimes it’s a BDF with
BDF cards and sometimes it’s not.
…On Mon, Sep 27, 2021 at 1:34 AM Jrois ***@***.***> wrote:
Hi Steve,
Thanks for the suggestion. I had not tried that yet. Unfortunately, I
couldn't get that working either.
I have tried writing the output using
PARAM,EXTOUT,DMIGOP2
After adding matrices to read using the method
model.set_additional_matrices_to_read (as suggested by arising errors) I
get an message saying there was a FATAL ERROR in the f06:
pyNastran.f06.errors.FatalError: There was a Nastran FATAL Error. Check
the F06.
last table=b'MUG1'; post=-2
However, upon inspecting the f06, I could not find any fatal errors or
other signs of errors.
I also tried to output using
EXTSEOUT(STIF, EXTID=30, DMIGOP2=13)
But that lead to the same results. Moreover, both small and large problems
yield the same error.
I understand that you don't have time to look at the problem now. So when
you do, please send me an update.
Enjoy you holiday!
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I am not using superelements, at least not explicitly. I use an API to recreate the model such that all elements have unique nodes. This way the whole model becomes decoupled, which allows me to extract element stiffness matrices for all elements. I am relatively new to Nastran and I'm not yet familiar with superelements so I can't say for sure that this process is related to superelements. As for the reading of the matrix, I didn't realise you could use the BDF reader to also read punch files. Instead I now wrote my own script that reads the matrix. This however can take some time when large matrices are concerned and I believe OP4 or OP2 would be faster. So if ever you fix the problem with large matrices I would definitely like to know! Thanks for your time and help Kind regards, |
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Hi,
I am having a issues reading in a stiffness matrix from an .op4 file.
Everything worked fine until I started scaling up the number of nodes, which led me to believe my issue is similar to a previous issue. However my error traceback was different so I decided to make a separate issue.
I have tried two set-ups and they both produce a different error:
Python v3.8 & pyNastran v1.3.1 give the following traceback:
When debug=True I get a different error:
Python v3.6 & pyNastran v1.2.1 gives this traceback:
Moreover, for some attempts I have gotten the same traceback as the first above (ending in AssertionError).
Below you can find a .zip containing the model and a code snippet to reproduce the error. I also added the op4 file produced since it can take some time to run the model.
Thanks in advance!
Kind regards,
Joris
test.zip
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