Beginner: invalid index to scalar variable. Help me please #158
Replies: 11 comments 8 replies
-
|
Hi @Suharyana61, thanks for checking out SaltProc! In order for me to best help you, I'll need the following information from you:
|
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-
|
Thank you very much for your replay.
1. I'm using Linux Mint 20.1 OS.
2. I.m unable to run the test suite. There are 2 failures.
```
FAILED
saltproc/tests/integration_tests/const_repr/test_const_reproc_run.py::test_integration_2step_constant_ideal_removal_heavy
- subprocess.CalledProcessError: Comm...
```
```
FAILED
saltproc/tests/integration_tests/no_repro/test_no_reproc_run.py::test_integration_2step_saltproc_no_reproc_heavy
- RuntimeError:
```
4. I changed the xsdata setting of the msbr.serpent file and then running
the code by typing python saltproc -i examples/msbr/msbr_main.json.
```
Step #1 has been started
Running serpent
Finished Serpent2 Run
Traceback (most recent call last):
File "/home/pc07/enter/lib/python3.8/runpy.py", line 194, in
_run_module_as_main
return _run_code(code, main_globals, None,
File "/home/pc07/enter/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "saltproc/__main__.py", line 4, in <module>
app.run()
File "/home/pc07/enter/lib/python3.8/site-packages/saltproc/app.py", line
441, in run
simulation.store_run_init_info()
File
"/home/pc07/enter/lib/python3.8/site-packages/saltproc/simulation.py", line
385, in store_run_init_info
self.sim_depcode.read_depcode_info()
File "/home/pc07/enter/lib/python3.8/site-packages/saltproc/depcode.py",
line 466, in read_depcode_info
self.sim_info['depletion_timestep'] = res['BURN_DAYS'][1][0]
IndexError: invalid index to scalar variable.
```
…On Mon, Jun 20, 2022 at 11:37 PM Olek ***@***.***> wrote:
Hi @Suharyana61 <https://github.com/Suharyana61>, thanks for checking out
SaltProc!
In order for me to best help you, I'll need the following information from
you:
- What operating system are you using?
- Are you able to run the test suite
<https://arfc.github.io/saltproc/master/installation.html#testing>
without any failures? If not, can you post the error messages in a reply using
a code formatting block
<https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/creating-and-highlighting-code-blocks>
?
- What is the *exact* command you are using to run the code?
—
Reply to this email directly, view it on GitHub
<#158 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AZTZFLO4G64AYVCBFSQ37VTVQCM4HANCNFSM5YWKXAHA>
.
You are receiving this because you were mentioned.Message ID:
***@***.***>
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Thanks for this info. Looking at this right now it's not immediately obvious as to what is happening. I'm away from my main office right now so don't have access to Serpent2, but I'll have access to it this weekend and will try to reproduce this behavior |
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-
|
Hi @Suharyana61, I've run both the test suites and the msbr example on my machine and have not been able to reproduce your issues. You said that you were unable to run the test suite without errors. I see that you posted the start of the error message, but didn't capture the entire message. Could you do the following for me?
|
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-
|
Thank you very much for your guidance.
1. I updated my saltproc to the latest commit on the master branch. I
downloaded the saltrproc-master.zip. I installed by running the command pip
install .
2. I run the test.
(base) ***@***.***:~/saltproc-master$ pytest saltproc
============================= test session starts
==============================
platform linux -- Python 3.8.5, pytest-6.1.1, py-1.9.0, pluggy-0.13.1
rootdir: /home/pc07/saltproc-master/saltproc, configfile: pytest.ini
collected 34 items
saltproc/tests/test_app.py ...... [
17%]
saltproc/tests/test_depcode.py .............. [
58%]
saltproc/tests/test_materialflow.py ... [
67%]
saltproc/tests/test_process.py . [
70%]
saltproc/tests/test_separator.py . [
73%]
saltproc/tests/test_simulation.py ...... [
91%]
saltproc/tests/test_sparger.py . [
94%]
saltproc/tests/integration_tests/const_repr/test_const_reproc_run.py F [
97%]
saltproc/tests/integration_tests/no_repro/test_no_reproc_run.py F
[100%]
=================================== FAILURES
===================================
_____________ test_integration_2step_constant_ideal_removal_heavy
______________
@pytest.mark.slow
# @pytest.mark.skip
def test_integration_2step_constant_ideal_removal_heavy():
# app.run()
subprocess.check_call([
'python',
'saltproc',
'-i',
'saltproc/tests/integration_tests/const_repr/tap_main_test.json'])
saltproc/tests/integration_tests/const_repr/test_const_reproc_run.py:125:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _
popenargs = (['python', 'saltproc', '-i',
'saltproc/tests/integration_tests/const_repr/tap_main_test.json'],)
kwargs = {}, retcode = 1
cmd = ['python', 'saltproc', '-i',
'saltproc/tests/integration_tests/const_repr/tap_main_test.json']
def check_call(*popenargs, **kwargs):
"""Run command with arguments. Wait for command to complete. If
the exit code was zero then return, otherwise raise
CalledProcessError. The CalledProcessError object will have the
return code in the returncode attribute.
The arguments are the same as for the call function. Example:
check_call(["ls", "-l"])
"""
retcode = call(*popenargs, **kwargs)
if retcode:
cmd = kwargs.get("args")
if cmd is None:
cmd = popenargs[0]
raise CalledProcessError(retcode, cmd)
E subprocess.CalledProcessError: Command '['python', 'saltproc',
'-i', 'saltproc/tests/integration_tests/const_repr/tap_main_test.json']'
returned non-zero exit status 1.
../enter/lib/python3.8/subprocess.py:364: CalledProcessError
----------------------------- Captured stdout call
-----------------------------
Initiating Saltproc:
Restart = False
Template File Path =
/home/pc07/saltproc-master/saltproc/tests/integration_tests/const_repr/tap_test.serpent
Input File Path =
/home/pc07/saltproc-master/saltproc/tests/integration_tests/const_repr/data/saltproc_serpent
Material File Path =
/home/pc07/saltproc-master/saltproc/tests/integration_tests/const_repr/data/saltproc_mat
Output HDF5 database Path =
/home/pc07/saltproc-master/saltproc/tests/integration_tests/const_repr/data/db_saltproc.h5
Step #1 has been started
Running serpent
_ .-=-. .-=-. .-==-.
{ } __ .' O o '. .' O o '. / -<' )--<
{ } .' O'. / o .-. O \ / o .-. O \ / .---`
{ } / .-. o\ /O / \ o\ /O / \ o\ /O /
\ `-` / \ O`-'o / \ O`-'o / \ O`-`o /
`-.-` '.____.' `._____.' `.____.'
Serpent 2 beta
A Continuous-energy Monte Carlo Reactor Physics Burnup Calculation Code
- Version 2.1.28 (February 6, 2017) -- Contact: ***@***.***
- Reference: J. Leppanen, et al. "The Serpent Monte Carlo code: Status,
development and applications in 2013." Ann. Nucl. Energy,
82 (2015) 142-150.
- Compiled Feb 21 2017 09:35:21
- MPI Parallel calculation mode not available
- OpenMP Parallel calculation mode available
- Geometry and mesh plotting available
- Default data path set to: "home/pc07/SERPENT/endfb7u.xsdata"
Begin calculation on Fri Jul 15 11:08:20 2022
Reading input file
"/home/pc07/saltproc-master/saltproc/tests/integration_tests/const_repr/./data/saltproc_serpent"...
Reading input file
"/home/pc07/saltproc-master/saltproc/tests/integration_tests/const_repr/./data/saltproc_mat"...
Reading input file "../../../../examples/tap/mats/non_burnable_mats.ini"...
Reading input file
"/home/pc07/saltproc-master/saltproc/tests/integration_tests/const_repr/./347_base.ini"...
***** Warning: Serpent 1 input option stabcut on line 49 of file
/home/pc07/saltproc-master/saltproc/tests/integration_tests/const_repr/./data/saltproc_serpent
not used
Checking duplicate input definitions...
OK.
Dividing burnable materials...
OK.
Creating geometry...
OK.
Counting geometry zones...
***** Warning: Universe 7 is used at multiple levels (5 and 4)
***** Warning: Universe 6 is used at multiple levels (4 and 5)
***** Warning: Universe 5 is used at multiple levels (2 and 5)
The geometry consists of 6 levels:
Level 0 size: max 11 zones
Level 1 size: max 100 zones
Level 2 size: max 25 zones
Level 3 size: max 5 zones
Level 4 size: max 4 zones
Level 5 size: max 1 zones
Processing cells...
OK.
Linking materials to geometry...
OK.
Counting cells...
OK.
Processing data for group constant generation:
- 70 energy groups in micro-group structure
- 2 energy groups in macro-group structure
- B1 fundamental mode calculation is not run
- Group constants generated in 1 universes
- Discontinuity factors are not calculated
- Pin-power distributions are not calculated
- Albedos are not calculated
- Poison cross sections are not calculated
Reading ACE directory files...
***** Fri Jul 15 11:08:20 2022
Input error:
Unable to locate cross section directory file "sss_jeff312.xsdata"
Environment variable SERPENT_DATA is set to
"home/pc07/SERPENT/endfb7u.xsdata"
----------------------------- Captured stderr call
-----------------------------
Traceback (most recent call last):
File "/home/pc07/enter/lib/python3.8/site-packages/saltproc/depcode.py",
line 586, in run_depcode
subprocess.check_output(
File "/home/pc07/enter/lib/python3.8/subprocess.py", line 411, in
check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/home/pc07/enter/lib/python3.8/subprocess.py", line 512, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '('sss2', '-omp', '1',
'/home/pc07/saltproc-master/saltproc/tests/integration_tests/const_repr/./data/saltproc_serpent')'
returned non-zero exit status 255.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/pc07/enter/lib/python3.8/runpy.py", line 194, in
_run_module_as_main
return _run_code(code, main_globals, None,
File "/home/pc07/enter/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "saltproc/__main__.py", line 4, in <module>
app.run()
File "/home/pc07/enter/lib/python3.8/site-packages/saltproc/app.py", line
438, in run
depcode.run_depcode(cores, nodes)
File "/home/pc07/enter/lib/python3.8/site-packages/saltproc/depcode.py",
line 592, in run_depcode
raise RuntimeError('\n %s RUN FAILED\n see error message above'
RuntimeError:
serpent RUN FAILED
see error message above
_______________ test_integration_2step_saltproc_no_reproc_heavy
________________
self = <saltproc.depcode.DepcodeSerpent object at 0x7f55289ed850>, cores = 1
nodes = 1
def run_depcode(self, cores, nodes):
"""Runs Serpent2 as a subprocess with the given parameters.
Parameters
----------
cores: int
Number of cores to use for Serpent2 run (`-omp` flag in
Serpent2).
nodes: int
Number of nodes to use for Serpent2 run (`-mpi` flag in
Serpent2).
"""
if self.exec_path.startswith('/projects/sciteam/bahg/'): # check
if BW
args = (
'aprun',
'-n',
str(nodes),
'-d', str(cores),
self.exec_path,
'-omp',
str(cores),
self.iter_inputfile)
elif self.exec_path.startswith('/apps/exp_ctl/'): # check if Falcon
args = (
'mpiexec',
self.exec_path,
self.iter_inputfile,
'-omp',
str(18))
else:
args = (self.exec_path, '-omp', str(cores), self.iter_inputfile)
print('Running %s' % (self.codename))
try:
subprocess.check_output(
args,
cwd=os.path.split(self.template_inputfile_path)[0],
stderr=subprocess.STDOUT)
saltproc/depcode.py:586:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _
timeout = None
popenargs = (('sss2', '-omp', '1',
'/home/pc07/saltproc-master/saltproc/tests/integration_tests/no_repro/int_test'),)
kwargs = {'cwd':
'/home/pc07/saltproc-master/saltproc/tests/integration_tests/no_repro',
'stderr': -2}
def check_output(*popenargs, timeout=None, **kwargs):
r"""Run command with arguments and return its output.
If the exit code was non-zero it raises a CalledProcessError. The
CalledProcessError object will have the return code in the
returncode
attribute and output in the output attribute.
The arguments are the same as for the Popen constructor. Example:
>> check_output(["ls", "-l", "/dev/null"])
b'crw-rw-rw- 1 root root 1, 3 Oct 18 2007 /dev/null\n'
The stdout argument is not allowed as it is used internally.
To capture standard error in the result, use stderr=STDOUT.
>> check_output(["/bin/sh", "-c",
... "ls -l non_existent_file ; exit 0"],
... stderr=STDOUT)
b'ls: non_existent_file: No such file or directory\n'
There is an additional optional argument, "input", allowing you to
pass a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it too will be used internally. Example:
>> check_output(["sed", "-e", "s/foo/bar/"],
... input=b"when in the course of fooman events\n")
b'when in the course of barman events\n'
By default, all communication is in bytes, and therefore any "input"
should be bytes, and the return value will be bytes. If in text
mode,
any "input" should be a string, and the return value will be a
string
decoded according to locale encoding, or by "encoding" if set. Text
mode
is triggered by setting any of text, encoding, errors or
universal_newlines.
"""
if 'stdout' in kwargs:
raise ValueError('stdout argument not allowed, it will be
overridden.')
if 'input' in kwargs and kwargs['input'] is None:
# Explicitly passing input=None was previously equivalent to
passing an
# empty string. That is maintained here for backwards
compatibility.
kwargs['input'] = '' if kwargs.get('universal_newlines', False)
else b''
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
**kwargs).stdout
../enter/lib/python3.8/subprocess.py:411:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (('sss2', '-omp', '1',
'/home/pc07/saltproc-master/saltproc/tests/integration_tests/no_repro/int_test'),)
kwargs = {'cwd':
'/home/pc07/saltproc-master/saltproc/tests/integration_tests/no_repro',
'stderr': -2, 'stdout': -1}
process = <subprocess.Popen object at 0x7f5528802220>
stdout = b'\n _ .-=-. .-=-. .-==-.
\n { } __ .\' O o \'. .\' O o
...data/jeff312/sss_jeff312.xsdata"\n\nEnvironment variable SERPENT_DATA is
set to "home/pc07/SERPENT/endfb7u.xsdata"\n\n'
stderr = None, retcode = 255
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False,
**kwargs):
"""Run command with arguments and return a CompletedProcess
instance.
The returned instance will have attributes args, returncode, stdout
and
stderr. By default, stdout and stderr are not captured, and those
attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to
capture them.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the
return code
in the returncode attribute, and output & stderr attributes if
those streams
were captured.
If timeout is given, and the process takes too long, a
TimeoutExpired
exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this
argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any
"input" should
be bytes, and the stdout and stderr will be bytes. If in text mode,
any
"input" should be a string, and stdout and stderr will be strings
decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or
universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be
used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is
not None:
raise ValueError('stdout and stderr arguments may not be
used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads.
communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled
that.
process.kill()
# We don't call process.wait() as .__exit__ does that for
us.
raise
retcode = process.poll()
if check and retcode:
raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '('sss2', '-omp',
'1',
'/home/pc07/saltproc-master/saltproc/tests/integration_tests/no_repro/int_test')'
returned non-zero exit status 255.
../enter/lib/python3.8/subprocess.py:512: CalledProcessError
During handling of the above exception, another exception occurred:
@pytest.mark.slow
# @pytest.mark.skip
def test_integration_2step_saltproc_no_reproc_heavy():
runsim_no_reproc(simulation, tap, 2)
saltproc/tests/integration_tests/no_repro/test_no_reproc_run.py:97:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _
saltproc/tests/integration_tests/no_repro/test_no_reproc_run.py:70: in
runsim_no_reproc
simulation.sim_depcode.run_depcode(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _
self = <saltproc.depcode.DepcodeSerpent object at 0x7f55289ed850>, cores = 1
nodes = 1
def run_depcode(self, cores, nodes):
"""Runs Serpent2 as a subprocess with the given parameters.
Parameters
----------
cores: int
Number of cores to use for Serpent2 run (`-omp` flag in
Serpent2).
nodes: int
Number of nodes to use for Serpent2 run (`-mpi` flag in
Serpent2).
"""
if self.exec_path.startswith('/projects/sciteam/bahg/'): # check
if BW
args = (
'aprun',
'-n',
str(nodes),
'-d', str(cores),
self.exec_path,
'-omp',
str(cores),
self.iter_inputfile)
elif self.exec_path.startswith('/apps/exp_ctl/'): # check if Falcon
args = (
'mpiexec',
self.exec_path,
self.iter_inputfile,
'-omp',
str(18))
else:
args = (self.exec_path, '-omp', str(cores), self.iter_inputfile)
print('Running %s' % (self.codename))
try:
subprocess.check_output(
args,
cwd=os.path.split(self.template_inputfile_path)[0],
stderr=subprocess.STDOUT)
except subprocess.CalledProcessError as error:
print(error.output.decode("utf-8"))
raise RuntimeError('\n %s RUN FAILED\n see error message above'
% (self.codename))
E RuntimeError:
E serpent RUN FAILED
E see error message above
saltproc/depcode.py:592: RuntimeError
----------------------------- Captured stdout call
-----------------------------
Step #1 has been started
Running serpent
_ .-=-. .-=-. .-==-.
{ } __ .' O o '. .' O o '. / -<' )--<
{ } .' O'. / o .-. O \ / o .-. O \ / .---`
{ } / .-. o\ /O / \ o\ /O / \ o\ /O /
\ `-` / \ O`-'o / \ O`-'o / \ O`-`o /
`-.-` '.____.' `._____.' `.____.'
Serpent 2 beta
A Continuous-energy Monte Carlo Reactor Physics Burnup Calculation Code
- Version 2.1.28 (February 6, 2017) -- Contact: ***@***.***
- Reference: J. Leppanen, et al. "The Serpent Monte Carlo code: Status,
development and applications in 2013." Ann. Nucl. Energy,
82 (2015) 142-150.
- Compiled Feb 21 2017 09:35:21
- MPI Parallel calculation mode not available
- OpenMP Parallel calculation mode available
- Geometry and mesh plotting available
- Default data path set to: "home/pc07/SERPENT/endfb7u.xsdata"
Begin calculation on Fri Jul 15 11:08:20 2022
Reading input file
"/home/pc07/saltproc-master/saltproc/tests/integration_tests/no_repro/int_test"...
Reading input file
"/home/pc07/saltproc-master/saltproc/tests/integration_tests/no_repro/int_test_mat"...
Reading input file
"/home/pc07/saltproc-master/saltproc/tests/integration_tests/no_repro/../../test_geo.inp"...
Checking duplicate input definitions...
OK.
Dividing burnable materials...
OK.
Creating geometry...
OK.
Counting geometry zones...
***** Warning: Universe 6 is used at multiple levels (4 and 5)
***** Warning: Universe 7 is used at multiple levels (4 and 5)
***** Warning: Universe 5 is used at multiple levels (2 and 5)
***** Warning: Universe 2 is used at multiple levels (1 and 4)
The geometry consists of 6 levels:
Level 0 size: max 9 zones
Level 1 size: max 100 zones
Level 2 size: max 25 zones
Level 3 size: max 5 zones
Level 4 size: max 6 zones
Level 5 size: max 1 zones
Processing cells...
OK.
Linking materials to geometry...
OK.
Counting cells...
OK.
Processing data for group constant generation:
- 70 energy groups in micro-group structure
- 2 energy groups in macro-group structure
- B1 fundamental mode calculation is not run
- Group constants generated in 1 universes
- Discontinuity factors are not calculated
- Pin-power distributions are not calculated
- Albedos are not calculated
- Poison cross sections are not calculated
Reading ACE directory files...
***** Fri Jul 15 11:08:20 2022
Input error:
Unable to locate cross section directory file
"/home/andrei2/serpent/xsdata/jeff312/sss_jeff312.xsdata"
Environment variable SERPENT_DATA is set to
"home/pc07/SERPENT/endfb7u.xsdata"
=========================== short test summary info
============================
FAILED
saltproc/tests/integration_tests/const_repr/test_const_reproc_run.py::test_integration_2step_constant_ideal_removal_heavy
FAILED
saltproc/tests/integration_tests/no_repro/test_no_reproc_run.py::test_integration_2step_saltproc_no_reproc_heavy
======================== 2 failed, 32 passed in 25.84s
=========================
(base) ***@***.***:~/saltproc-master$
…On Wed, Jul 13, 2022 at 2:51 AM Olek ***@***.***> wrote:
Hi @Suharyana61 <https://github.com/Suharyana61>, I've run both the test
suites and the msbr example on my machine and have not been able to
reproduce your issues.
You said that you were unable to run the test suite without errors. I see
that you posted the start of the error message, but didn't capture the
entire message.
Could you do the following for me?
1. Update your local git repository of saltproc to the latest commit
on the master branch.
2. Run the tests and example again.
3. If you get any errors, post the *full* error message stack in a
gist and link to it in a reply.
4. If you don't get any errors, please let me know in a reply.
—
Reply to this email directly, view it on GitHub
<#158 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AZTZFLLFYOQIFREZJHTEDDTVTXEC7ANCNFSM5YWKXAHA>
.
You are receiving this because you were mentioned.Message ID:
***@***.***>
|
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-
|
Hello @Suharyana61, that is quite a nasty error. It looks like all the unit tests are running fine, and the only thing failing are the integration tests. I was able to pick out that you haven't set up the cross section libraries that the unit test is expecting. It looks like you are providing a cross section library than SaltProc isn't expecting for it's integration tests:
As explained on this page, SaltProc needs a very specific library to run the integration tests. Please follow the instructions there, and once you have done so try running the integration tests again. |
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-
|
Thank you very much. I did not follow the instruction properly. Now the
data path is correct, "/home/pc07/SALTPROC/jeff312/sss_jeff312.xsdata".
However when I tried running the pytest, another 2 failures occurred.
Please find the report attached this email. Best reagard
…On Tue, Jul 19, 2022 at 4:04 AM Olek ***@***.***> wrote:
Hello @Suharyana61 <https://github.com/Suharyana61>, that is quite a
nasty error. It looks like all the unit tests are running fine, and the
only thing failing are the integration tests. I was able to pick out that
you haven't set up the cross section libraries that the unit test is
expecting. It looks like you are providing a cross section library than
SaltProc isn't expecting for it's integration tests:
Reading ACE directory files...
***** Fri Jul 15 11:08:20 2022
Input error:
Unable to locate cross section directory file "sss_jeff312.xsdata"
Environment variable SERPENT_DATA is set to
"home/pc07/SERPENT/endfb7u.xsdata"
As explained on this page
<https://arfc.github.io/saltproc/master/installation.html#testing>,
SaltProc needs a very specific library to run the integration tests. Please
follow the instructions there, and once you have done so try running the
integration tests again.
—
Reply to this email directly, view it on GitHub
<#158 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AZTZFLK6BSKS7ONNG3N7QV3VUXBGTANCNFSM5YWKXAHA>
.
You are receiving this because you were mentioned.Message ID:
***@***.***>
|
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Hi @Suharyana61, I'm not seeing the attachment in question. Could you copy and paste your terminal output into a gist, and post the link to it in a comment below? |
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I'm sorry yesterday I sent the report by email since I have not familiar with a gits. These are the 2 failures. Thank you very much (base) pc07@PC-07:~/SALTPROC$ pytest saltproc saltproc/tests/test_app.py ...... [ 17%] =================================== FAILURES ===================================
saltproc/tests/integration_tests/const_repr/test_const_reproc_run.py:125: popenargs = (['python', 'saltproc', '-i', 'saltproc/tests/integration_tests/const_repr/tap_main_test.json'],)
E subprocess.CalledProcessError: Command '['python', 'saltproc', '-i', 'saltproc/tests/integration_tests/const_repr/tap_main_test.json']' returned non-zero exit status 1. ../enter/lib/python3.8/subprocess.py:364: CalledProcessError Step #1 has been started _ .-=-. .-=-. .-==-. Serpent 2 beta A Continuous-energy Monte Carlo Reactor Physics Burnup Calculation Code
Begin calculation on Tue Jul 26 08:53:44 2022 Reading input file "/home/pc07/SALTPROC/saltproc/tests/integration_tests/const_repr/./data/saltproc_serpent"... ***** Warning: Serpent 1 input option stabcut on line 54 of file /home/pc07/SALTPROC/saltproc/tests/integration_tests/const_repr/./data/saltproc_serpent not used Checking duplicate input definitions... Dividing burnable materials... Creating geometry... Counting geometry zones... ***** Warning: Universe 7 is used at multiple levels (5 and 4) ***** Warning: Universe 6 is used at multiple levels (4 and 5) ***** Warning: Universe 5 is used at multiple levels (2 and 5) The geometry consists of 6 levels: Level 0 size: max 11 zones Processing cells... Linking materials to geometry... Counting cells... Processing data for group constant generation:
Reading ACE directory files... Reading decay data files... ***** Tue Jul 26 08:53:44 2022 (seed = 7812324546562) Suspicious line spectrum energy 0.000000E+00 (ZAI = 190360) ***** Tue Jul 26 08:53:44 2022 (seed = 7812324546562) Suspicious line spectrum energy 0.000000E+00 (ZAI = 190360) ***** Tue Jul 26 08:53:44 2022 (seed = 7812324546562) Suspicious line spectrum energy 0.000000E+00 (ZAI = 190360) ***** Tue Jul 26 08:53:44 2022 (seed = 7812324546562) Suspicious line spectrum energy 0.000000E+00 (ZAI = 190360) ***** Tue Jul 26 08:53:44 2022 (seed = 7812324546562) Suspicious line spectrum energy 0.000000E+00 (ZAI = 190360) ***** Tue Jul 26 08:53:44 2022 (seed = 7812324546562) Sum of decay branching ratios is 0.450000 (ZAI = 771690) ***** Tue Jul 26 08:53:44 2022 (seed = 7812324546562) Sum of decay branching ratios is 0.940000 (ZAI = 791730) ***** Tue Jul 26 08:53:45 2022 (seed = 7812324546562) Sum of decay branching ratios is 0.910000 (ZAI = 1022510) ***** Tue Jul 26 08:53:45 2022 (seed = 7812324546562) Sum of decay branching ratios is 0.850000 (ZAI = 1022570) OK. Reading neutron-induced fission yields... Reading spontaneous fission yields... Adding nuclides in material fuel... Nuclide 1001.09c -- hydrogen at 900K (H-1) Adding nuclides in material ctrlPois... Adding nuclides in material zrh... Adding nuclides in material sic... Nuclide 6000.09c -- natural carbon at 900K (C-nat) Adding nuclides in material hast... Nuclide 28058.09c -- nickel 58 at 900K (Ni-58) Adding nuclides in material air... Adding activation products... Nuclide 20044.09c -- calcium 44 at 900K (Ca-44) Adding actinide data... Adding fission product data... Adding remaining data and forming paths... Running Doppler-broadening preprocessor: Adding thermal scattering data... Nuclide hzr05.32t -- hydrogen at 800K (H-1) Checking data and printing output... ***** Tue Jul 26 08:54:02 2022:
Fatal error in function CheckNuclideData: Duplicate found ZAI 20060 id = 09c T = 900.0T Simulation aborted. ----------------------------- Captured stderr call ----------------------------- During handling of the above exception, another exception occurred: Traceback (most recent call last): self = <saltproc.depcode.DepcodeSerpent object at 0x7fed73a0e730>, cores = 1
saltproc/depcode.py:586: timeout = None
../enter/lib/python3.8/subprocess.py:411: input = None, capture_output = False, timeout = None, check = True
E subprocess.CalledProcessError: Command '('sss2', '-omp', '1', '/home/pc07/SALTPROC/saltproc/tests/integration_tests/no_repro/int_test')' returned non-zero exit status 255. ../enter/lib/python3.8/subprocess.py:512: CalledProcessError During handling of the above exception, another exception occurred:
saltproc/tests/integration_tests/no_repro/test_no_reproc_run.py:97: saltproc/tests/integration_tests/no_repro/test_no_reproc_run.py:70: in runsim_no_reproc self = <saltproc.depcode.DepcodeSerpent object at 0x7fed73a0e730>, cores = 1
E RuntimeError: saltproc/depcode.py:592: RuntimeError Step #1 has been started _ .-=-. .-=-. .-==-. Serpent 2 beta A Continuous-energy Monte Carlo Reactor Physics Burnup Calculation Code
Begin calculation on Tue Jul 26 08:54:02 2022 Reading input file "/home/pc07/SALTPROC/saltproc/tests/integration_tests/no_repro/int_test"... Checking duplicate input definitions... Dividing burnable materials... Creating geometry... Counting geometry zones... ***** Warning: Universe 6 is used at multiple levels (4 and 5) ***** Warning: Universe 7 is used at multiple levels (4 and 5) ***** Warning: Universe 5 is used at multiple levels (2 and 5) ***** Warning: Universe 2 is used at multiple levels (1 and 4) The geometry consists of 6 levels: Level 0 size: max 9 zones Processing cells... Linking materials to geometry... Counting cells... Processing data for group constant generation:
Reading ACE directory files... Reading decay data files... ***** Tue Jul 26 08:54:02 2022 (seed = 46549345296) Suspicious line spectrum energy 0.000000E+00 (ZAI = 190360) ***** Tue Jul 26 08:54:02 2022 (seed = 46549345296) Suspicious line spectrum energy 0.000000E+00 (ZAI = 190360) ***** Tue Jul 26 08:54:02 2022 (seed = 46549345296) Suspicious line spectrum energy 0.000000E+00 (ZAI = 190360) ***** Tue Jul 26 08:54:02 2022 (seed = 46549345296) Suspicious line spectrum energy 0.000000E+00 (ZAI = 190360) ***** Tue Jul 26 08:54:02 2022 (seed = 46549345296) Suspicious line spectrum energy 0.000000E+00 (ZAI = 190360) ***** Tue Jul 26 08:54:02 2022 (seed = 46549345296) Sum of decay branching ratios is 0.450000 (ZAI = 771690) ***** Tue Jul 26 08:54:02 2022 (seed = 46549345296) Sum of decay branching ratios is 0.940000 (ZAI = 791730) ***** Tue Jul 26 08:54:02 2022 (seed = 46549345296) Sum of decay branching ratios is 0.910000 (ZAI = 1022510) ***** Tue Jul 26 08:54:02 2022 (seed = 46549345296) Sum of decay branching ratios is 0.850000 (ZAI = 1022570) OK. Reading neutron-induced fission yields... Reading spontaneous fission yields... Adding nuclides in material fuel... Nuclide 1001.09c -- hydrogen at 900K (H-1) Adding nuclides in material ctrlPois... Adding nuclides in material zrh... Adding nuclides in material sic... Nuclide 6000.09c -- natural carbon at 900K (C-nat) Adding nuclides in material hast... Nuclide 28058.09c -- nickel 58 at 900K (Ni-58) Adding nuclides in material air... Adding activation products... Nuclide 20044.09c -- calcium 44 at 900K (Ca-44) Adding actinide data... Adding fission product data... Adding remaining data and forming paths... Running Doppler-broadening preprocessor: Adding thermal scattering data... Nuclide hzr05.32t -- hydrogen at 800K (H-1) Checking data and printing output... ***** Tue Jul 26 08:54:20 2022:
Fatal error in function CheckNuclideData: Duplicate found ZAI 20060 id = 09c T = 900.0T Simulation aborted. =========================== short test summary info ============================ |
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Hi @Suharyana61, thank you for the error report. I saw the following error reported by Serpent2 in both of the integration tests: This is a bug in Serpent2 and is not related to SaltProc. I see you are using Serpent 2.1.28. Please update to the latest version of Serpent2 if possible. If the problem persists after that, or you are unable to upgrade, you should make a post on the serpent forums and ask for help there on how to fix this bug. P.S. The bugs linked on this page may be related to your issue. |
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Thank you very much for your comment, it's very helpful. I will upgrade my Serpent to the latest version. Greetings from Indonesia. |
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Hello @Suharyana61, were you able to update your Serpent version? If so, were you able to get the simulation to work? |
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I just updated my Serpent version, 2.1.32 a couple hours ago, but failed running the pytest. Thank you very much (base) pc07@PC-07:~/SALTPROC$ pytest saltproc saltproc/tests/test_app.py ...... [ 17%] =================================== FAILURES ===================================
saltproc/tests/integration_tests/const_repr/test_const_reproc_run.py:125: popenargs = (['python', 'saltproc', '-i', 'saltproc/tests/integration_tests/const_repr/tap_main_test.json'],)
E subprocess.CalledProcessError: Command '['python', 'saltproc', '-i', 'saltproc/tests/integration_tests/const_repr/tap_main_test.json']' returned non-zero exit status 1. ../enter/lib/python3.8/subprocess.py:364: CalledProcessError Step #1 has been started
saltproc/tests/integration_tests/no_repro/test_no_reproc_run.py:97: saltproc/tests/integration_tests/no_repro/test_no_reproc_run.py:70: in runsim_no_reproc self = <subprocess.Popen object at 0x7f9d978ccd00>
E PermissionError: [Errno 13] Permission denied: 'sss2' ../enter/lib/python3.8/subprocess.py:1702: PermissionError Step #1 has been started What should I do? Thank you very much |
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Ups I'm sorry I was wrong. My report above is not accurate. After I refresh my computer after updating, I re-run the pytest but still failed. Is the failures caused by my desktop does not have memory? Below the complete report after i run the pytest with my Serpent 2.1.32 version (base) pc07@PC-07:~/SALTPROC$ pytest saltproc saltproc/tests/test_app.py ...... [ 17%] =================================== FAILURES ===================================
saltproc/tests/integration_tests/const_repr/test_const_reproc_run.py:125: popenargs = (['python', 'saltproc', '-i', 'saltproc/tests/integration_tests/const_repr/tap_main_test.json'],)
E subprocess.CalledProcessError: Command '['python', 'saltproc', '-i', 'saltproc/tests/integration_tests/const_repr/tap_main_test.json']' returned non-zero exit status 1. ../enter/lib/python3.8/subprocess.py:364: CalledProcessError Step #1 has been started _ .-=-. .-=-. .-==-. Serpent 2 beta A Continuous-energy Monte Carlo Reactor Physics Burnup Calculation Code
Begin calculation on Wed Sep 14 12:30:19 2022 at PC-07 Reading input file "/home/pc07/SALTPROC/saltproc/tests/integration_tests/const_repr/./data/saltproc_serpent"... ***** Warning: Serpent 1 input option stabcut on line 54 of file /home/pc07/SALTPROC/saltproc/tests/integration_tests/const_repr/./data/saltproc_serpent not used Checking duplicate input definitions... Dividing burnable materials... Creating geometry... Counting geometry zones... ***** Warning: Universe 7 is used at multiple levels (5 and 4) ***** Warning: Universe 6 is used at multiple levels (4 and 5) ***** Warning: Universe 5 is used at multiple levels (2 and 5) The geometry consists of 6 levels: Level 0 size: max 11 zones Processing cells... Linking materials to geometry... Processing detector definitions... Counting cells... Processing data for group constant generation:
Reading ACE directory files... Reading radioactive decay data files... ***** Wed Sep 14 12:30:19 2022 (seed = 7812324546562) Sum of decay branching ratios is 0.450000 (ZAI = 771690) ***** Wed Sep 14 12:30:19 2022 (seed = 7812324546562) Sum of decay branching ratios is 0.940000 (ZAI = 791730) ***** Wed Sep 14 12:30:20 2022 (seed = 7812324546562) Sum of decay branching ratios is 0.910000 (ZAI = 1022510) ***** Wed Sep 14 12:30:20 2022 (seed = 7812324546562) Sum of decay branching ratios is 0.850000 (ZAI = 1022570) OK. Reading neutron-induced fission yields... Reading spontaneous fission yields... Adding nuclides in material fuel... Nuclide 1001.09c -- hydrogen at 900K (H-1) Adding nuclides in material ctrlPois... Adding nuclides in material zrh... Adding nuclides in material sic... Nuclide 6000.09c -- natural carbon at 900K (C-nat) Adding nuclides in material hast... Nuclide 28058.09c -- nickel 58 at 900K (Ni-58) Adding nuclides in material air... Adding activation products... Nuclide 20044.09c -- calcium 44 at 900K (Ca-44) Adding actinide data... Adding fission product data... Nuclide 38084.09c -- strontium 84 at 900K (Sr-84) Adding remaining data and forming paths... OK. Running Doppler-broadening preprocessor: Adding thermal scattering data... Nuclide hzr05.32t -- hydrogen at 800K (H-1) Interpolating to 900.00K... Checking data and printing output... Adding all nuclides in inventory list... Generating unionize energy grids... Adding points: 1001.09c -- Points added in neutron grid: 693 Performing grid thinning for neutron grid:
OK. Processing cross sections and ENDF reaction laws... Nuclide 1001.09c -- hydrogen at 900K (H-1) ----------------------------- Captured stderr call ----------------------------- During handling of the above exception, another exception occurred: Traceback (most recent call last): self = <saltproc.depcode.DepcodeSerpent object at 0x7fa357ba7af0>, cores = 1
saltproc/depcode.py:586: timeout = None
../enter/lib/python3.8/subprocess.py:411: input = None, capture_output = False, timeout = None, check = True
E subprocess.CalledProcessError: Command '('sss2', '-omp', '1', '/home/pc07/SALTPROC/saltproc/tests/integration_tests/no_repro/int_test')' died with <Signals.SIGSEGV: 11>. ../enter/lib/python3.8/subprocess.py:512: CalledProcessError During handling of the above exception, another exception occurred:
saltproc/tests/integration_tests/no_repro/test_no_reproc_run.py:97: saltproc/tests/integration_tests/no_repro/test_no_reproc_run.py:70: in runsim_no_reproc self = <saltproc.depcode.DepcodeSerpent object at 0x7fa357ba7af0>, cores = 1
E RuntimeError: saltproc/depcode.py:592: RuntimeError Step #1 has been started _ .-=-. .-=-. .-==-. Serpent 2 beta A Continuous-energy Monte Carlo Reactor Physics Burnup Calculation Code
Begin calculation on Wed Sep 14 12:33:00 2022 at PC-07 Reading input file "/home/pc07/SALTPROC/saltproc/tests/integration_tests/no_repro/int_test"... Checking duplicate input definitions... Dividing burnable materials... Creating geometry... Counting geometry zones... ***** Warning: Universe 6 is used at multiple levels (4 and 5) ***** Warning: Universe 7 is used at multiple levels (4 and 5) ***** Warning: Universe 5 is used at multiple levels (2 and 5) ***** Warning: Universe 2 is used at multiple levels (1 and 4) The geometry consists of 6 levels: Level 0 size: max 9 zones Processing cells... Linking materials to geometry... Processing detector definitions... Counting cells... Processing data for group constant generation:
Reading ACE directory files... Reading radioactive decay data files... ***** Wed Sep 14 12:33:02 2022 (seed = 46549345296) Sum of decay branching ratios is 0.450000 (ZAI = 771690) ***** Wed Sep 14 12:33:02 2022 (seed = 46549345296) Sum of decay branching ratios is 0.940000 (ZAI = 791730) ***** Wed Sep 14 12:33:02 2022 (seed = 46549345296) Sum of decay branching ratios is 0.910000 (ZAI = 1022510) ***** Wed Sep 14 12:33:02 2022 (seed = 46549345296) Sum of decay branching ratios is 0.850000 (ZAI = 1022570) OK. Reading neutron-induced fission yields... Reading spontaneous fission yields... Adding nuclides in material fuel... Nuclide 1001.09c -- hydrogen at 900K (H-1) Adding nuclides in material ctrlPois... Adding nuclides in material zrh... Adding nuclides in material sic... Nuclide 6000.09c -- natural carbon at 900K (C-nat) Adding nuclides in material hast... Nuclide 28058.09c -- nickel 58 at 900K (Ni-58) Adding nuclides in material air... Adding activation products... Nuclide 20044.09c -- calcium 44 at 900K (Ca-44) Adding actinide data... Adding fission product data... Nuclide 38084.09c -- strontium 84 at 900K (Sr-84) Adding remaining data and forming paths... OK. Running Doppler-broadening preprocessor: Adding thermal scattering data... Nuclide hzr05.32t -- hydrogen at 800K (H-1) Interpolating to 900.00K... Checking data and printing output... Adding all nuclides in inventory list... Generating unionize energy grids... Adding points: 1001.09c -- Points added in neutron grid: 693 Performing grid thinning for neutron grid:
OK. Processing cross sections and ENDF reaction laws... Nuclide 1001.09c -- hydrogen at 900K (H-1) =========================== short test summary info ============================ |
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Hi @Suharyana61 This appears to be an issue with your Serpent2 installation. I'd recommend asking the folks at the Serpent forums for assistance. |
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Also, if you are on Ubuntu, you could try using this installer I wrote to install serpent 2.1.32 and apply some patches that may fix the issue you are running into |
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Hi, thank you very much for your guidance. Finished SERPENT Run Storing material data for depletion step #5. Mass and volume of fuel before reproc: 219999750.600000 g, 44353000.000000 cm3 Process: sparger, divisor=1.0 Process: entrainment_separator, divisor=1.0 Process: nickel_filter, divisor=1.0 Process: bypass, divisor=0.9 Process: heat_exchanger, divisor=1.0 Process: core_inlet, divisor=1.0 Process: core_outlet, divisor=1.0 Process: sparger, divisor=1.0 Process: entrainment_separator, divisor=1.0 Process: nickel_filter, divisor=1.0 Process: liquid_metal, divisor=0.1 Process: heat_exchanger, divisor=1.0 Process: core_inlet, divisor=1.0 1 Materal mass on path 0: 197998896.2535113 Mass and volume of fuel after reproc: 219998525.752663 g, 44352753.064929 cm3 Mass and volume of fuel after REFILL: 219999750.600000 g, 44353000.000000 cm3 Storing material data for depletion step #5. Time at the end of current depletion step: 10.000000d (saltproc-env) mint-pc3@mintpc3-MS-7C56:~/saltproc$ |
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Hi @Suharyana61,
This again sounds like a Serpent error, but it could be on the SaltProc side. Please give me the error message you get from the program. If you could use code formatting blocks for the error instead of having it in plain text along with the rest of your message, that will help me differentiate between the error and your own writing. |
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Hi @Suharyana61, sorry for the long wait. I made a PR a while back to fix this issue. Please let me know if it works in the most recent SaltProc version |
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Hi, I'm interested in Saltproc and I have installed it. When I run the mbsr example input file, a message appear:
File "/home/pc07/enter/lib/python3.8/site-packages/saltproc/depcode.py", line 466, in read_depcode_info
self.sim_info['depletion_timestep'] = res['BURN_DAYS'][1][0]
IndexError: invalid index to scalar variable.
Could you please let me know what should I do? Thank you very much
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