2 level template error

[shakespeare]

I'm working with the 2LevelImpute ebook, first example in the tutorial in DEEP. When I get down to submitting the job, it throws an error. I can't tell if I made a mistake in the setup, or if there's another problem, e.g., my install. Seems to be saying there's a missing file. I would appreciate guidance on how to resolve the issue. Thx.

Here's the error log:

Traceback (most recent call last): File "ebooktest.py", line 126, in new_resource
File "ebooktest.py", line 236, in new_input File "ebooktest.py", line 265, in check_run
File "ebooktest.py", line 548, in run_input File "ebooktest.py", line 275, in run_model
File "C:\StatJR\packages\Python_script.py", line 71, in run self.eng.run('script.py')
File "O:\StatJR\estat\trunk\src\lib\EStat\engines\Engine.py", line 43, in decorated
File "O:\StatJR\estat\trunk\src\lib\EStat\engines\Python.py", line 16, in run File "", line 187, in
File "O:\StatJR\estat\trunk\src\apps\cmdtest\cmdtest.py", line 128, in RunStatJR
File "C:\StatJR\packages\CustomC.py", line 890, in run self.runcode(str(self.eng.outputs['modelcode.cpp'].content), self.vars[chainnum], self.data)
File "C:\StatJR\packages\CustomC.py", line 563, in runcode extra_compile_args = ['-w', '-O3', '-std=c++11']) File "c:\Python27\lib\site-packages\scipy\weave\inline_tools.py", line 361, in inline
File "c:\Python27\lib\site-packages\scipy\weave\inline_tools.py", line 491, in compile_function
File "c:\Python27\lib\site-packages\scipy\weave\ext_tools.py", line 373, in compile
File "c:\Python27\lib\site-packages\scipy\weave\build_tools.py", line 242
, in build_extension
File "c:\Python27\lib\site-packages\scipy\weave\platform_info.py", line 120, in get_compiler_dir
File "c:\Python27\lib\site-packages\scipy\weave\platform_info.py", line 57, in create_compiler_instance
File "c:\Python27\lib\site-packages\numpy\distutils\ccompiler.py", line 562, in new_compiler
File "c:\Python27\lib\site-packages\numpy\distutils\mingw32ccompiler.py", line 94, in __init__
File "c:\Python27\lib\site-packages\numpy\distutils\mingw32ccompiler.py", line 361, in build_msvcr_library File "c:\Python27\lib\site-packages\numpy\distutils\mingw32ccompiler.py", line 273, in generate_def
File "c:\Python27\lib\site-packages\numpy\distutils\mingw32ccompiler.py", line 265, in dump_table File "c:\Python27\lib\subprocess.py", line 709, in __init__
File "c:\Python27\lib\subprocess.py", line 957, in _execute_child WindowsError: [Error 2] The system cannot find the file specified

[ChrisCharlton]

Can you confirm that Stat-JR is picking up the change in settings recommended in:

http://www.bristol.ac.uk/cmm/software/s ... evelImpute

by opening the TREE interface and clicking the Settings button in the top-right corner of the page?

Under EStat in the subsection eStat executable it should read:

Code: Select all

C:\StatJR\eStat\bin\Release\eStat.exe

(or the equivalent if you have installed Stat-JR elsewhere).

Could you also confirm that you are able to run other models using the TREE interface, as this will confirm whether the compiler, etc are set up correctly?

[shakespeare]

The path is set correctly. What models should I try to run?

[ChrisCharlton]

Could you try a couple of the example models in Chapter 4 of the Stat-JR beginner's guide (http://www.bris.ac.uk/cmm/software/stat ... inners.pdf)?

[shakespeare]

Ok. I tried to run the first example in Chapter 4. I received the error below. Clearly something amiss. My IT team did this install for me, so if there are instructions I can give to them, please forward. Thx.

Traceback (most recent call last): File "webtest.py", line 416, in go
File "C:\StatJR\packages\eStat.py", line 1208, in run self.runcode(str(self.eng.outputs['modelcode.cpp'].content), self.vars[chainnum], self.data)
File "C:\StatJR\packages\eStat.py", line 838, in runcode extra_compile_args = ['-w', '-O3', '-std=c++11' ])
File "c:\Python27\lib\site-packages\scipy\weave\inline_tools.py", line 361, in inline
File "c:\Python27\lib\site-packages\scipy\weave\inline_tools.py", line 491, in compile_function
File "c:\Python27\lib\site-packages\scipy\weave\ext_tools.py", line 373, in compile
File "c:\Python27\lib\site-packages\scipy\weave\build_tools.py", line 242, in build_extension
File "c:\Python27\lib\site-packages\scipy\weave\platform_info.py", line 125, in get_compiler_dir ValueError: The 'gcc' compiler was not found.

[ChrisCharlton]

The error message you are getting indicates that either step 2 or 3 of the instructions at http://www.bris.ac.uk/cmm/software/stat ... stallation hasn't worked. If someone else installed this for you then my guess would be that the correct path (step 3) may not be set for your user account.

[shakespeare]

We found the problem to be an uninstalled compiler. Fixed that and the first example in Chapter 4 works flawlessly. I tried to run the 2-level example and received this error:

Traceback (most recent call last):
File "ebooktest.py", line 126, in new_resource
File "ebooktest.py", line 236, in new_input
File "ebooktest.py", line 265, in check_run
File "ebooktest.py", line 548, in run_input
File "ebooktest.py", line 275, in run_model
File "C:\StatJR\packages\Python_script.py", line 71, in run
self.eng.run('script.py')
File "O:\StatJR\estat\trunk\src\lib\EStat\engines\Engine.py", line 43, in decorated
File "O:\StatJR\estat\trunk\src\lib\EStat\engines\Python.py", line 16, in run
File "", line 259, in
File "c:\Python27\lib\multiprocessing\pool.py", line 554, in get
CompileError: error: c:\users\sc014459\appdata\local\temp\4\tmpzdrka6\virozz: The process cannot access the file because it is being used by another process

I'll try running some of the other examples in Chapter 4, but I'd appreciate feedback if anything obvious jumps out in this error message. To my best knowledge, I have no other software that uses the C++ compiler. Thx.

[ChrisCharlton]

There may be another application on your computer that automatically opens newly created files (a virus scanner may do this for example), so it might be worth checking whether this is the case.

[shakespeare]

Apparently that was the case. I tried running this template again later and it worked. I'm not having so much luck with the 2-level template, however. On Step 2. Specifying the variables in the MOI, I get the following error:

Traceback (most recent call last):
File "ebooktest.py", line 126, in new_resource
File "ebooktest.py", line 236, in new_input
File "ebooktest.py", line 265, in check_run
File "ebooktest.py", line 548, in run_input
File "ebooktest.py", line 275, in run_model
File "C:\StatJR\packages\Python_script.py", line 71, in run
self.eng.run('script.py')
File "O:\StatJR\estat\trunk\src\lib\EStat\engines\Engine.py", line 43, in decorated
File "O:\StatJR\estat\trunk\src\lib\EStat\engines\Python.py", line 16, in run
File "", line 259, in
File "c:\Python27\lib\multiprocessing\pool.py", line 554, in get
KeyError: 's'

I've tried re-running this template repeatedly and received this message. I think I have everything set up correctly, so I'd appreciate feedback on potential corrective action.

[ChrisCharlton]

This may be due to variable naming, do any of your variable names contain underscore characters? If not, could you post the generated input string (you can find this beneath the input questions)?