sskutnik/cyborg

Cyclus-Based ORIGEN (CYBORG) - a reactor depletion analysis tool for Cyclus using ORIGEN

cyborg's Issues

Cycamore link broken in README.md

Need to create build / use documentation for Cyborg

Need to update the README.rst to reflect the usage and build options for Cyborg, including how SCALE libraries are found and how to set the ORIGEN library default location.

Eventually need to also add usage documentation.

CYBORG build error with Find_QT

After successfully locating the SCALE directory, the CYBORG build outputs this error message:

dkadkf@arfc-100 ~/github/cyborg (master) $ python install.py --orglib_root=~/SCALE-6.2.2/data/arplibs
/usr/bin/cmake
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- CMake Build type: 
-- Using /home/dkadkf/.local as CYCLUS_ROOT_DIR.
-- Found Cyclus Core Headers : /home/dkadkf/.local/include/cyclus
-- Found Cyclus Core Test Headers : /home/dkadkf/.local/include/cyclus
-- Found Cyclus Core Shared Data : /home/dkadkf/.local/share/cyclus
-- Found Cyclus Core Library : /home/dkadkf/.local/lib/libcyclus.so
-- Found Cyclus Test Libraries : /home/dkadkf/.local/lib/cyclus/libgtest.so/home/dkadkf/.local/lib/cyclus/libbaseagentunittests.so
-- LibXML++ find package args: LibXml2;REQUIRED
-- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.3") 
-- LibXML++ find package args: Glibmm;REQUIRED
-- Glibmm find package args: Glib;REQUIRED
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") 
-- Checking for module 'glib-2.0'
--   Found glib-2.0, version 2.48.2
-- Found glib-2.0: /home/dkadkf/anaconda3/include/glib-2.0, /home/dkadkf/anaconda3/lib/libglib-2.0.so
-- Glibmm find package args: SigC++;REQUIRED
-- Checking for module 'sigc++-2.0'
--   Found sigc++-2.0, version 2.6.2
-- Found SigC++ 
-- Checking for module 'glibmm-2.4'
--   Found glibmm-2.4, version 2.46.3
-- Found Glibmm 
-- Checking for module 'libxml++-2.6'
--   Found libxml++-2.6, version 2.40.1
-- Found LibXML++ 
--LIBS: /home/dkadkf/.local/lib/libcyclus.so;/usr/lib/x86_64-linux-gnu/libxml++-2.6.so;/usr/lib/x86_64-linux-gnu/libxml2.so;/usr/lib/x86_64-linux-gnu/libglibmm-2.4.so;/home/dkadkf/anaconda3/lib/libglib-2.0.so;/usr/lib/x86_64-linux-gnu/libsigc-2.0.so
--LD_LIBRARY_PATH: 
-- Boost version: 1.58.0
-- Found the following Boost libraries:
--   program_options
--   filesystem
--   system
--    Boost Root: 
--    Boost Include directory: /usr/include
--    Boost Library directories: /usr/lib/x86_64-linux-gnu
--    Boost Program Options location: /usr/lib/x86_64-linux-gnu/libboost_program_options.so
--    Boost Filesystem location: /usr/lib/x86_64-linux-gnu/libboost_filesystem.so
--    Boost Serialization location: 
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- A library with BLAS API found.
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
	Found LAPACK Libraries: /usr/lib/liblapack.so;/usr/lib/libblas.so
-- Found HDF5: /home/dkadkf/anaconda3/lib/libhdf5_hl.so;/home/dkadkf/anaconda3/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/dkadkf/anaconda3/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so  
--    HDF5 Root: 
--    HDF5 Include directory: /home/dkadkf/anaconda3/include
--    HDF5 Library directories: /home/dkadkf/anaconda3/lib
--    HDF5 Libraries: /home/dkadkf/anaconda3/lib/libhdf5_hl.so;/home/dkadkf/anaconda3/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/home/dkadkf/anaconda3/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- Found Sqlite3 header file in /home/dkadkf/anaconda3/include
-- Found Sqlite3 libraries: /home/dkadkf/anaconda3/lib/libsqlite3.so
--    SQLITE3 Include directories: /home/dkadkf/anaconda3/include
--    SQLITE3 Libraries: /home/dkadkf/anaconda3/lib/libsqlite3.so
CMake Error at CMakeLists.txt:155 (include):
  include called with wrong number of arguments.  include() only takes one
  file.


-- Using /home/dkadkf/SCALE-6.2.2 as SCALE_ROOT_DIR.
SCALE_INCLUDE_DIR: /home/dkadkf/SCALE-6.2.2/include
SCALE JSON LIBRARY: /home/dkadkf/SCALE-6.2.2/lib/libStandard_Json.so
-- Found SCALE Headers: /home/dkadkf/SCALE-6.2.2/include
-- Found SCALE Libraries: /home/dkadkf/SCALE-6.2.2/lib/libScaleUtils_IO.so/home/dkadkf/SCALE-6.2.2/lib/libStandard_Json.so/home/dkadkf/SCALE-6.2.2/lib/libOrigenCore.so/home/dkadkf/SCALE-6.2.2/lib/libOrigenSolver.so
-- Setting ORGLIB_DIR to: /home/dkadkf/SCALE-6.2.2/data/arplibs
-- Starting construction of build files for agent: reactor
-- Copying /home/dkadkf/github/cyborg/src/cyclus_origen_interface.h to /home/dkadkf/github/cyborg/build/cyborg/cyclus_origen_interface.h.
-- Copying /home/dkadkf/github/cyborg/src/orglib_default_location.h to /home/dkadkf/github/cyborg/build/cyborg/orglib_default_location.h.
dstcustomheaders: cyclus_origen_interface.h;orglib_default_location.h
-- Executing /home/dkadkf/.local/include/cyclus/../../bin/cycpp.py /home/dkadkf/github/cyborg/src/reactor.cc --cpp-path=cpp -o=/home/dkadkf/github/cyborg/build/cyborg/reactor.cc --pass3-use-orig -I=:/home/dkadkf/SCALE-6.2.2/include:/home/dkadkf/.local/include/cyclus:/usr/include/libxml++-2.6:/usr/include/glibmm-2.4:/usr/lib/x86_64-linux-gnu/glibmm-2.4/include:/home/dkadkf/anaconda3/include/glib-2.0:/usr/lib/x86_64-linux-gnu/glib-2.0/include:/usr/include/sigc++-2.0:/usr/lib/x86_64-linux-gnu/sigc++-2.0/include:/usr/lib/x86_64-linux-gnu/libxml++-2.6/include:/usr/include:/home/dkadkf/anaconda3/include:/home/dkadkf/anaconda3/include:/home/dkadkf/github/cyborg/src
Traceback (most recent call last):
  File "/home/dkadkf/.local/include/cyclus/../../bin/cycpp.py", line 2369, in <module>
    main()
  File "/home/dkadkf/.local/include/cyclus/../../bin/cycpp.py", line 2353, in main
    context, superclasses = accumulate_state(canon)   # pass 2
  File "/home/dkadkf/.local/include/cyclus/../../bin/cycpp.py", line 908, in accumulate_state
    state.accumulate(statement, sep)
  File "/home/dkadkf/.local/include/cyclus/../../bin/cycpp.py", line 714, in accumulate
    filter.transform(statement, sep)
  File "/home/dkadkf/.local/include/cyclus/../../bin/cycpp.py", line 475, in transform
    state.var_annotations = self._eval()
  File "/home/dkadkf/.local/include/cyclus/../../bin/cycpp.py", line 454, in _eval
    self._add_gbl_proxies(glb, clspaths, val['vars'])
KeyError: 'vars'
CMake Error at /home/dkadkf/.local/share/cyclus/cmake/UseCyclus.cmake:128 (message):
  cycpp failed on '/home/dkadkf/github/cyborg/src/reactor.cc' with exit code
  '1'
Call Stack (most recent call first):
  src/CMakeLists.txt:53 (USE_CYCLUS)


-- Configuring incomplete, errors occurred!
See also "/home/dkadkf/github/cyborg/build/CMakeFiles/CMakeOutput.log".
See also "/home/dkadkf/github/cyborg/build/CMakeFiles/CMakeError.log".
Traceback (most recent call last):
  File "install.py", line 142, in <module>
    main()
  File "install.py", line 139, in main
    install(args)
  File "install.py", line 64, in install
    shell=(os.name == 'nt'))
  File "/home/dkadkf/anaconda3/lib/python3.6/subprocess.py", line 291, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['cmake', '/home/dkadkf/github/cyborg', '-DCMAKE_INSTALL_PREFIX=/home/dkadkf/.local', '-DCYCLUS_ROOT_DIR=/home/dkadkf/.local', '-DUSER_ORGLIB_DIR=/home/dkadkf/SCALE-6.2.2/data/arplibs']' returned non-zero exit status 1.

Tagged libraries fail?

@sskutnik
Error Message with libraries?
arp2obl.py script was (i think) successful (here)

dkadkf@arfc-100 ~/github/cyborg/inputs/MOX-BWR (master) $ cyclus MOX_src_1_Reactor_1_year.xml 
              :                                                               
          .CL:CC CC             _Q     _Q  _Q_Q    _Q    _Q              _Q   
        CC;CCCCCCCC:C;         /_\)   /_\)/_/\\)  /_\)  /_\)            /_\)  
        CCCCCCCCCCCCCl       __O|/O___O|/O_OO|/O__O|/O__O|/O____________O|/O__
     CCCCCCf     iCCCLCC     /////////////////////////////////////////////////
     iCCCt  ;;;;;.  CCCC                                                      
    CCCC  ;;;;;;;;;. CClL.                          c                         
   CCCC ,;;       ;;: CCCC  ;                   : CCCCi                       
    CCC ;;         ;;  CC   ;;:                CCC`   `C;                     
  lCCC ;;              CCCC  ;;;:             :CC .;;. C;   ;    :   ;  :;;   
  CCCC ;.              CCCC    ;;;,           CC ;    ; Ci  ;    :   ;  :  ;  
   iCC :;               CC       ;;;,        ;C ;       CC  ;    :   ; .      
  CCCi ;;               CCC        ;;;.      .C ;       tf  ;    :   ;  ;.    
  CCC  ;;               CCC          ;;;;;;; fC :       lC  ;    :   ;    ;:  
   iCf ;;               CC         :;;:      tC ;       CC  ;    :   ;     ;  
  fCCC :;              LCCf      ;;;:         LC :.  ,: C   ;    ;   ; ;   ;  
  CCCC  ;;             CCCC    ;;;:           CCi `;;` CC.  ;;;; :;.;.  ; ,;  
    CCl ;;             CC    ;;;;              CCC    CCL                     
   tCCC  ;;        ;; CCCL  ;;;                  tCCCCC.                      
    CCCC  ;;     :;; CCCCf  ;                     ,L                          
     lCCC   ;;;;;;  CCCL                                                      
     CCCCCC  :;;  fCCCCC                                                      
      . CCCC     CCCC .                                                       
       .CCCCCCCCCCCCCi                                                        
          iCCCCCLCf                                                           
           .  C. ,                                                            
              :                                                               
Experimental Warning: MatlSellPolicy is experimental and its API may be subject to change
Experimental Warning: The CyBORG Reactor is highly experimental.
Experimental Warning: MatlSellPolicy is experimental and its API may be subject to change
Experimental Warning: The CyBORG Reactor is highly experimental.
Experimental Warning: MatlSellPolicy is experimental and its API may be subject to change
Experimental Warning: The CyBORG Reactor is highly experimental.
Experimental Warning: MatlSellPolicy is experimental and its API may be subject to change
Experimental Warning: The CyBORG Reactor is highly experimental.
Experimental Warning: MatlSellPolicy is experimental and its API may be subject to change
Experimental Warning: The CyBORG Reactor is highly experimental.
Interp tag name: Plutonium Content, value: 4.50005.
Interp tag name: Plutonium-239 Content, value: 61.9993.
Key Warning: Recipe lookup failed: Invalid recipe name {
   "Assembly Type" : "mox_ge10x10-8",
   "Moderator Density" : 0.550,
   "Plutonium Content" : 4.500050000000001,
   "Plutonium-239 Content" : 61.99931111876536,
   "Powers (W)" : "3.33333e+07,0,3.33333e+07,0,3.33333e+07",
   "Times (y)" : "0,1,1.08333,2.08333,2.16667,3.16667"
}

Cyborg::reactor::interpolate(937) : No libraries found that match specified ID tags!

Do you have any ideas what might be wrong?

CyBORG does not appear to be correctly handling fuel discharges

Looks like CyBORG is not discharging fuel correctly; spent fuel commodity in the database is not present, and the input fuel recipe on subsequent cycles appears to be depleted materials (i.e., somehow getting shoved back to the front of the queue instead of being discharged). Need to investigate further.