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simple detector example

Runtime Mavericks ROOT/python issue with root-5.34.11 AVOIDED

(chroma_env)delta:test blyth$ python -i
Python 2.7.6 (default, Nov 18 2013, 15:12:51)
[GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.2.79)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from chroma.io.root import RootWriter
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/env/chroma_env/src/chroma/chroma/io/root.py", line 6, in <module>
    from chroma.rootimport import ROOT
  File "/usr/local/env/chroma_env/src/chroma/chroma/rootimport.py", line 6, in <module>
    import ROOT
  File "/usr/local/env/chroma_env/src/root-v5.34.11/lib/ROOT.py", line 257, in <module>
    _root.gPad         = _ExpandMacroFunction( "TVirtualPad",  "Pad" )
  File "/usr/local/env/chroma_env/src/root-v5.34.11/lib/ROOT.py", line 237, in __init__
    c = _root.MakeRootClass( klass )
AttributeError: type object 'string' has no attribute 'c_str'
>>>
  • http://root.cern.ch/phpBB3/viewtopic.php?f=14&t=17238
    • suggests this issue fixed after root-5.34.11
  • Moving to 5.34.14 avoids this issue, but get a freetype build issue, using internal freetype in configure chroma-kludge-root avoids that. Fix is expected in as yet unreleased 5.34.15

Runtime hang, probably zmq ? INVALID

Nope, this was just waiting around to close a hidden mathplotlib window. How zmq being used is still a bit mysterious.

Initially suspected issue with zmq, starts 5 processes which dont take CPU and seems to hang.:

blyth           39070   0.0  0.8  2778456 136152 s010  S+    2:06PM   0:02.19 python ./simple_detector.py
blyth           39069   0.0  1.0  2798476 159416 s010  S+    2:06PM   0:02.01 python ./simple_detector.py
blyth           39068   0.0  0.9  2796412 143680 s010  S+    2:06PM   0:01.73 python ./simple_detector.py
blyth           39067   0.0  1.0  2804252 159648 s010  S+    2:06PM   0:01.96 python ./simple_detector.py
blyth           39063   0.0  2.8 32545740 468452 s010  S+    2:06PM   0:05.30 python ./simple_detector.py

After 10 mins of seemingly hanging interrupted and then killed by closing tab:

(chroma_env)delta:test blyth$ ./simple_detector.py
Info in <TUnixSystem::ACLiC>: creating shared library /Users/blyth/.chroma/root_C.so

RooFit v3.59 -- Developed by Wouter Verkerke and David Kirkby
                Copyright (C) 2000-2013 NIKHEF, University of California & Stanford University
                All rights reserved, please read http://roofit.sourceforge.net/license.txt


^CProcess G4GeneratorProcess-2:
Process G4GeneratorProcess-3:
Process G4GeneratorProcess-4:
Process G4GeneratorProcess-1:
Traceback (most recent call last):
Traceback (most recent call last):
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
    self.run()
    self.run()
    self.run()
  File "/usr/local/env/chroma_env/src/chroma/chroma/generator/photon.py", line 32, in run
  File "/usr/local/env/chroma_env/src/chroma/chroma/generator/photon.py", line 32, in run
  File "/usr/local/env/chroma_env/src/chroma/chroma/generator/photon.py", line 32, in run
  File "/usr/local/env/chroma_env/src/chroma/chroma/generator/photon.py", line 32, in run
    ev = vertex_socket.recv_pyobj()
    ev = vertex_socket.recv_pyobj()
    ev = vertex_socket.recv_pyobj()
  File "/usr/local/env/chroma_env/lib/python2.7/site-packages/zmq/sugar/socket.py", line 344, in recv_pyobj
  File "/usr/local/env/chroma_env/lib/python2.7/site-packages/zmq/sugar/socket.py", line 344, in recv_pyobj
    ev = vertex_socket.recv_pyobj()
  File "/usr/local/env/chroma_env/lib/python2.7/site-packages/zmq/sugar/socket.py", line 344, in recv_pyobj
  File "/usr/local/env/chroma_env/lib/python2.7/site-packages/zmq/sugar/socket.py", line 344, in recv_pyobj
    s = self.recv(flags)
    s = self.recv(flags)
  File "socket.pyx", line 622, in zmq.backend.cython.socket.Socket.recv (zmq/backend/cython/socket.c:5403)
    s = self.recv(flags)
  File "socket.pyx", line 622, in zmq.backend.cython.socket.Socket.recv (zmq/backend/cython/socket.c:5403)
  File "socket.pyx", line 622, in zmq.backend.cython.socket.Socket.recv (zmq/backend/cython/socket.c:5403)
    s = self.recv(flags)
  File "socket.pyx", line 622, in zmq.backend.cython.socket.Socket.recv (zmq/backend/cython/socket.c:5403)
  File "socket.pyx", line 656, in zmq.backend.cython.socket.Socket.recv (zmq/backend/cython/socket.c:5222)
  File "socket.pyx", line 656, in zmq.backend.cython.socket.Socket.recv (zmq/backend/cython/socket.c:5222)
  File "socket.pyx", line 656, in zmq.backend.cython.socket.Socket.recv (zmq/backend/cython/socket.c:5222)
  File "socket.pyx", line 656, in zmq.backend.cython.socket.Socket.recv (zmq/backend/cython/socket.c:5222)
  File "socket.pyx", line 139, in zmq.backend.cython.socket._recv_copy (zmq/backend/cython/socket.c:1711)
  File "socket.pyx", line 139, in zmq.backend.cython.socket._recv_copy (zmq/backend/cython/socket.c:1711)
  File "checkrc.pxd", line 11, in zmq.backend.cython.checkrc._check_rc (zmq/backend/cython/socket.c:5713)
  File "checkrc.pxd", line 11, in zmq.backend.cython.checkrc._check_rc (zmq/backend/cython/socket.c:5713)
  File "socket.pyx", line 139, in zmq.backend.cython.socket._recv_copy (zmq/backend/cython/socket.c:1711)
  File "socket.pyx", line 139, in zmq.backend.cython.socket._recv_copy (zmq/backend/cython/socket.c:1711)
  File "/usr/local/env/chroma_env/lib/python2.7/site-packages/Geant4/__init__.py", line 242, in _run_abort
  File "/usr/local/env/chroma_env/lib/python2.7/site-packages/Geant4/__init__.py", line 242, in _run_abort
  File "checkrc.pxd", line 11, in zmq.backend.cython.checkrc._check_rc (zmq/backend/cython/socket.c:5713)
  File "checkrc.pxd", line 11, in zmq.backend.cython.checkrc._check_rc (zmq/backend/cython/socket.c:5713)
    raise KeyboardInterrupt
    raise KeyboardInterrupt
KeyboardInterrupt
KeyboardInterrupt
  File "/usr/local/env/chroma_env/lib/python2.7/site-packages/Geant4/__init__.py", line 242, in _run_abort
  File "/usr/local/env/chroma_env/lib/python2.7/site-packages/Geant4/__init__.py", line 242, in _run_abort
    raise KeyboardInterrupt
KeyboardInterrupt
    raise KeyboardInterrupt
KeyboardInterrupt

XQuartz DISPLAY issue : RESOLVED

Initially xclock and root fail to work saying:

root: can't figure out DISPLAY, set it manually
In case you run a remote ssh session, restart your ssh session with:
=========>  ssh -Y

Resolved by logging out and back in again, following the XQuartz install.

zombie test.root file : INVALID

This was due to the above “hang” and killing the session.

(chroma_env)delta:test blyth$ root test.root
  *******************************************
  *                                         *
  *        W E L C O M E  to  R O O T       *
  *                                         *
  *   Version   5.34/14  16 December 2013   *
  *                                         *
  *  You are welcome to visit our Web site  *
  *          http://root.cern.ch            *
  *                                         *
  *******************************************

ROOT 5.34/14 (v5-34-14@v5-34-14, Dec 16 2013, 12:23:58 on macosx64)

CINT/ROOT C/C++ Interpreter version 5.18.00, July 2, 2010
Type ? for help. Commands must be C++ statements.
Enclose multiple statements between { }.
root [0]
Attaching file test.root as _file0...
Warning in <TFile::Init>: file test.root probably not closed, trying to recover
Warning in <TFile::Init>: no keys recovered, file has been made a Zombie
root [1]
root [1]

working

Curiously try again with some logging added and it seems to work. Order 10 “Photon hit time” matplotlib windows are popped up. Have to close them in turn for script to complete:

(chroma_env)delta:test blyth$ ./simple_detector.py
INFO:__main__:start other import
INFO:__main__:after import
INFO:__main__:starting
INFO:__main__:build_detector
INFO:chroma:Flattening detector mesh...
INFO:chroma:  triangles: 107928
INFO:chroma:  vertices:  44970
INFO:__main__:load_bvh
INFO:chroma:Loading BVH "default" for geometry from cache.
INFO:chroma:Optimization: Sufficient memory to move triangles onto GPU
INFO:chroma:Optimization: Sufficient memory to move vertices onto GPU
INFO:chroma:device usage:
----------
nodes           142.2K   2.3M
total                    2.3M
----------
device total             2.1G
device used            157.5M
device free              2.0G

INFO:__main__:start photon_bomb simulation
INFO:__main__:ev <chroma.event.Event object at 0x112a7a190>
INFO:__main__:start gun simulation
(chroma_env)delta:test blyth$

A root file is created:

(chroma_env)delta:test blyth$ du -h test.root
253M    test.root

Examining distributions in root with TBrowser shows a lot of distributions suggesting the propagation is working:

root [7] TBrowser b

with more logging

(chroma_env)delta:test blyth$ ./simple_detector.py
INFO:__main__:start simple_detector
INFO:__main__:after imports
INFO:__main__:after first defs
INFO:__main__:after second defs
INFO:__main__:starting main
INFO:__main__:after main imports
INFO:__main__:after build_detector
INFO:chroma:Flattening detector mesh...
INFO:chroma:  triangles: 107928
INFO:chroma:  vertices:  44970
INFO:__main__:after flatten
INFO:chroma:Loading BVH "default" for geometry from cache.
INFO:__main__:after load_bvh
INFO:chroma:Optimization: Sufficient memory to move triangles onto GPU
INFO:chroma:Optimization: Sufficient memory to move vertices onto GPU
INFO:chroma:device usage:
----------
nodes           142.2K   2.3M
total                    2.3M
----------
device total             2.1G
device used            174.1M
device free              2.0G

INFO:__main__:after sim instanciation
INFO:__main__:start photon_bomb simulation
INFO:__main__:ev <chroma.event.Event object at 0x116ce1250>
INFO:__main__:start gun simulation
INFO:__main__:write ev <chroma.event.Event object at 0x116ce1310>
INFO:__main__:detected [False False False ..., False False False] 328430
INFO:__main__:show plot
INFO:__main__:after show plot
INFO:__main__:write ev <chroma.event.Event object at 0x12c63e710>
INFO:__main__:detected [False False False ..., False  True False] 242802
INFO:__main__:show plot
INFO:__main__:after show plot
INFO:__main__:write ev <chroma.event.Event object at 0x12c6a2090>
INFO:__main__:detected [False False False ..., False False False] 306569
INFO:__main__:show plot
INFO:__main__:after show plot
INFO:__main__:write ev <chroma.event.Event object at 0x12c66ded0>
INFO:__main__:detected [False False False ..., False False False] 327345
INFO:__main__:show plot
INFO:__main__:after show plot
INFO:__main__:write ev <chroma.event.Event object at 0x12c6a23d0>
INFO:__main__:detected [False False False ..., False False False] 336813
INFO:__main__:show plot
INFO:__main__:after show plot
INFO:__main__:write ev <chroma.event.Event object at 0x12c690750>
INFO:__main__:detected [False False False ..., False False False] 391338
INFO:__main__:show plot
INFO:__main__:after show plot
INFO:__main__:write ev <chroma.event.Event object at 0x12c6f3290>
INFO:__main__:detected [False False False ..., False False False] 390456
INFO:__main__:show plot
INFO:__main__:after show plot
INFO:__main__:write ev <chroma.event.Event object at 0x12c738cd0>
INFO:__main__:detected [False False False ..., False False False] 380238
INFO:__main__:show plot
INFO:__main__:after show plot
INFO:__main__:write ev <chroma.event.Event object at 0x12c72fe90>
INFO:__main__:detected [False False False ..., False False False] 328344
INFO:__main__:show plot
INFO:__main__:after show plot
INFO:__main__:write ev <chroma.event.Event object at 0x12c66c810>
INFO:__main__:detected [False False False ..., False False False] 279567
INFO:__main__:show plot
INFO:__main__:after show plot
INFO:__main__:after gun loop
INFO:__main__:after close
(chroma_env)delta:test blyth$