GrUMPy
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coin-or
easy_install installs an old version.
I found easy_install installed 0.84, while the current version is 0.85. And, the 0.84 version is not working.
Coorection: The version 0.84 I referred was actually 0.8.4.
The latest release version is 0.8.4 (not 0.84). Incidentally, it looks like I never actually tagged 0.8.4 (at least in the version on Github). That should be what you get when you easy_install. There hasn't been a 0.85.0 release yet. I made some substantial changes in recent commits and need to make sure everything is in order before making a first release. It's pure Python, though, so it should work fine if you just clone the repo and do python setup.py install. If you were having trouble with 0.8, though, I doubt 0.85 will be much differents. Can you say what's not working with 0.8.4? When I released it, it seemed to be working.
There are some known issues with xdot and PyGtk on OS X and Linux, which I think will be difficult to resolve. I can give you some advice on that if you are running into those problems. I will try to update the README with some information about this now that you have reminded me of the problem.
Thanks for the reply. You also answered the question I have (in mind) for xdot on OSX.
The version 0.8.4 I could install from easy_install or pip did not work for p0201_GLPK.vbc. So I cloned the master branch and was able to run and visualize on my OSX.
Then I wanted to make it pretty. Assuming that xdot would make the picture prettier, I have installed xdot via brew. Now I am getting this error, even after re-installing coinor.grumpy and xdot several times.
I hope this helps.
By the way, the version described in README of the master branch is 0.85.
Process: Python [95577]
Path: /usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier: org.python.python
Version: 2.7.12 (2.7.12)
Code Type: X86-64 (Native)
Parent Process: bash [83111]
Responsible: iTerm2 [268]
User ID: 501
Date/Time: 2016-12-02 11:26:36.009 -0600
OS Version: Mac OS X 10.10.5 (14F2009)
Report Version: 11
Anonymous UUID: 6713AA5A-D296-6BCD-7FB6-57AB41A9A1B3
Sleep/Wake UUID: 2D1C73D3-8164-441B-B3CE-5F46083260A8
Time Awake Since Boot: 180000 seconds
Time Since Wake: 13000 seconds
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000008
VM Regions Near 0x8:
-->
__TEXT 0000000103c79000-0000000103c7b000 [ 8K] r-x/rwx SM=COW /usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 org.python.python 0x000000010b6cdd35 PyImport_AddModule + 24
1 gurobipy.so 0x000000010b136967 __Pyx_FetchCommonType + 23
2 gurobipy.so 0x000000010b10c99b initgurobipy + 299
Thread 1:: Dispatch queue: com.apple.libdispatch-manager
0 libsystem_kernel.dylib 0x00007fff939c5232 kevent64 + 10
1 libdispatch.dylib 0x00007fff8d68926e _dispatch_mgr_thread + 52
Thread 2:
0 libsystem_kernel.dylib 0x00007fff939c494a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff86c093dd start_wqthread + 13
Thread 3:
0 libsystem_kernel.dylib 0x00007fff939c494a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff86c093dd start_wqthread + 13
Thread 4:
0 libsystem_kernel.dylib 0x00007fff939c494a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff86c093dd start_wqthread + 13
Thread 5:
0 libsystem_kernel.dylib 0x00007fff939c494a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff86c093dd start_wqthread + 13
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000000000000 rcx: 0x0000000000000001 rdx: 0x0000000000000003
rdi: 0x000000010b22ff01 rsi: 0x0000000000000010 rbp: 0x00007fff5bf83c30 rsp: 0x00007fff5bf83c10
r8: 0x000000010b78e030 r9: 0x000000010b790088 r10: 0x0000000000000000 r11: 0x00000000000880b9
r12: 0x0000000000000002 r13: 0x00007fb951969e00 r14: 0x000000010b22ff01 r15: 0x00007fff748b9070
rip: 0x000000010b6cdd35 rfl: 0x0000000000010206 cr2: 0x0000000000000008
Logical CPU: 2
Error Code: 0x00000004
Trap Number: 14
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External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 1
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 12415290
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=219.2M resident=134.1M(61%) swapped_out_or_unallocated=85.0M(39%)
Writable regions: Total=78.3M written=12.4M(16%) resident=18.6M(24%) swapped_out=4K(0%) unallocated=59.7M(76%)
REGION TYPE VIRTUAL
=========== =======
CG shared images 144K
Dispatch continuations 16.0M
Kernel Alloc Once 8K
MALLOC 43.0M
MALLOC (admin) 32K
STACK GUARD 56.0M
Stack 10.1M
VM_ALLOCATE 8044K
__DATA 17.5M
__IMAGE 528K
__LINKEDIT 76.3M
__TEXT 142.9M
__UNICODE 552K
mapped file 51.1M
shared memory 4K
=========== =======
TOTAL 422.1M
There are probably a couple of different things going on here. The crash is probably due to mixing libraries from Apple's Python and Homebrew's python. This is a recurrent problem that almost everyone who switches to homebrew seems to encounter. The Homebrew python path still includes the site-packages directory for Apple's python and it ends up pulling in libraries from the Apple Python site-package directory. If you grep the above error output and look for packages in /Library/Python/2.7/site-packages/, e.g.,
/Library/Python/2.7/site-packages/PIL/.dylibs/libjpeg.9.dylib
those are the problematic ones. I would suggest you just go ahead and delete everything in /Library/Python/2.7/site-packages/ (back it up to be sure). I think that will fix the problem (you may need to reinstall some of the packages under homebrew). Alternatively, you could install GrUMPy in a virtual environment using virtualenv with the --no-site-packages option, which I guess would also fix the problem.
It's hard to tell what the problem is with 0.8.4 on OS X without some more details. I don't think i changed anything that should make the difference between working and not working on OS X, but I guess it's good that you got it working with 0.85.
As for making the graphs prettier with xdot, this may not be quite what you expect. There are two different styles of tree pics you can get. One is the one you already got working, which is made with old-school gnuplot and pictures the nodes at the level of their bound. The other is the pretty tree pictures like this one, which are made using graphviz and then displayed using either pygame, xdot, or simply saved as files. Once you have a tree read in, you can produce either kind of image, but the commands for the two different image types are different, which goes back to the fact that GrUMPy is a merger of two separately developed projects. So just installing xdot and running p0201_GLPK.vbc won't change anything.
If you tell me what you want to do exactly, I can try to point you to some documentation.
Thanks for the comments. I have (indirectly) resolved the issue.
Short: I made it work by removing /Library/Python/ and reinstalling python from brew.
Details: python installed by brew on my mac seems to read packages from both /Library/Python/2.7/site-packages/ and /usr/local/lib/python2.7/site-packages/. I also found multiple directories under /Library/Python/ (e.g., 2.5, 2.6, 2.7). I renamed /Library/Python/ to '/Library/Python_bak/and reinstallpython. To run grumpy, I needed to install pulpandpygame` from this clean version.
Prettier: I would like to generate a tree image like this. Here are the images for p0201_GLPK.vbc and p0201_SYMPHONY.vbc: p0201_GLPK.vbc.pdf and p0201_SYMPHONY.vbc.pdf. One is gray-colored, whereas the other is not.
More notes:
- Version
0.8.4still does not work. Forp0201_SYMPHONY.vbc, I am getting this:
Invalid line: 0.288516 branched 1 None M 7125.000000 11.368421 24 19000000 100000
Should match: <time> branched <node id> <parent id>
<branch direction> <lp bound>
<sum of integer infeasibilities> <number of integer
infeasibilities>
- Things under
/Library/Pythonmay not be necessary to runpython. -
xdotseems to requirepython 3.0(requirements). I could installxdotusingpip, but I got this messsage:
Xdot is not installed. Display is set to off.
-
pygamedoes not give me this pretty tree by default. It may require some parameter tunes.
Test script
from coinor.grumpy import BBTree
bt = BBTree()
file_ = open('../GrUMPy/src/grumpy/examples/p0201_SYMPHONY.vbc', 'r')
# file_ = open('../GrUMPy/src/grumpy/examples/p0201_GLPK.vbc', 'r')
for line in file_:
bt.ProcessLine(line)
bt.set_display_mode('PIL')
bt.display()
Thanks for the comments. I have (indirectly) resolved the issue.
Short: I made it work by removing /Library/Python/ and reinstalling python from brew.
Details: python installed by brew on my mac seems to read packages from both /Library/Python/2.7/site-packages/ and /usr/local/lib/python2.7/site-packages/. I also found multiple directories under /Library/Python/ (e.g., 2.5, 2.6, 2.7). I renamed /Library/Python/ to '/Library/Python_bak/and reinstall python. To run grumpy, I needed to install pulp and pygame` from this clean version.
Yes, exactly, this is the conflict between packages meant to work with Apple's python and the homebrew version that I was referrring to. Just to clarify, you shouldn't need to install pulp and pygame for GrUMPy to work---they are only required for some optional things you might want to do with GrUMPy. That is why they are not listed as requirements in setup.py.
Prettier: I would like to generate a tree image like this. Here are the images for p0201_GLPK.vbc and p0201_SYMPHONY.vbc: p0201_GLPK.vbc.pdf and p0201_SYMPHONY.vbc.pdf. One is gray-colored, whereas the other is not.
The "pretty" trees are generated by populating a BBTree object with data coming from some external application (a solver, another Python script, etc.) and displaying it. Whether the nodes are colored or not, etc. is just a function of the application itself. The two trees you are pointed out above were generated for a particular application where we wanted greyscale coloring of the nodes to indicate certain properties. If you take a look at how the nodes are added to the tree in BranchAndBound.py, you should see how it works.
More notes:
Version 0.8.4 still does not work. For p0201_SYMPHONY.vbc, I am getting this: Invalid line: 0.288516 branched 1 None M 7125.000000 11.368421 24 19000000 100000 Should match:
Ah, OK, this is useful to know I'm surprised because I'm sure this was working previously. I will look at it. In any case, I'll probably make a release of 0.85 in the near future and then it will be moot.
Things under /Library/Python may not be necessary to run python.
They are definitely not needed for homebrew python, but would be needed if you are using Apple's python. They just use different directories to store site-packages and the packages are not mutually compatible.
xdot seems to require python 3.0 (requirements). I could install xdot using pip, but I got this messsage: Xdot is not installed. Display is set to off.
GrUMPy is implemented in Python 2. You can't import Python 3 packages in Python 2, so this is why xdot is not seen as installed. This must have changed recently, as xdot was previously working with Python 2. Hmm, I'll have to look into this, might be time to start porting all my projects to Python 3.
pygame does not give me this pretty tree by default. It may require some parameter tunes.
pygame just provides a way of displaying an image file. The image itself is generated independent of pygame. Whether it is "pretty" or not has to do with what display function is called and the data describing the tree, which comes from an external application.
Hope this helps clarify some things!
@kibaekkim I've updated the README now to indicate how to successfully get the current release of GrUMPy working with xdot on all platforms.