Use Gurobi 5.5.0 in Python 2.7.5 installed via Homebrew (OS X 10.8.4)
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Nagae Takeshi
Sep 5, 2013, 3:42:25 AM9/5/13
to gur...@googlegroups.com
Dear all,
I would like to use Gurobi 5.5.0 from python 2.7.5 that is installed via homebrew (OS X 10.8.4) with latest X Code Command Line Tools (CLT).
My brew --config says:
-----
$ brew --config
HOMEBREW_VERSION: 0.9.4
ORIGIN: https://github.com/mxcl/homebrew
HEAD: cc03fbde87c4f94b5463598bbfe138f69e6d4900
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
CPU: 8-core 64-bit ivybridge
OS X: 10.8.4-x86_64
CLT: 4.6.0.0.1.1365549073
LLVM-GCC: build 2336
Clang: 4.2 build 425
X11: 2.7.4 => /opt/X11
System Ruby: 1.8.7-358
Perl: /usr/bin/perl
Python: /usr/local/bin/python => /usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/bin/python2.7
Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
-----
Python 2.7.5 is installed via homebrew in /usr/local/bin:
-----
$ which python
/usr/local/bin/python
$ python --version
Python 2.7.5
-----
In /usr/bin folder, there is another python, which might be embedded in X Code CLT:
-----
$ /usr/bin/python --version
Python 2.7.2
-----
I download Gurobi 5.5.0 package for Mac OS X and installed it:
-----
$ cd /Library/gurobi550/mac64/
$ python setup.py install
running install
running build
running build_py
running install_lib
copying build/lib/gurobipy/__init__.py -> /usr/local/lib/python2.7/site-packages/gurobipy
copying build/lib/gurobipy/gurobipy.so -> /usr/local/lib/python2.7/site-packages/gurobipy
byte-compiling /usr/local/lib/python2.7/site-packages/gurobipy/__init__.py to __init__.pyc
running install_egg_info
Removing /usr/local/lib/python2.7/site-packages/gurobipy-5.5.0-py2.7.egg-info
Writing /usr/local/lib/python2.7/site-packages/gurobipy-5.5.0-py2.7.egg-info
-----
However, import gurobipy from python fails:
-----
-----
$ python
Python 2.7.5 (default, Aug 27 2013, 11:16:28)
[GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import gurobipy
Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6
-----
I put the error message at the end of this post.
It is noteworthy gurobipy can be imported from the older (or OS X preinstalled) python:
---
$ /usr/bin/python
Python 2.7.2 (default, Oct 11 2012, 20:14:37)
[GCC 4.2.1 Compatible Apple Clang 4.0 (tags/Apple/clang-418.0.60)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import gurobipy
>>> # no warning/error message is shown
---
As I installed many modules (e.g. numpy, scipy, matplotlib, iPython, etc) via homebrew for python 2.7.5,
it is not willing to call /usr/bin/python only for Gurobi.
What can I unify Gurobi and other modules on python 2.7.5?
# The error message is as below:
=====================================================
Process: Python [44809]
Path: /usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: 2.7.5 (2.7.5)
Code Type: X86-64 (Native)
Parent Process: bash [44668]
User ID: 501
Date/Time: 2013-09-05 16:20:22.472 +0900
OS Version: Mac OS X 10.8.4 (12E55)
Report Version: 10
Interval Since Last Report: 3891 sec
Crashes Since Last Report: 21
Per-App Crashes Since Last Report: 7
Anonymous UUID: 5D95BB85-C00E-4467-C7EE-09E68EA59B1A
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Application Specific Information:
abort() called
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff8765bd46 __kill + 10
1 libsystem_c.dylib 0x00007fff86fe7df0 abort + 177
2 org.python.python 0x0000000104937eaa Py_FatalError + 49
3 org.python.python 0x0000000104936370 PyThreadState_Get + 28
4 org.python.python 0x0000000104931f16 Py_InitModule4_64 + 58
5 gurobipy.so 0x000000010455352f initgurobipy + 511
6 org.python.python 0x0000000104231bab _PyImport_LoadDynamicModule + 150
7 org.python.python 0x00000001042318c2 import_submodule + 274
8 org.python.python 0x00000001042314a1 load_next + 268
9 org.python.python 0x000000010422f597 PyImport_ImportModuleLevel + 596
10 org.python.python 0x0000000104215e16 builtin___import__ + 132
11 org.python.python 0x00000001041a44fd PyObject_Call + 101
12 org.python.python 0x0000000104220274 PyEval_CallObjectWithKeywords + 93
13 org.python.python 0x000000010421d61a PyEval_EvalFrameEx + 11727
14 org.python.python 0x000000010421a721 PyEval_EvalCodeEx + 1638
15 org.python.python 0x000000010421a0b5 PyEval_EvalCode + 54
16 org.python.python 0x000000010422e354 PyImport_ExecCodeModuleEx + 247
17 org.python.python 0x0000000104230e88 load_source_module + 1068
18 org.python.python 0x0000000104231104 load_package + 298
19 org.python.python 0x00000001042318c2 import_submodule + 274
20 org.python.python 0x00000001042314a1 load_next + 268
21 org.python.python 0x000000010422f597 PyImport_ImportModuleLevel + 596
22 org.python.python 0x0000000104215e16 builtin___import__ + 132
23 org.python.python 0x00000001041a44fd PyObject_Call + 101
24 org.python.python 0x0000000104220274 PyEval_CallObjectWithKeywords + 93
25 org.python.python 0x000000010421d61a PyEval_EvalFrameEx + 11727
26 org.python.python 0x000000010421a721 PyEval_EvalCodeEx + 1638
27 org.python.python 0x000000010421a0b5 PyEval_EvalCode + 54
28 org.python.python 0x0000000104238eb8 run_mod + 53
29 org.python.python 0x0000000104238cda PyRun_InteractiveOneFlags + 365
30 org.python.python 0x00000001042387cb PyRun_InteractiveLoopFlags + 188
31 org.python.python 0x000000010423867c PyRun_AnyFileExFlags + 60
32 org.python.python 0x000000010424958b Py_Main + 3039
33 libdyld.dylib 0x00007fff844607e1 start + 1
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x00007fff5ba6d9f0 rcx: 0x00007fff5ba6d9d8 rdx: 0x0000000000000000
rdi: 0x000000000000af09 rsi: 0x0000000000000006 rbp: 0x00007fff5ba6da00 rsp: 0x00007fff5ba6d9d8
r8: 0x00000000000003f5 r9: 0x0000000000000004 r10: 0x00007fff8765d342 r11: 0x0000000000000206
r12: 0x00007fd7c1032200 r13: 0x00000001045fba2c r14: 0x00000000000003f5 r15: 0x0000000000000000
rip: 0x00007fff8765bd46 rfl: 0x0000000000000206 cr2: 0x00007fff729a8ff0
Logical CPU: 0
Binary Images:
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External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
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: 8250
thread_create: 2
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=76.0M resident=36.4M(48%) swapped_out_or_unallocated=39.6M(52%)
Writable regions: Total=20.4M written=2272K(11%) resident=2860K(14%) swapped_out=0K(0%) unallocated=17.6M(86%)
REGION TYPE VIRTUAL
=========== =======
MALLOC 12.0M
MALLOC guard page 32K
STACK GUARD 56.0M
Stack 8192K
__DATA 2032K
__LINKEDIT 52.7M
__TEXT 23.3M
__UNICODE 544K
shared memory 12K
=========== =======
TOTAL 154.6M
(Following message is suppressed as it seems not relevant)
=====================================================
Nagae Takeshi
Sep 5, 2013, 10:09:23 PM9/5/13
to gur...@googlegroups.com
Dear all,
Here is my tentative step: just give up to use homebrew-ed python.
$ brew unlink python
Unlinking /usr/local/Cellar/python/2.7.5... 37 links removed
$ which python
/usr/bin/python
Then I added the following to '~/.bash_profile'
export PYTHONPATH=`brew --prefix`/lib/python2.7/site-packages:$PYTHONPATH
However, I can't use neither pip nor easy_install to get another module unless linking homebrew-ed python :-(
Greg Glockner
Sep 6, 2013, 9:43:15 AM9/6/13
to gur...@googlegroups.com
The only version of Python that is supported on OS X is the default version from Apple.
Jakob Sch.
Sep 6, 2013, 10:16:15 AM9/6/13
to gur...@googlegroups.com
Hi Nagae,
You might want to try SciPySuperpack (http://fonnesbeck.github.io/ScipySuperpack/).
It installs a bunch of useful packages (scipy, numpy, ipython, etc.) for the native MacPython (which can then be used alongside gurobi).
Hope this helps,
Jakob
You might want to try SciPySuperpack (http://fonnesbeck.github.io/ScipySuperpack/).
It installs a bunch of useful packages (scipy, numpy, ipython, etc.) for the native MacPython (which can then be used alongside gurobi).
Hope this helps,
Jakob
Nagae Takeshi
Sep 9, 2013, 9:19:42 PM9/9/13
to gur...@googlegroups.com
It is a concise and perfect information which I need.
Thank you.
Nagae Takeshi
Sep 9, 2013, 9:23:45 PM9/9/13
to gur...@googlegroups.com
Thank you for fascinating recommendation.
But I still like homebrew and thus I may try the following homebrew-based packages with the native MacPython:
(i.e. I skip "brew install python" and add "sudo /usr/bin/easy_install pip")
Chien-Chun Ni
Feb 17, 2014, 2:06:17 AM2/17/14
to gur...@googlegroups.com
Hi all.
Nagae Takeshi於 2013年9月9日星期一UTC-4下午9時23分45秒寫道：
I found a solution for this problem,
1. find your 'gurobipy.so', should be in `/usr/local/lib/python2.7/site-packages/gurobipy`
2. type 'otool -l gurobipy.so' to find out which lib it used.
The log should look like follows, and you are searching for the default interpreter like location, for me, the log looks like follows:
Load command 10
cmd LC_LOAD_DYLIB
cmdsize 88
name /System/Library/Frameworks/Python.framework/Versions/2.7/Python (offset 24)
time stamp 2 Wed Dec 31 19:00:02 1969
current version 2.7.1
compatibility version 2.7.0
3. change that to homebrew one, using install_name_tool like following:
'install_name_tool -change /System/Library/Frameworks/Python.framework/Versions/2.7/Python /usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib gurobipy.so'
For me, now my gurobipy work smoothly on brew python, hope this help.
For me, now my gurobipy work smoothly on brew python, hope this help.
Nagae Takeshi於 2013年9月9日星期一UTC-4下午9時23分45秒寫道：
Matthew Oster
Aug 2, 2017, 3:10:32 PM8/2/17
to Gurobi Optimization
Thanks Chien-Chun! This helped me successfully install 7.0.1 a few months ago and (after forgetting that I used your advice) has recently helped install 7.5.1. To (hopefully) slightly improve your answer, I'd do the following:
-Matt
1. Find (and cd to) your base gurobipy.so (should be at /Library/gurobi751/mac64/lib/python2.7/gurobipy/gurobipy.so).
2. Execute 'otool -l gurobipy.so | grep [Pp]ython' (should return at least one line with the system python library you've linked to, call it OLD).
3. Find your desired homebrew python library (should be in /usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib, call it NEW).
4. Execute 'install_name_tool -change OLD NEW gurobipy.so' (obviously replacing OLD and NEW with your paths above).
Now I'm able to create virtual environments, 'python setup.py install' gurobipy-7.5.1, and 'python -c "import gurobipy"' without any seg faults or other problems.
Now I'm able to create virtual environments, 'python setup.py install' gurobipy-7.5.1, and 'python -c "import gurobipy"' without any seg faults or other problems.
-Matt
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