Hi Edward.
I was looking for a solution where I could use a package manager
to easily install dependencies.
I tried anaconda. There I had problems with wxPython.
I tried dmg installs, but ran into problems with matplotlib.
I don't think I had problems with wxPython.
So I settled for brew, which nicely installed python and pypi.
And then ipython, xmgrace was much easier.
---- My setup is now:----
tlinnet@linmac:bin$ relax -i
relax repository checkout r21734
svn://svn.gna.org/svn/relax/trunk
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2013 the relax development team
This is free software which you are welcome to modify and redistribute
under the conditions of the
GNU General Public License (GPL). This program, including all
modules, is licensed under the GPL
and comes with absolutely no warranty. For details type 'GPL' within
the relax prompt.
Assistance in using the relax prompt and scripting interface can be
accessed by typing 'help' within
the prompt.
Processor fabric: Uni-processor.
Hardware information:
Machine: x86_64
Processor: i386
Endianness: little
Total RAM size: ? Mb
Total swap size: ? Mb
Operating system information:
System: Darwin
Release: 13.0.0
Version: Darwin Kernel Version 13.0.0: Thu Sep 19
22:22:27 PDT 2013; root:xnu-2422.1.72~6/RELEASE_X86_64
Mac version: 10.9 (, , ) x86_64
Distribution:
Full platform string: Darwin-13.0.0-x86_64-i386-64bit
Python information:
Architecture: 64bit
Python version: 2.7.6
Python branch:
Python build: default, Dec 2 2013 13:01:42
Python compiler: GCC 4.2.1 Compatible Apple LLVM 5.0
(clang-500.2.79)
Libc version:
Python implementation: CPython
Python revision:
Python executable:
/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Python flags: sys.flags(debug=0, py3k_warning=0,
division_warning=0, division_new=0, inspect=0, interactive=0,
optimize=0, dont_write_bytecode=0, no_user_site=0, no_site=0,
ignore_environment=0, tabcheck=0, verbose=0, unicode=0,
bytes_warning=0, hash_randomization=0)
Python float info:
sys.float_info(max=1.7976931348623157e+308, max_exp=1024,
max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021,
min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.220446049250313e-16,
radix=2, rounds=1)
Python module path: ['/Users/tlinnet/software/relax_trunk',
'/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools-1.3.2-py2.7.egg',
'/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.4.1-py2.7.egg',
'/usr/local/lib/python2.7/site-packages/setuptools-1.3.2-py2.7.egg',
'/usr/local/lib/python2.7/site-packages/pip-1.4.1-py2.7.egg',
'/usr/local/lib/wxPython-2.9.5.0/lib/python2.7/site-packages',
'/usr/local/lib/wxPython-2.9.5.0/lib/python2.7/site-packages/wx-2.9.5-osx_cocoa',
'/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python27.zip',
'/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7',
'/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin',
'/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac',
'/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages',
'/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk',
'/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old',
'/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload',
'/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages',
'/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/wx-2.9.5-osx_cocoa',
'/Library/Python/2.7/site-packages',
'/usr/local/lib/wxPython-2.9.5.0/lib/python2.7',
'/usr/local/lib/python2.7/site-packages',
'/usr/local/lib/python2.7/site-packages/wx-2.9.5-osx_cocoa']
Python packages and modules (most are optional):
Name Installed Version Path
minfx True 1.0.5
/Library/Python/2.7/site-packages/minfx
bmrblib True 1.0.3
/Library/Python/2.7/site-packages/bmrblib
numpy True 1.8.0
/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy
scipy True 0.13.1
/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy
wxPython True 2.9.5.0 osx-cocoa (classic)
/usr/local/lib/wxPython-2.9.5.0/lib/python2.7/site-packages/wx-2.9.5-osx_cocoa/wx
mpi4py False
epydoc True 3.0.1
/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/epydoc
optparse True 1.5.3
/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/optparse.pyc
readline True
/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/readline.so
profile True
/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/profile.pyc
bz2 True
/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/bz2.so
gzip True
/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/gzip.pyc
io True
/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/io.pyc
xml True 0.8.4 (internal)
/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xml/__init__.pyc
xml.dom.minidom True
/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xml/dom/minidom.pyc
relax information:
Version: repository checkout r21734
svn://svn.gna.org/svn/relax/trunk
Processor fabric: Uni-processor.
relax C modules:
Module Compiled File type
Path
target_functions.relax_fit True Mach-O 64-bit bundle x86_64
/Users/tlinnet/software/relax_trunk/target_functions/relax_fit.so
Troels Emtekær Linnet
2013/12/2 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
Hi,
If there is a wxPython problem, did you report it upstream to the
wxPython developers so they can fix it? There are many, many
different ways of setting up a Python install to run relax. I've
tried Fink, DMG, manually compiling, building frameworks, but not
Homebrew yet. Anyway, the DMG file route is normally the easiest.
Note that if Homebrew bundles an older wxPython version, then you
might see those iCCP messages from wxPython itself rather than relax.
Regards,
Edward
On 2 December 2013 17:39, Troels Emtekær Linnet <tlinnet@xxxxxxxxx> wrote:
For the record.
I had problems setting up wxPython on Mavericks.
I decided to go with brew:
1) Install brew
http://crosstown.coolestguidesontheplanet.com/os-x/55-setting-up-os-x-mavericks-and-homebrew
Notes: I could not and I did not have to do: xcode-select --install
2) Install python+numpy+scipy+matplotlib+ipython over brew
http://www.lowindata.com/2013/installing-scientific-python-on-mac-os-x/
Notes: Skipped virtualenv
For matplotlib, I had to do:
pip install git+git://github.com/matplotlib/matplotlib.git
(It was due to a package error ... )
After finishing to pygments, I could also install spyder as an editor
pip install spyder
3) wxPython
http://superuser.com/questions/196197/installing-wxpython-via-pip-or-easy-install
brew install --python wxmac --devel
4) minfx and bmrblib
http://wiki.nmr-relax.com/Installation_mac#Minfx_and_Bmrblib
----- .bash_profile used ----
##Setting color for terminal
export CLICOLOR=1
export LSCOLORS=ExFxCxDxBxegedabagacad
## black background
# export LSCOLORS=gxBxhxDxfxhxhxhxhxcxcx
# Directory to show in basj
export PS1='\u@\H:\W$ '
## Setting path for git
PATH="/usr/local/git/bin:${PATH}"
export PATH
## From: http://hackercodex.com/guide/mac-osx-mavericks-10.9-configuration/
# Set architecture flags
# export ARCHFLAGS="-arch x86_64"
## Ensure user-installed binaries take precedence
export PATH=/usr/local/bin:$PATH
export PATH=/usr/local/share/python:$PATH
## Test
# export PYTHONPATH=/usr/local/lib/python:$PYTHONPATH
# Load .bashrc if it exists
# test -f ~/.bashrc && source ~/.bashrc
alias ipyt='ipython qtconsole --pylab=inline'
alias textedit='open -a TextEdit'
alias relax=$HOME/software/relax_trunk/relax
Troels Emtekær Linnet
2013/12/2 Troels Emtekær Linnet <tlinnet@xxxxxxxxx>:
By the way, I get this error when I start in GUI mode
----
iCCP: known incorrect sRGB profile
----
Troels Emtekær Linnet
2013/12/2 Troels Emtekær Linnet <tlinnet@xxxxxxxxx>:
Hi Edward.
For a long time I thought it was a problem with xcode.
And I have tried alot...
But it was simple, I just altered the archs, and it worked.
-----------
def det_arch(self):
"""Nasty hack to make Scons behave properly with
cross-compilation on Mac OS X!
@return: The list of CPU architects to cross compile.
@rtype: list of str
"""
# The list of archectures to try.
#archs = ['i386', 'ppc', 'x86_64']
archs = ['x86_64']
-----------------
Troels Emtekær Linnet
2013/12/2 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
Hi,
I'm not sure what is happening here. This normally works. Maybe you
should look at the det_arch() method in the 'sconstruct' script, as
that is the likely failure point. I would guess that it is not able
to correctly determine the supported architectures on your system.
This has worked on numerous Macs before, so maybe there is something
different with the setup (Xcode is a likely culprit).
Regards,
Edward
On 1 December 2013 23:33, Troels Emtekær Linnet <tlinnet@xxxxxxxxx>
wrote:
Hi Edward.
I tried compiling relax on mac OS X Mavericks.
Should I in some way specify which kernel to build for?
I get these errors:
----------
linmac:relax_trunk tlinnet$ scons
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
###########################
# Compiling the C modules #
###########################
Building the relaxation curve fitting module
'target_functions/relax_fit.so'
gcc -o target_functions/c_chi2.os -c
-I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
-arch i386 -arch ppc -arch x86_64 -fPIC target_functions/c_chi2.c
In file included from target_functions/c_chi2.c:20:
In file included from /usr/include/stdio.h:64:
/usr/include/sys/cdefs.h:655:2: error: Unsupported architecture
#error Unsupported architecture
^
In file included from target_functions/c_chi2.c:20:
In file included from /usr/include/stdio.h:67:
In file included from /usr/include/_types.h:27:
In file included from /usr/include/sys/_types.h:33:
/usr/include/machine/_types.h:34:2: error: architecture not supported
#error architecture not supported
^
In file included from target_functions/c_chi2.c:20:
In file included from /usr/include/stdio.h:67:
In file included from /usr/include/_types.h:27:
/usr/include/sys/_types.h:94:9: error: unknown type name '__int64_t'
typedef __int64_t __darwin_blkcnt_t; /* total blocks */
^
/usr/include/sys/_types.h:95:9: error: unknown type name '__int32_t'
typedef __int32_t __darwin_blksize_t; /* preferred block
size */
^
/usr/include/sys/_types.h:96:9: error: unknown type name '__int32_t'
typedef __int32_t __darwin_dev_t; /* dev_t */
^
/usr/include/sys/_types.h:99:9: error: unknown type name '__uint32_t'
typedef __uint32_t __darwin_gid_t; /* [???] process and
group IDs */
^
/usr/include/sys/_types.h:100:9: error: unknown type name '__uint32_t'
typedef __uint32_t __darwin_id_t; /* [XSI] pid_t, uid_t,
or gid_t*/
^
/usr/include/sys/_types.h:101:9: error: unknown type name '__uint64_t'
typedef __uint64_t __darwin_ino64_t; /* [???] Used for 64
bit inodes */
^
/usr/include/sys/_types.h:107:9: error: unknown type name
'__darwin_natural_t'
typedef __darwin_natural_t __darwin_mach_port_name_t; /* Used by mach
*/
^
/usr/include/sys/_types.h:109:9: error: unknown type name '__uint16_t'
typedef __uint16_t __darwin_mode_t; /* [???] Some file
attributes */
^
/usr/include/sys/_types.h:110:9: error: unknown type name '__int64_t'
typedef __int64_t __darwin_off_t; /* [???] Used for file
sizes */
^
/usr/include/sys/_types.h:111:9: error: unknown type name '__int32_t'
typedef __int32_t __darwin_pid_t; /* [???] process and
group IDs */
^
/usr/include/sys/_types.h:131:9: error: unknown type name '__uint32_t'
typedef __uint32_t __darwin_sigset_t; /* [???] signal set */
^
/usr/include/sys/_types.h:132:9: error: unknown type name '__int32_t'
typedef __int32_t __darwin_suseconds_t; /* [???] microseconds
*/
^
/usr/include/sys/_types.h:133:9: error: unknown type name '__uint32_t'
typedef __uint32_t __darwin_uid_t; /* [???] user IDs */
^
/usr/include/sys/_types.h:134:9: error: unknown type name '__uint32_t'
typedef __uint32_t __darwin_useconds_t; /* [???] microseconds
*/
^
In file included from target_functions/c_chi2.c:20:
In file included from /usr/include/stdio.h:71:
/usr/include/sys/_types/_va_list.h:31:9: error: unknown type name
'__darwin_va_list'; did you mean '__builtin_va_list'?
typedef __darwin_va_list va_list;
^
note: '__builtin_va_list' declared here
In file included from target_functions/c_chi2.c:20:
In file included from /usr/include/stdio.h:72:
/usr/include/sys/_types/_size_t.h:30:9: error: unknown type name
'__darwin_size_t'; did you mean '__darwin_ino_t'?
typedef __darwin_size_t size_t;
^
/usr/include/sys/_types.h:103:26: note: '__darwin_ino_t' declared here
typedef __darwin_ino64_t __darwin_ino_t; /* [???] Used for
inodes */
^
In file included from target_functions/c_chi2.c:20:
In file included from /usr/include/stdio.h:434:
/usr/include/sys/_types/_ssize_t.h:30:9: error: unknown type name
'__darwin_ssize_t'
typedef __darwin_ssize_t ssize_t;
^
19 errors generated.
scons: *** [target_functions/c_chi2.os] Error 1
scons: building terminated because of errors.
linmac:relax_trunk tlinnet$
Troels Emtekær Linnet
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Re: Building relax trunk on mac OS X 10.9