OSX 10.12

[andyse...@gmail.com]

Dear all,

Slightly off the line question. My macs (including Mac Pros) have gone very slow after I upgraded them to macOS Sierra. Its taking longer for computation. More specifically, the mac pro froze couple of times  while visualizing class averages. 

Has anybody faced such issues or its just my systems?

Best 

Andy

[Steve Ludtke]

Hi Andy.  I haven't experienced this on any of our Macs.  I understand that perhaps for as long as a couple/few days after upgrading it may be rebuilding indices in the background for the new way they are handing that, and since that involves a lot of disk/network, even if running in the background, it can impact performance significantly. Indeed, Apple is claiming that the people who have experienced poorer than expected battery life on their new macbook pros are likely encountering this initial period of indexing.

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----------------------------------------------------------------------------

Steven Ludtke, Ph.D.

Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem)

Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)

Co-Director CIBR Center                          (www.bcm.edu/research/cibr)

Baylor College of Medicine                             

slu...@bcm.edu

[Paul Penczek]

Hi

What is the general situation with Sierra?  Should we all upgrade?

Regards,

Pawel

[Steve Ludtke]

We updated pretty much all of our macs soon after release. I haven't had any issues with it at all. Nothing like when they introduced the new rootkit security a year or two ago which screwed things up so much.

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Paul Penczek]

This is news to me.  I thought you told us not to upgrade. 

Maybe I'll use winter break to play with it. Do you have any instructions, or is it straightforward?  I mean source installation. 

Regards,

Pawel

[Steve Ludtke]

Hmm, I don't remember commenting on this release. I think I may have commented on last year's update. I didn't change anything on my machines after updating. Note that I continue to do most of my actual development on Linux machines, so I use the binary release on most of my Macs

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Paul Penczek]

Regards,

Pawel

[Paul Penczek]

Hi,

The upgrade did not quite work.  It did compile all right, but then it failed on import:

pawel-Air:/Users/pawel 208> sx.py

Python 2.7.10 (default, Jul 30 2016, 19:40:32) 

Type "copyright", "credits" or "license" for more information.

IPython 1.2.1 -- An enhanced Interactive Python.

?         -> Introduction and overview of IPython's features.

%quickref -> Quick reference.

help      -> Python's own help system.

object?   -> Details about 'object', use 'object??' for extra details.

---------------------------------------------------------------------------

ImportError                               Traceback (most recent call last)

/Library/Python/2.7/site-packages/IPython/utils/py3compat.pyc in execfile(fname, *where)

    202             else:

    203                 filename = fname

--> 204             __builtin__.execfile(filename, *where)

/Users/pawel/EMAN2/bin/sx_real.py in <module>()

     35 #

     36 

---> 37 import EMAN2

     38 from EMAN2 import *

     39 

/Users/pawel/EMAN2/lib/EMAN2.py in <module>()

     42 import socket

     43 import subprocess

---> 44 from EMAN2_cppwrap import *

     45 from pyemtbx.imagetypes import *

     46 from pyemtbx.box import *

/Users/pawel/EMAN2/lib/EMAN2_cppwrap.py in <module>()

     31 #

     32 

---> 33 from libpyAligner2 import *

     34 from libpyAverager2 import *

     35 from libpyBoxingTools2 import *

ImportError: dlopen(/Users/pawel/EMAN2/lib/libpyAligner2.so, 2): Library not loaded: libboost_python.dylib

  Referenced from: /Users/pawel/EMAN2/lib/libpyAligner2.so

  Reason: unsafe use of relative rpath libboost_python.dylib in /Users/pawel/EMAN2/lib/libpyAligner2.so with restricted binary

Thanks,

Pawel.

[Steve Ludtke]

Perhaps you skipped a version. You seem to be running into the rootkit prevention system they added a year or two ago. This page may help:

http://stackoverflow.com/questions/33281753/unsafe-use-of-relative-rpath-libboost-dylib-when-making-boost-python-helloword-d

[Paul Penczek]

Hi,

driiving safely?

The page helped somewhat.  Now at least the system starts.  However:

1. it turns out each time I recompile eman2 I have to repeat the fix.

2.  display did not work and I could not figure how to fix it.

Pawel.

/Users/pawel/EMAN2/lib/EMAN2_cppwrap.py in <module>()

     31 #

     32 

---> 33 from libpyAligner2 import *

     34 from libpyAverager2 import *

     35 from libpyBoxingTools2 import *

ImportError: dlopen(/Users/pawel/EMAN2/lib/libpyAligner2.so, 2): Library not loaded: libboost_python.dylib

  Referenced from: /Users/pawel/EMAN2/lib/libpyAligner2.so

  Reason: unsafe use of relative rpath libboost_python.dylib in /Users/pawel/EMAN2/lib/libpyAligner2.so with restricted binary

In [1]: quit

pawel-Air:/Users/pawel 250> !for

foreach n ( /Users/pawel/EMAN2/lib/libpy*so )

foreach? install_name_tool -change libboost_python.dylib /usr/local/lib/libboost_python.dylib $n

foreach? end

pawel-Air:/Users/pawel 253> sx.py

Python 2.7.10 (default, Jul 30 2016, 19:40:32) 

Type "copyright", "credits" or "license" for more information.

IPython 1.2.1 -- An enhanced Interactive Python.

?         -> Introduction and overview of IPython's features.

%quickref -> Quick reference.

help      -> Python's own help system.

object?   -> Details about 'object', use 'object??' for extra details.

/Library/Python/2.7/site-packages/bsddb3-5.3.0-py2.7-macosx-10.9-intel.egg/bsddb3/_pybsddb.py:3: UserWarning: Module readline was already imported from /Library/Python/2.7/site-packages/IPython/utils/rlineimpl.pyc, but /Library/Python/2.7/site-packages/readline-6.2.4.1-py2.7-macosx-10.7-intel.egg is being added to sys.path

Welcome to the interactive SPARX-NoGUI Python interface, provided by ipython

   SPARX v4.0 (GITHUB: Tue Dec 20 08:42:41 2016)

In [1]: display(test_image())

Traceback (most recent call last):

  File "/Users/pawel/EMAN2/bin/e2display.py", line 36, in <module>

    from emapplication import EMApp

  File "/Users/pawel/EMAN2/lib/emapplication.py", line 34, in <module>

    from PyQt4 import QtGui, QtCore, QtOpenGL

ImportError: dlopen(/Library/Python/2.7/site-packages/PyQt4/QtGui.so, 2): Library not loaded: QtGui.framework/Versions/4/QtGui

  Referenced from: /Library/Python/2.7/site-packages/PyQt4/QtGui.so

  Reason: unsafe use of relative rpath QtGui.framework/Versions/4/QtGui in /Library/Python/2.7/site-packages/PyQt4/QtGui.so with restricted binary

In [2]: quit

pawel-Air:/Users/pawel 254> 

---

From: Steve Ludtke <slud...@gmail.com>
To: em...@googlegroups.com
Sent: Monday, December 19, 2016 10:26 PM
Subject: Re: [EMAN2] OSX 10.12

[Paul Penczek]

I also did this:

pawel-Air:/Users/pawel 256> otool -L /Library/Python/2.7/site-packages/PyQt4/QtGui.so

/Library/Python/2.7/site-packages/PyQt4/QtGui.so:

QtGui.framework/Versions/4/QtGui (compatibility version 4.8.0, current version 4.8.2)

QtCore.framework/Versions/4/QtCore (compatibility version 4.8.0, current version 4.8.2)

/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)

/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)

---

From: Paul Penczek <pawe...@att.net>
To: "em...@googlegroups.com" <em...@googlegroups.com>
Sent: Tuesday, December 20, 2016 8:45 AM

[Jesus Montoya]

Hi Pawel,

I'm getting the same errors compiling on Sierra.

For the first error, related to libboost, the fix is to change "libboost_python.dylib" to "/usr/local/lib/libboost_python.dylib" in all *.so files inside of "/Users/pawel/EMAN2/lib/".

I did this with a similar command as yours and it worked:

cd $EMAN2DIR/lib
for i in *.so
do
install_name_tool $i -change libboost_python.dylib /usr/local/lib/libboost_python.dylib
done

However, for the second error, "QtGui.framework/Versions/4/QtGui" seems to be problematic in all *.so files inside "/Library/Python/2.7/site-packages/PyQt4/" (correct?).
What do I need to change it to? What should the value be of the red question marks below?
Thanks for your help!

cd /Library/Python/2.7/site-packages/PyQt4/
for i in *.so
do
install_name_tool $i -change QtGui.framework/Versions/4/QtGui <???>
done

I'm assuming /Library/Frameworks/QtGui.framework/Versions/4/QtGui might be the correct answer, but I cannot seem to run the command unless I use sudo, so I'm a bit wary of running the wrong command.
Thanks!
 

cd /Library/Python/2.7/site-packages/PyQt4/
for i in *.so
do
sudo install_name_tool $i -change QtGui.framework/Versions/4/QtGui /Library/Frameworks/QtGui.framework/Versions/4/QtGui 
done

[Paul Penczek]

Hi

I never managed the graphics. What I posted earlier fixes basic operations. I tried this and that with graphics, I believe I also recompiled the relevant libraries but no luck. 

So I was waiting for you guys to figure it out😜

Regards,

Pawel

[Jesus Montoya]

Oh, OK ^_^

I think I've fixed it :-) 

Indeed, one seems to need to run the commands with sudo:

cd /Library/Python/2.7/site-packages/PyQt4/

for i in *.so; do sudo install_name_tool $i -change QtGui.framework/Versions/4/QtGui /Library/Frameworks/QtGui.framework/Versions/4/QtGui; done

for i in *.so; do sudo install_name_tool $i -change QtCore.framework/Versions/4/QtCore /Library/Frameworks/QtCore.framework/Versions/4/QtCore; done

for i in *.so; do sudo install_name_tool $i -change QtOpenGL.framework/Versions/4/QtOpenGL /Library/Frameworks/QtOpenGL.framework/Versions/4/QtOpenGL; done

cd /Library/Frameworks/QtOpenGL.framework/Versions/4/ 

sudo install_name_tool QtOpenGL -change QtCore.framework/Versions/4/QtCore /Library/Frameworks/QtCore.framework/Versions/4/QtCore

sudo install_name_tool QtOpenGL -change QtGui.framework/Versions/4/QtGui /Library/Frameworks/QtGui.framework/Versions/4/QtGui

cd /Library/Frameworks/QtGui.framework/Versions/4/

sudo install_name_tool QtGui -change QtCore.framework/Versions/4/QtCore /Library/Frameworks/QtCore.framework/Versions/4/QtCore

I hope I didn't miss any; but basically, depending on the error triggered, you change the library the fails to import, for one that actually exists (you can figure the latter out doing a terminal search; for example, "locate QtGui.Framework/Versions/4/QtGui", which is on the offending lines in the import, spits out "/Library/Frameworks/QtGui.framework/Versions/4/QtGui", which seems to be the correct replacement.

e2display now launches and displays EM maps without issues, so I'm assuming the issue is fixed.

I wonder whether Steve or someone else might be able to figure out a more efficient fix??

[Paul Penczek]

Didn't work.

I had to translate your script to csh:

foreach n ( /Users/pawel/EMAN2/lib/libpy*so )

install_name_tool -change libboost_python.dylib /usr/local/lib/libboost_python.dylib $n

end

cd /Library/Python/2.7/site-packages/PyQt4

foreach n ( *so )

sudo install_name_tool -change QtGui.framework/Versions/4/QtGui /Library/Frameworks/QtGui.framework/Versions/4/QtGui  $n

sudo install_name_tool -change QtCore.framework/Versions/4/QtCore  /Library/Frameworks/QtCore.framework/Versions/4/QtCore  $n

sudo install_name_tool -change QtOpenGL.framework/Versions/4/QtOpenGL /Library/Frameworks/QtOpenGL.framework/Versions/4/QtOpenGL  $n

end

cd /Library/Frameworks/QtOpenGL.framework/Versions/4/ 

sudo install_name_tool -change  QtOpenGL QtCore.framework/Versions/4/QtCore /Library/Frameworks/QtCore.framework/Versions/4/QtCore

sudo install_name_tool -change  QtOpenGL QtGui.framework/Versions/4/QtGui /Library/Frameworks/QtGui.framework/Versions/4/QtGui

cd /Library/Frameworks/QtGui.framework/Versions/4/

sudo install_name_tool -change  QtGui QtCore.framework/Versions/4/QtCore /Library/Frameworks/QtCore.framework/Versions/4/QtCore

cd  ~/

And then I get the same error:

  File "/Users/pawel/EMAN2/lib/emapplication.py", line 34, in <module>

    from PyQt4 import QtGui, QtCore, QtOpenGL

ImportError: dlopen(/Library/Python/2.7/site-packages/PyQt4/QtGui.so, 2): Library not loaded: QtCore.framework/Versions/4/QtCore

  Referenced from: /Library/Frameworks/QtGui.framework/Versions/4/QtGui

  Reason: unsafe use of relative rpath QtCore.framework/Versions/4/QtCore in /Library/Frameworks/QtGui.framework/Versions/4/QtGui with restricted binary

And this is content of the directory:

pawel-Air:/Library/Python/2.7/site-packages/PyQt4 271> ll

total 22632

-rwxr-xr-x   1      8752 Feb  7 19:23 Qt.so*

-rwxr-xr-x   1   2629840 Feb  7 19:23 QtCore.so*

-rwxr-xr-x   1   8470352 Feb  7 19:23 QtGui.so*

-rwxr-xr-x   1    308432 Feb  7 19:23 QtOpenGL.so*

-rwxr-xr-x   1    116296 Feb  7 19:23 QtSvg.so*

-rw-r--r--@  1      1111 May 25  2014 __init__.py

-rw-r--r--   1       138 Nov  9  2013 __init__.pyc

-rw-r--r--   1     13925 May 25  2014 pyqtconfig.py

-rw-r--r--   1     16348 Nov  9  2013 pyqtconfig.pyc

drwxr-xr-x  15       510 Oct 16  2014 uic/

pawel-Air:/Library/Python/2.7/site-packages/PyQt4 272> 

Any ideas?

Pawel.

---

From: Jesus Montoya <jga...@gmail.com>
To: EMAN2 <em...@googlegroups.com>
Cc: jga...@gmail.com
Sent: Tuesday, February 7, 2017 6:36 PM

Subject: Re: [EMAN2] OSX 10.12

Oh, OK ^_^

I think I've fixed it :-) 

Indeed, one seems to need to run the commands with sudo:

cd /Library/Python/2.7/site-packages/PyQt4/

for i in *.so; do sudo install_name_tool $i -change QtGui.framework/Versions/4/QtGui /Library/Frameworks/QtGui.framework/Versions/4/QtGui; done

for i in *.so; do sudo install_name_tool $i -change QtCore.framework/Versions/4/QtCore /Library/Frameworks/QtCore.framework/Versions/4/QtCore; done

for i in *.so; do sudo install_name_tool $i -change QtOpenGL.framework/Versions/4/QtOpenGL /Library/Frameworks/QtOpenGL.framework/Versions/4/QtOpenGL; done

cd /Library/Frameworks/QtOpenGL.framework/Versions/4/ 

sudo install_name_tool QtOpenGL -change QtCore.framework/Versions/4/QtCore /Library/Frameworks/QtCore.framework/Versions/4/QtCore

sudo install_name_tool QtOpenGL -change QtGui.framework/Versions/4/QtGui /Library/Frameworks/QtGui.framework/Versions/4/QtGui

cd /Library/Frameworks/QtGui.framework/Versions/4/

sudo install_name_tool QtGui -change QtCore.framework/Versions/4/QtCore /Library/Frameworks/QtCore.framework/Versions/4/QtCore

I hope I didn't miss any; but basically, depending on the error triggered, you change the library the fails to import, for one that actually exists (you can figure the latter out doing a terminal search; for example, "locate QtGui.Framework/Versions/4/QtGui", which is on the offending lines in the import, spits out "/Library/Frameworks/QtGui.framework/Versions/4/QtGui", which seems to be the correct replacement.

e2display now launches and displays EM maps without issues, so I'm assuming the issue is fixed.

I wonder whether Steve or someone else might be able to figure out a more efficient fix??

On Tuesday, February 7, 2017 at 6:09:03 PM UTC-6, pawe...@att.net wrote:

Hi

I never managed the graphics. What I posted earlier fixes basic operations. I tried this and that with graphics, I believe I also recompiled the relevant libraries but no luck. 

So I was waiting for you guys to figure it out😜

Regards,

Pawel

On Feb 7, 2017, at 5:54 PM, Jesus Montoya <jga...@gmail.com> wrote:

Hi Pawel,

I'm getting the same errors compiling on Sierra.

For the first error, related to libboost, the fix is to change "libboost_python.dylib" to "/usr/local/lib/libboost_ python.dylib" in all *.so files inside of "/Users/pawel/EMAN2/lib/".

I did this with a similar command as yours and it worked:

cd $EMAN2DIR/lib
for i in *.so
do
install_name_tool $i -change libboost_python.dylib /usr/local/lib/libboost_python .dylib
done

However, for the second error, "QtGui.framework/Versions/4/ QtGui" seems to be problematic in all *.so files inside "/Library/Python/2.7/site- packages/PyQt4/" (correct?).

What do I need to change it to? What should the value be of the red question marks below?
Thanks for your help!

cd 

/Library/Python/2.7/site- packages/PyQt4/

for i in *.so
do

install_name_tool $i -change QtGui.framework/ Versions/4/QtGui <???>
done

I'm assuming /Library/Frameworks/ QtGui.framework/Versions/4/ QtGui might be the correct answer, but I cannot seem to run the command unless I use sudo, so I'm a bit wary of running the wrong command.
Thanks!
 

cd /Library/Python/2.7/site- packages/PyQt4/

for i in *.so
do
sudo install_name_tool $i -change QtGui.framework/ Versions/4/QtGui 

/Library/ Frameworks/QtGui.framework/ Versions/4/QtGui 
done

On Tuesday, December 20, 2016 at 9:00:20 AM UTC-6, pawe...@att.net wrote:

I also did this:

pawel-Air:/Users/pawel 256> otool -L /Library/Python/2.7/site- packages/PyQt4/QtGui.so

/Library/Python/2.7/site- packages/PyQt4/QtGui.so:

QtGui.framework/Versions/4/ QtGui (compatibility version 4.8.0, current version 4.8.2)

QtCore.framework/Versions/4/ QtCore (compatibility version 4.8.0, current version 4.8.2)

/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)

/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)

---

From: Paul Penczek <pawe...@att.net>
To: "em...@googlegroups.com" <em...@googlegroups.com>
Sent: Tuesday, December 20, 2016 8:45 AM
Subject: Re: [EMAN2] OSX 10.12

Hi,

driiving safely?

The page helped somewhat.  Now at least the system starts.  However:

1. it turns out each time I recompile eman2 I have to repeat the fix.

2.  display did not work and I could not figure how to fix it.

Pawel.

/Users/pawel/EMAN2/lib/EMAN2_ cppwrap.py in <module>()

     31 #

     32 

---> 33 from libpyAligner2 import *

     34 from libpyAverager2 import *

     35 from libpyBoxingTools2 import *

ImportError: dlopen(/Users/pawel/EMAN2/lib/ libpyAligner2.so, 2): Library not loaded: libboost_python.dylib

  Referenced from: /Users/pawel/EMAN2/lib/ libpyAligner2.so

  Reason: unsafe use of relative rpath libboost_python.dylib in /Users/pawel/EMAN2/lib/ libpyAligner2.so with restricted binary

In [1]: quit

pawel-Air:/Users/pawel 250> !for

foreach n ( /Users/pawel/EMAN2/lib/libpy* so )

foreach? install_name_tool -change libboost_python.dylib /usr/local/lib/libboost_ python.dylib $n

foreach? end

pawel-Air:/Users/pawel 253> sx.py

Python 2.7.10 (default, Jul 30 2016, 19:40:32) 

Type "copyright", "credits" or "license" for more information.

IPython 1.2.1 -- An enhanced Interactive Python.

?         -> Introduction and overview of IPython's features.

%quickref -> Quick reference.

help      -> Python's own help system.

object?   -> Details about 'object', use 'object??' for extra details.

/Library/Python/2.7/site- packages/bsddb3-5.3.0-py2.7- macosx-10.9-intel.egg/bsddb3/_ pybsddb.py:3: UserWarning: Module readline was already imported from /Library/Python/2.7/site- packages/IPython/utils/ rlineimpl.pyc, but /Library/Python/2.7/site- packages/readline-6.2.4.1-py2. 7-macosx-10.7-intel.egg is being added to sys.path

Welcome to the interactive SPARX-NoGUI Python interface, provided by ipython

   SPARX v4.0 (GITHUB: Tue Dec 20 08:42:41 2016)

In [1]: display(test_image())

Traceback (most recent call last):

  File "/Users/pawel/EMAN2/bin/ e2display.py", line 36, in <module>

    from emapplication import EMApp

  File "/Users/pawel/EMAN2/lib/ emapplication.py", line 34, in <module>

    from PyQt4 import QtGui, QtCore, QtOpenGL

ImportError: dlopen(/Library/Python/2.7/ site-packages/PyQt4/QtGui.so, 2): Library not loaded: QtGui.framework/Versions/4/ QtGui

  Referenced from: /Library/Python/2.7/site- packages/PyQt4/QtGui.so

  Reason: unsafe use of relative rpath QtGui.framework/Versions/4/ QtGui in /Library/Python/2.7/site- packages/PyQt4/QtGui.so with restricted binary

[Steve Ludtke]

Over my trip to Australia I finally got around to a complete reconfiguration of my MacBook Pro so I can compile from source. I did this basically in the airport lounge between flights (with some advice), so clearly it didn't take terribly long to do it. I completely removed all of the old cr4p I had on there previously via custom builds of dependencies.  With one small exception, I did this using Anaconda:

1) Install current Python2 Anaconda

2) configure account to use this anaconda. I have a "useconda2" command which does this:

useconda2='export PYTHONPATH=$HOME/EMAN2/lib:$HOME/EMAN2/bin; export PATH=$HOME/anaconda2/bin:$HOME/EMAN2/bin:.:/users/stevel/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Developer/usr/bin:/Applications/Chimera.app/Contents/MacOS'

(I just reset the entire PATH to avoid building up redundancies)

3) Install FFTW from source. Compile both normal (double) and --enable-single. While there are a dozen different versions available from anaconda, I didn't want to try and find one that had the necessary versions, so I just built it. If someone figures out one that works, let me know. You will also need --enable-shared and I used --prefix=$HOME (so you don't have to deal with the Mac's annoying security subsystem).

4) Install other necessary Anaconda modules (conda install). This includes specific versions for a few. I don't recall how many of these were already installed and how many I had to do. Note that some need a specific version, eg:

conda install qt=4 pyqt=4

and a couple are from other channels, eg:

conda install -c conda-forge boost boost-cpp

boost                     1.63.0                   py27_4    conda-forge

boost-cpp                 1.63.0                        1    conda-forge

bsddb                     1.0                      py27_1  

freetype                  2.5.5                         2  

ftgl                      2.1.3                         2    jmbell

gsl                       2.2.1                         0  

hdf5                      1.8.17                        1  

ipython                   5.1.0                    py27_0  

ipython_genutils          0.1.0                    py27_0  

jpeg                      9b                            0  

libpng                    1.6.27                        0  

libtiff                   4.0.6                         3  

matplotlib                1.5.3               np111py27_0  

numpy                     1.11.1                   py27_0  

pyopengl                  3.0.2                    py27_0  

pyqt                      4.11.4                   py27_4  

qt                        4.8.7                         4  

scikit-learn              0.17.1              np111py27_2  

scipy                     0.18.1              np111py27_0  

theano                    0.8.2                    py27_0  

tk                        8.5.18                        0  

5) Once all of this is done, all you have to do is get your CMake configuration to point at all of the right files. Unfortunately, since the current CMakeLists file doesn't search anaconda at the moment, this is a manual process:

BOOST_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include/boost

BOOST_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libboost_python.dylib

FREETYPE_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include/freetype2

FREETYPE_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libfreetype.dylib

FTGL_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include

FTGL_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libftgl.2.dylib

GSL_CBLAS_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include

GSL_CBLAS_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libgslcblas.dylib

GSL_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include

GSL_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libgsl.dylib

HDF5_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include

HDF5_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libhdf5.dylib

JPEG_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include

JPEG_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libjpeg.dylib

NUMPY_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/lib/python2.7/site-packages/numpy/core/include

PNG_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include

PNG_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libpng.dylib

PYTHON_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include/python2.7

PYTHON_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libpython2.7.dylib

TIFF_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include

TIFF_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libtiff.dylib

ZLIB_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libz.dylib

FFTW3_INCLUDE_PATH:PATH=/Users/stevel/include

FFTW3_LIBRARY:FILEPATH=/Users/stevel/lib/libfftw3f.dylib

FFTW3d_INCLUDE_PATH:PATH=/Users/stevel/include

FFTW3d_LIBRARY:FILEPATH=/Users/stevel/lib/libfftw3.dylib

Once this was done (it really didn't take very long to do), everything works for me, including the GUI. While I haven't tested absolutely everything, I did go through a lot of the tutorial and everything seemed fine.

[Steve Ludtke]

I've updated the installation instructions on the Wiki to reflect what I wrote below with a few additional notes.

[Paul Penczek]

Hmmm...  Flight to Australia is very long which explains your impression it did not take long. Still, if it works it is worth trying. It does not look like you had to remove any old installs (except one which seems uncommon). 

Regards,

Pawel

[Steve Ludtke]

Not on the flight, in the lounge between flights  :^)   Hard to download a bunch of packages from the plane. Plane internet not up to that sort of thing.

'completely removed all of the old cr4p' means I deleted the entire contents of /usr/local (I did keep a copy just in case), so that wasn't entirely trivial.  I now have things configured so I can use either the binary install (for testing, etc.) or build from source. Seems to be working very nicely, except for the Qt4 bug on recent MacOS versions which puts the window resizing handle near the top of the window, and that's an internal Qt4 problem as far as I know.  Would like to switch to Qt5, but the changes they made means this may be a fair bit of work...

[Paul Penczek]

/usr/local contains only user-installed stuff, so removing it should not be excessively dangerous. 

Maybe over the weekend...

Regards,

Pawel

[Jesus Montoya]

Pawel, on the computer (iMac) where I got things to work (not as cleanly as Steve) I was indeed using anaconda2, per Steve's recommendation a few days ago.

Steve, thanks for updating the instructions. I followed them for my laptop and things seem to work fine (e2.py, e2speedtest.py, e2display.py).

As you mentioned, FFTW wasn't found by anaconda, so I compiled from source. Does using version 3.3.4 make any difference, vs version 3.3.5?

FTGL wasn't initially found either, so I did:

conda install -c mlgill ftgl=2.1.3

On a (perhaps separate) note, the CMAKE_OSX_SYSROOT was empty when running cmake ../eman2.
Is that OK/normal/expected? I just manually set it to /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk 

[Jesus Montoya]

Hm. The process updated by Steve worked like a charm on  my laptop. But now that I'm trying to replicate things to work cleanly on my iMac, following the same protocol, cmake fails to build EMAN2.

                        if (verbose>0) printf("%d orientations to test (%d)\n",(int)(transforms.size()*(360.0/astep)),transforms.size());

                                                                        ~~                                            ^~~~~~~~~~~~~~~~~

                                                                        %lu

/Users/jgalaz/srcgit/eman2/libEM/aligner.cpp:3368:29: warning: format specifies type 'int' but the argument has type 'size_type'

      (aka 'unsigned long') [-Wformat]

                                        printf("  %d/%d \r",it,transforms.size());

                                                     ~~        ^~~~~~~~~~~~~~~~~

                                                     %lu

/Users/jgalaz/srcgit/eman2/libEM/aligner.cpp:3477:44: warning: expression result unused [-Wunused-value]

                                                for (int j=0; j<3; j++) s_step[i*3+j]*-0.75;

                                                                        ~~~~~~~~~~~~~^~~~~~

/Users/jgalaz/srcgit/eman2/libEM/aligner.cpp:4026:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean

      'delete[]'? [-Wmismatched-new-delete]

        delete cr;

        ^

              []

/Users/jgalaz/srcgit/eman2/libEM/aligner.cpp:3891:12: note: allocated with 'new[]' here

        float* cr=new float[size*(bw+1)];

                  ^

/Users/jgalaz/srcgit/eman2/libEM/aligner.cpp:4028:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean

      'delete[]'? [-Wmismatched-new-delete]

        delete ci;

        ^

              []

/Users/jgalaz/srcgit/eman2/libEM/aligner.cpp:3892:12: note: allocated with 'new[]' here

        float* ci=new float[size*(bw+1)];

                  ^

15 warnings and 15 errors generated.

make[2]: *** [libEM/CMakeFiles/EM2.dir/aligner.o] Error 1

make[1]: *** [libEM/CMakeFiles/EM2.dir/all] Error 2

make: *** [all] Error 2 

[Steve Ludtke]

Right, but you didn't show us any of the errors?

Is your OSX up to date?

Is your XCode up to date?

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Steve Ludtke]

A further note. I installed from source on one more Mac completely from scratch, and used this as an opportunity to tweak the new installation instructions, and the CMakeLists file. The instructions are now much shorter and simpler, and everything seems to work like a charm for me. Be sure to update to a current copy of the source from GitHub.

http://eman2.org/COMPILE_EMAN2_MAC_OS_X

[Paul Penczek]

Steve:

I started the anaconda install.  Should I damage my laptop expect my visit in the afternoon...

Pawel.

---

[Steve Ludtke]

One thing not mentioned on the page. If you have previously installed a bunch of dependencies manually or via one of the Mac package managers, you may wish to remove them if you don't need them for something else. As I mentioned before, the first thing I did was to completely remove the contents of /usr/local

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Paul Penczek]

Yes, this you mentioned in a letter early and I did clean it. 

However as I wrote just few moments ago I cannot execute conda. I hope for hints. 

Regards,

Pawel

[Paul Penczek]

I got to point #5 of your instructions.  The condo stuff indeed went smoothly and quickly, but I have no way to say whether it was successful.

 Now I am trying to do the ccmake:

I did the below

PYTHON_INCLUDE_PATH=$HOME/anaconda2/include/python2.7
PYTHON_LIBRARY=$HOME/anaconda2/lib/libpython2.7.dylib
ZLIB_LIBRARY=$HOME/anaconda2/lib/libz.dylib

and for some reason I had to change Sdk

However, ccmake complains (see attached snapshot) and if I push it anyway the compilation failed on multiple errors.

???

[Steve Ludtke]

I see the warning as well, and haven't decided whether to do something about it yet, but it is harmless for now.  I don't get compile errors, so I'd probably need to see one...

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

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<ccmakeproblems.tiff>

[Paul Penczek]

Maybe I should have wiped out the previous eman2 directory, or is it not necessary?

Regards,

Pawel

[Paul Penczek]

I will send you examples of errors in10 minutes. 

Regards,

Pawel

[Paul Penczek]

Now that I checked it carefully I realized that the problems are earlier.

libfftw3f is obviously under anaconda2, but I do not know about libEM2.dylib.  What is it??

pawel-Air:/Users/pawel/EMAN2/src/build 209> cmake ../eman2

-- Configuring done

CMake Warning (dev):

  Policy CMP0042 is not set: MACOSX_RPATH is enabled by default.  Run "cmake

  --help-policy CMP0042" for policy details.  Use the cmake_policy command to

  set the policy and suppress this warning.

  MACOSX_RPATH is not specified for the following targets:

   EM2

   GLEM2

   pyAligner2

   pyAnalyzer2

   pyAverager2

   pyBoxingTools2

   pyCmp2

   pyEMData2

   pyEMObject2

   pyFundamentals2

   pyGLUtils2

   pyGeometry2

   pyMarchingCubes2

   pyPDBReader2

   pyPointArray2

   pyPolarData2

   pyProcessor2

   pyProjector2

   pyReconstructor2

   pyTomoSeg2

   pyTransform2

   pyTypeConverter2

   pyUtils2

This warning is for project developers.  Use -Wno-dev to suppress it.

-- Generating done

-- Build files have been written to: /Users/pawel/EMAN2/src/build

pawel-Air:/Users/pawel/EMAN2/src/build 210> make -j

Scanning dependencies of target EM2

make[2]: *** No rule to make target `/usr/local/lib/libfftw3f.dylib', needed by `lib/libEM2.dylib'.  Stop.

make[2]: *** Waiting for unfinished jobs....

[Steve Ludtke]

Yes, I would suggest starting completely from scratch with this project. I completely removed my Git checkout as well as all installed EMAN2 folders.

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Steve Ludtke]

I think you may just need to remove your eman2 folder and do a fresh Git checkout. It should find the FFTW version installed in anaconda automatically, but if you didn't start from scratch, the cache will have all sorts of incorrect paths.

You are following the instructions from the Wiki, not the ones I emailed, right?

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Paul Penczek]

Yes, I was following the wiki stuff.

You may want to add helpful hints for morons:

that one should use binary anaconda install.  I lost couple of hours struggling with the GUI one.

Also, it was not immediately apparent to me where to put stuff in point #5.

Finally, I think it might be necessary, not only advisable, to remove the old eman2 install first.

I will try to repeat everything tonight.  Now the weather is too nice to deal with it.

Pawel.

---

From: Steve Ludtke <slud...@gmail.com>
To: em...@googlegroups.com

Sent: Sunday, February 12, 2017 2:31 PM

Subject: Re: [EMAN2] OSX 10.12

[Paul Penczek]

I am biking around and thinking. 

Completely from scratch means including removal what anaconda installed?

It also puzzles me there is no pydusa in your instructions. So where is mpirun step?

Regards,

Pawel

[Steve Ludtke]

I considered that a separate step. Instructions for that are elsewhere, since EMAN only uses MPI on clusters, not workstations.  It is true, though, that we should consider how to integrate it into the anaconda environment since we seem to be going that way. OpenMPI is no problem 

conda install openmpi

I just added that now to the Wiki install instructions. Pydusa may require some thought. While I'm sure it can be made to install in the anaconda environment, we can probably make it easier. Perhaps we can add it to a channel somewhere so 'conda' can be used to install it. Anaconda uses the (now widely used) mpi4py. I have not investigated whether it's worth considering a change, given how deprecated Pydusa is.

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Paul Penczek]

I noticed your changes in instructions. Greatly appreciated!

Outside of simple utilities my programs require mpi. I also need it to develop the code. 

pydusa not only is outdated but it is also extremely slow. 

I'll try to run it tonight and see whether it still works with the new install. 

So what about installation on unix particularly clusters?  One still has to use the old way?  No anaconda?

Regards,

Pawel

[Steve Ludtke]

We are in the process of developing a new binary installation strategy which is based on Anaconda

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Paul Penczek]

I took a break. I'll try again tomorrow. 

Regards,

Pawel

[Paul Penczek]

Hi,

unless I am confused (which normally I am) you mentioned that now you prepare binary snapshot

using gcc V.5 that is supposedly 50% faster.

Is that correct?  Is it the one that is posted on the daily snapshots?  If not, how one can get it?

Thanks,

Pawel.

[Jesus Galaz-Montoya]

Hi Steve,

Following the new protocol on my iMac, with a fresh clone from git, NUMPY isn't found automatically, and many variables link to /usr/local.

 CMake Error: The following variables are used in this project, but they are set to NOTFOUND.

 Please set them or make sure they are set and tested correctly in the CMake files:

 NUMPY_INCLUDE_PATH

    used as include directory in directory /Users/jgalaz/srcgit/eman2

    used as include directory in directory /Users/jgalaz/srcgit/eman2/rt

    used as include directory in directory /Users/jgalaz/srcgit/eman2/rt/pyem

I changed linked all options manually to /Users/jgalaz/anaconda2/include and the appropriate /Users/jgalaz/anaconda2/lib/libxxxxxx.dylib, but am still getting these errors:

[ 94%] Built target pyTransform2

1 warning generated.

[ 95%] Linking CXX shared library ../lib/libpyEMData2.dylib

cd /Users/jgalaz/srcgit/eman2/libpyEM && /Users/jgalaz/anaconda2/bin/cmake -E cmake_link_script CMakeFiles/pyEMData2.dir/link.txt --verbose=1

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++    -O3 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -dynamiclib -Wl,-headerpad_max_install_names  -o ../lib/libpyEMData2.dylib -install_name @rpath/libpyEMData2.dylib CMakeFiles/pyEMData2.dir/libpyEMData2.o CMakeFiles/pyEMData2.dir/emdata_wrapitems.o ../lib/libEM2.dylib /Users/jgalaz/anaconda2/lib/libboost_python.dylib /Users/jgalaz/anaconda2/lib/libpython2.7.dylib /Users/jgalaz/anaconda2/lib/libfftw3f.dylib /Users/jgalaz/anaconda2/lib/libfftw3.dylib /Users/jgalaz/anaconda2/lib/libgsl.dylib /Users/jgalaz/anaconda2/lib/libgslcblas.dylib -lm /Users/jgalaz/anaconda2/lib/libtiff.dylib /Users/jgalaz/anaconda2/lib/libjpeg.dylib /Users/jgalaz/anaconda2/lib/libhdf5.dylib /Users/jgalaz/anaconda2/lib/libz.dylib /Users/jgalaz/anaconda2/lib/libpng.dylib /Users/jgalaz/anaconda2/lib/libz.dylib /Users/jgalaz/anaconda2/lib/libpng.dylib -Wl,-rpath,/Users/jgalaz/srcgit/eman2/lib -Wl,-rpath,/Users/jgalaz/anaconda2/lib 

[ 95%] Built target pyEMData2

1 warning generated.

[ 96%] Linking CXX shared library ../lib/libpyUtils2.dylib

cd /Users/jgalaz/srcgit/eman2/libpyEM && /Users/jgalaz/anaconda2/bin/cmake -E cmake_link_script CMakeFiles/pyUtils2.dir/link.txt --verbose=1

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++    -O3 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -dynamiclib -Wl,-headerpad_max_install_names  -o ../lib/libpyUtils2.dylib -install_name @rpath/libpyUtils2.dylib CMakeFiles/pyUtils2.dir/libpyUtils2.o ../lib/libEM2.dylib /Users/jgalaz/anaconda2/lib/libboost_python.dylib /Users/jgalaz/anaconda2/lib/libpython2.7.dylib /Users/jgalaz/anaconda2/lib/libfftw3f.dylib /Users/jgalaz/anaconda2/lib/libfftw3.dylib /Users/jgalaz/anaconda2/lib/libgsl.dylib /Users/jgalaz/anaconda2/lib/libgslcblas.dylib -lm /Users/jgalaz/anaconda2/lib/libtiff.dylib /Users/jgalaz/anaconda2/lib/libjpeg.dylib /Users/jgalaz/anaconda2/lib/libhdf5.dylib /Users/jgalaz/anaconda2/lib/libz.dylib /Users/jgalaz/anaconda2/lib/libpng.dylib /Users/jgalaz/anaconda2/lib/libz.dylib /Users/jgalaz/anaconda2/lib/libpng.dylib -Wl,-rpath,/Users/jgalaz/srcgit/eman2/lib -Wl,-rpath,/Users/jgalaz/anaconda2/lib 

[ 96%] Built target pyUtils2

make: *** [all] Error 2

[Steve Ludtke]

If you read the current instructions (they were updated earlier today), there are some specific points which should resolve these issues. Are you sure you had your shell configured to use anaconda2 when you ran ccmake?  Are you sure you completely removed the old eman2 folder before doing the fresh git checkout?

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Steve Ludtke]

The current 2.2alpha download has a binary complied with GCC5.  It probably is a week or so out of date (from the current Git snapshot). Note that this is only for Linux, and then, only for Linux versions which are compatible with GCC5. Some, like CentOS6, which don't support GCC5 out of the box, can supposedly be made compatible. GCC6 is even better, though only a small amount, so we went with 5.

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Paul Penczek]

Ok, I hope Toshio will give it a try. 

Regards,

Pawel

[Jesus Montoya]

Yes, Xcode is up to date; the errors are there, they're just (strangely) colored white, so one has to highlight the white empty space to see them. I'll repaste them bellow in a visible color:

[Steve Ludtke]

What you pasted was warnings. No errors.

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Paul Penczek]

Hi,

it pulls incorrect version of openmpi.  The system will not work with it.

You need version 1.10.2

Thanks,

Pawel.

[Paul Penczek]

More problems.

First a request:  you want to add at the beginning of #6 that one should open new window.

Otherwise the just installed ccmake cannot be found.

Then I ran ccmake as per instructions and I got this:

 CMake Error at CMakeLists.txt:206 (if):

   if given arguments:

     "STREQUAL" "BUILD"

   Unknown arguments specified

This means full stop, as I have no idea what to do next.

Pawel.

---

From: Paul Penczek <pawe...@att.net>
To: "em...@googlegroups.com" <em...@googlegroups.com>

Sent: Monday, February 13, 2017 6:12 PM
Subject: [EMAN2] Error in anaconda installer

[Jesus Galaz-Montoya]

All of this is on the latest MacOSX, Sierra 10.2.

Xcode seems functional:

jesuss-imac:build jgalaz$ g++ --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 8.0.0 (clang-800.0.42.1)
Target: x86_64-apple-darwin16.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

I've started cleanly from scratch for the billionth time now:
I did sudo rm -rf ~/EMAN2 ~/srcgit/eman2 ~/src/build, then cloned eman2 freshly from git.

I installed anaconda2 in my home directory more than a week ago when you originally suggested to use anaconda.

I've defined the same 'useconda2' alias as in your e-mail (and the updated Wiki), and ran the alias before compiling.

I opened a fresh terminal, ran all the "conda install" commands in the updated instructions, then ccmake, configured all options manually (since cmake didn't find them automatically) to use the appropriate include and lib directories at /Users/jgalaz/anacoda2/. 

Still, I got the same error as before.

I've now deleted /usr/local/lib altogether, ran the HomeBrew uninstaller to get rid of whatever I installed with HomreBrew long ago, deleted many old irrelevant things from /usr/local/bin. I can't get rid of all of it because Git and IMOD seem to have stuff in there. 

I repeated the whole process from scratch yet again (remove the ~/EMAN2, ~/srcgit/eman2, and ~/srcgit/build directories; clone eman2 from git, run conda install for all dependencies just in case, etc).

Cmake upgraded to 3.6.3 and is now giving a weirder error...

CMake Error at CMakeLists.txt:206 (if):
   if given arguments:
   "STREQUAL" "BUILD"
   Unknown arguments specified

I wonder whether the culprit might be my environment; do any variables other than PATH and PYTHONPATH need to be reset or defined? (LD_LIBRARY_PATH, LIBRARY_PATH, etc.)? (I'm tempted to just copy the ~/.profile file from my laptop, where things are working). 

[Steve Ludtke]

Sorry, someone committed a bad patch today that I didn't catch. Temporarily just set a shell variable before running ccmake:

CONDA_BUILD_STATE=x

Well get it fixed soon.

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Paul Penczek]

THESE ARE ALL numpys I could find.

pawel-Air:/Users/pawel 212> ff numpy

./anaconda2/include/boost/python/numpy

./anaconda2/lib/python2.7/site-packages/astropy/utils/compat/numpy

./anaconda2/lib/python2.7/site-packages/Cython/Includes/numpy

./anaconda2/lib/python2.7/site-packages/numpy

./anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy

./anaconda2/lib/python2.7/site-packages/pandas/compat/numpy

./anaconda2/pkgs/astropy-1.3-np111py27_0/lib/python2.7/site-packages/astropy/utils/compat/numpy

./anaconda2/pkgs/boost-1.63.0-py27_5/include/boost/python/numpy

./anaconda2/pkgs/cython-0.25.2-py27_0/lib/python2.7/site-packages/Cython/Includes/numpy

./anaconda2/pkgs/numpy-1.11.3-py27_0/lib/python2.7/site-packages/numpy

./anaconda2/pkgs/numpy-1.11.3-py27_0/lib/python2.7/site-packages/numpy/core/include/numpy

./anaconda2/pkgs/pandas-0.19.2-np111py27_1/lib/python2.7/site-packages/pandas/compat/numpy

./Desktop/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy

./Desktop/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy

./Desktop/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/numarray/include/numpy

[Paul Penczek]

That got me we step further.  Now it looks like bumpy is not found.

 FFTW3F_LIBRARIES:

 FFTW_INCLUDE_PATH: /Users/pawel/anaconda2/include

 NUMPY_INCLUDE_PATH: NUMPY_INCLUDE_PATH-NOTFOUND

 INCLUDE_DIRECTORIES---START

 INCLUDE_DIRECTORIES---END

 CMake Error: The following variables are used in this project, but they are set to NOTFOUND.

 Please set them or make sure they are set and tested correctly in the CMake files:

 NUMPY_INCLUDE_PATH

    used as include directory in directory /Users/pawel/eman2

    used as include directory in directory /Users/pawel/eman2

    used as include directory in directory /Users/pawel/eman2

    used as include directory in directory /Users/pawel/eman2

    used as include directory in directory /Users/pawel/eman2

    used as include directory in directory /Users/pawel/eman2

    used as include directory in directory /Users/pawel/eman2

    used as include directory in directory /Users/pawel/eman2/rt

    used as include directory in directory /Users/pawel/eman2/rt

    used as include directory in directory /Users/pawel/eman2/rt

    used as include directory in directory /Users/pawel/eman2/rt

    used as include directory in directory /Users/pawel/eman2/rt

    used as include directory in directory /Users/pawel/eman2/rt

    used as include directory in directory /Users/pawel/eman2/rt/pyem

    used as include directory in directory /Users/pawel/eman2/rt/pyem

    used as include directory in directory /Users/pawel/eman2/rt/pyem

    used as include directory in directory /Users/pawel/eman2/rt/pyem

    used as include directory in directory /Users/pawel/eman2/rt/pyem

    used as include directory in directory /Users/pawel/eman2/rt/pyem

    used as include directory in directory /Users/pawel/eman2/rt/emdata

    used as include directory in directory /Users/pawel/eman2/rt/emdata

Errors occurred during the last pass                                                                                                              

                                                                                                                               CMake Version 3.6.3

---

From: Steve Ludtke <slud...@gmail.com>

To: em...@googlegroups.com
Sent: Monday, February 13, 2017 6:42 PM
Subject: Re: [EMAN2] Error in anaconda installer

[Steve Ludtke]

I just tested the current snapshot and it doesn't require the env variable any more.  I also have no problems with it finding my numpy. If you do have problems look at the troubleshooting section of the page...

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Paul Penczek]

I had to edit CM file to put proper numpy location.

After that it compiled properly.

After couple of false starts I made it to respond.  I think it had problem initiating ipython.

Finally, I decided to try display.  That produced a window with some garbage in it, but also

many errors.  They keep appearing when I tried to resize the window, so something 

is still deeply wrong.  One more thing, it is not clear to me whether when I start sparx

I should do useconda2 environment or not.

pawel-Air:/Users/pawel 210% sx.py

Python 2.7.13 |Anaconda custom (x86_64)| (default, Dec 20 2016, 23:05:08) 

Type "copyright", "credits" or "license" for more information.

IPython 5.1.0 -- An enhanced Interactive Python.

?         -> Introduction and overview of IPython's features.

%quickref -> Quick reference.

help      -> Python's own help system.

object?   -> Details about 'object', use 'object??' for extra details.

/Users/pawel/EMAN2/bin/sx_real.py:48: DeprecationWarning: `IPython.lib.inputhook` is deprecated since IPython 5.0 and will be removed in future versions.

  import IPython.lib.inputhook

Welcome to the interactive SPARX-NoGUI Python interface, provided by ipython

   SPARX v4.0 (GITHUB: Mon Feb 13 22:31:37 2017)

In [1]: b=test_image()

In [2]: fft(b)

Out[2]: <libpyEMData2.EMData at 0x125c00590>

In [3]: display(b)

/Users/pawel/anaconda2/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.

  warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')

Traceback (most recent call last):

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 214, in paintGL

    self.render()

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 1032, in render

    if self.tex_name != 0: glDeleteTextures(self.tex_name)

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/latebind.py", line 61, in __call__

    return self.wrapperFunction( self.baseFunction, *args, **named )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/GL/exceptional.py", line 59, in glDeleteTextures

    ptr = arrays.GLuintArray.asArray( size )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 149, in asArray

    return cls.getHandler(value).asArray( value, typeCode or cls.typeConstant )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 53, in __call__

    typ.__module__, type.__name__, repr(value)[:50]

TypeError: No array-type handler for type numpy.type (value: 1) registered

Traceback (most recent call last):

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 214, in paintGL

    self.render()

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 1032, in render

    if self.tex_name != 0: glDeleteTextures(self.tex_name)

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/latebind.py", line 61, in __call__

    return self.wrapperFunction( self.baseFunction, *args, **named )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/GL/exceptional.py", line 59, in glDeleteTextures

    ptr = arrays.GLuintArray.asArray( size )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 149, in asArray

    return cls.getHandler(value).asArray( value, typeCode or cls.typeConstant )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 53, in __call__

    typ.__module__, type.__name__, repr(value)[:50]

TypeError: No array-type handler for type numpy.type (value: 1) registered

Traceback (most recent call last):

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 214, in paintGL

    self.render()

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 1032, in render

    if self.tex_name != 0: glDeleteTextures(self.tex_name)

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/latebind.py", line 61, in __call__

    return self.wrapperFunction( self.baseFunction, *args, **named )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/GL/exceptional.py", line 59, in glDeleteTextures

    ptr = arrays.GLuintArray.asArray( size )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 149, in asArray

    return cls.getHandler(value).asArray( value, typeCode or cls.typeConstant )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 53, in __call__

    typ.__module__, type.__name__, repr(value)[:50]

TypeError: No array-type handler for type numpy.type (value: 1) registered

Traceback (most recent call last):

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 214, in paintGL

    self.render()

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 1032, in render

    if self.tex_name != 0: glDeleteTextures(self.tex_name)

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/latebind.py", line 61, in __call__

    return self.wrapperFunction( self.baseFunction, *args, **named )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/GL/exceptional.py", line 59, in glDeleteTextures

    ptr = arrays.GLuintArray.asArray( size )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 149, in asArray

    return cls.getHandler(value).asArray( value, typeCode or cls.typeConstant )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 53, in __call__

    typ.__module__, type.__name__, repr(value)[:50]

TypeError: No array-type handler for type numpy.type (value: 1) registered

Traceback (most recent call last):

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 214, in paintGL

    self.render()

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 1032, in render

    if self.tex_name != 0: glDeleteTextures(self.tex_name)

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/latebind.py", line 61, in __call__

    return self.wrapperFunction( self.baseFunction, *args, **named )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/GL/exceptional.py", line 59, in glDeleteTextures

    ptr = arrays.GLuintArray.asArray( size )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 149, in asArray

    return cls.getHandler(value).asArray( value, typeCode or cls.typeConstant )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 53, in __call__

    typ.__module__, type.__name__, repr(value)[:50]

TypeError: No array-type handler for type numpy.type (value: 1) registered

Traceback (most recent call last):

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 214, in paintGL

    self.render()

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 1032, in render

    if self.tex_name != 0: glDeleteTextures(self.tex_name)

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/latebind.py", line 61, in __call__

    return self.wrapperFunction( self.baseFunction, *args, **named )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/GL/exceptional.py", line 59, in glDeleteTextures

    ptr = arrays.GLuintArray.asArray( size )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 149, in asArray

    return cls.getHandler(value).asArray( value, typeCode or cls.typeConstant )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 53, in __call__

    typ.__module__, type.__name__, repr(value)[:50]

TypeError: No array-type handler for type numpy.type (value: 1) registered

Traceback (most recent call last):

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 214, in paintGL

    self.render()

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 1032, in render

    if self.tex_name != 0: glDeleteTextures(self.tex_name)

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/latebind.py", line 61, in __call__

    return self.wrapperFunction( self.baseFunction, *args, **named )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/GL/exceptional.py", line 59, in glDeleteTextures

    ptr = arrays.GLuintArray.asArray( size )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 149, in asArray

    return cls.getHandler(value).asArray( value, typeCode or cls.typeConstant )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 53, in __call__

    typ.__module__, type.__name__, repr(value)[:50]

TypeError: No array-type handler for type numpy.type (value: 1) registered

Traceback (most recent call last):

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 214, in paintGL

    self.render()

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 1032, in render

    if self.tex_name != 0: glDeleteTextures(self.tex_name)

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/latebind.py", line 61, in __call__

    return self.wrapperFunction( self.baseFunction, *args, **named )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/GL/exceptional.py", line 59, in glDeleteTextures

    ptr = arrays.GLuintArray.asArray( size )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 149, in asArray

    return cls.getHandler(value).asArray( value, typeCode or cls.typeConstant )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 53, in __call__

    typ.__module__, type.__name__, repr(value)[:50]

TypeError: No array-type handler for type numpy.type (value: 1) registered

Traceback (most recent call last):

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 214, in paintGL

    self.render()

  File "/Users/pawel/EMAN2/lib/emimage2d.py", line 1032, in render

    if self.tex_name != 0: glDeleteTextures(self.tex_name)

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/latebind.py", line 61, in __call__

    return self.wrapperFunction( self.baseFunction, *args, **named )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/GL/exceptional.py", line 59, in glDeleteTextures

    ptr = arrays.GLuintArray.asArray( size )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 149, in asArray

    return cls.getHandler(value).asArray( value, typeCode or cls.typeConstant )

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 53, in __call__

    typ.__module__, type.__name__, repr(value)[:50]

TypeError: No array-type handler for type numpy.type (value: 1) registered

T

[Steve Ludtke]

Yes, you must have your account configured to use the anaconda environment when you run any sx* or e2* programs. I would suggest rebooting the computer after a successful install. I have no idea why, but I also had some strange errors just after installing, but a reboot cured it.

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Paul Penczek]

Now I am struggling with MPI.  Th first attempt failed, so I am trying to overwrite the old version you loaded with conda.  If you could upgraded to the current 1.10.2 it would simplify the matter.

I will try the reboot next.

---

From: Steve Ludtke <slud...@gmail.com>
To: em...@googlegroups.com

Sent: Monday, February 13, 2017 11:07 PM

Subject: Re: [EMAN2] Error in anaconda installer

[Paul Penczek]

No, rebooting did not help the display issue.

Nor did pydusa work.

I will wait until you upgrade openmpi version in conda and then try again from scratch.

Pawel.

---

From: Steve Ludtke <slud...@gmail.com>
To: em...@googlegroups.com

Sent: Monday, February 13, 2017 11:07 PM

Subject: Re: [EMAN2] Error in anaconda installer

[Steve Ludtke]

I think you are confused. We don't compile the dependencies in Anaconda. They are compiled and provided by the creators of Anaconda. The only one we compiled was FTGL which you can tell by which channel it's in.  What's wrong with the MPI version they provide?  That's a similar version to the one we use on one of our clusters with no problems...

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Paul Penczek]

This version is outdated. It does not have SHARED directives.  So if you run pydusa it will fail on missing symbols. 

In addition if you provide precompiled version of openmpi isn't it in conflict with the current approach that allows pydusa to figure preinstalled version on a given system?

Shouldn't you rather skip openmpi in conda installation?

Regards,

Pawel

[Steve Ludtke]

You can try this and see if this version is sufficient:

conda install -c conda-forge openmpi

[Paul Penczek]

It jumps too far:

openmpi:     1.6.3-1                   --> 2.0.2-0       conda-forge

We did not test v.2 at all.  Would take some effort...

---

From: Steve Ludtke <slud...@gmail.com>
To: em...@googlegroups.com

Sent: Tuesday, February 14, 2017 7:09 AM

[Paul Penczek]

Hi,

I upgraded openmpi to v.2 and at least pydusa worked and all symbols are there.  Whether it actually works I have no way to say, particularly that openmpi folks have a nasty custom

of removing some functions.

Can you replace permanently in your conda?

So now all what is left is the display :-(

Pawel.

---

From: Steve Ludtke <slud...@gmail.com>
To: em...@googlegroups.com

Sent: Tuesday, February 14, 2017 7:09 AM

[Paul Penczek]

Steve:

I started adding new variable "phase_shift" to the ctf machinery.

I thought I did everything correctly as I did with dfdiff in the past, but I clearly

missed something as despite my changes ctf object does not know about the new variables

even though I can set the value through a dictionary.

I chanced it in so you (or somebody who knows classes) can have a look.

I will wait with my further work until you have a chance to correct it (or comment on it).

I am also concerned that if I add another variable the hardwired positions of snr might be affected,

but I am not familiar with the way it is coded.

Thanks,

Pawel

Here is the problem:

c = EMAN2Ctf()

c.dfdiff works

but 

c.phase_shift does not

[Paul Penczek]

Now it failed entire on make.

Maybe the problem is with PYTHONPATH?

Pawel.

      ...

  "boost::python::objects::register_dynamic_id_aux(boost::python::type_info, std::__1::pair<void*, boost::python::type_info> (*)(void*))", referenced from:

      init_module_libpyGLUtils2() in libpyGLUtils2.o

      boost::python::class_<EMAN::GLUtil, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>::class_<boost::python::init<mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_> >(char const*, boost::python::init_base<boost::python::init<mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_> > const&) in libpyGLUtils2.o

ld: symbol(s) not found for architecture x86_64

clang: error: linker command failed with exit code 1 (use -v to see invocation)

make[2]: *** [lib/libpyGLUtils2.dylib] Error 1

make[1]: *** [libpyEM/CMakeFiles/pyGLUtils2.dir/all] Error 2

make: *** [all] Error 2

pawel-Air:/Users/pawel/EMAN2/src/eman2 217> setenv

TMPDIR=/var/folders/v1/pql9t6rd0r175_r6_n0wx81r0000gr/T/

XPC_FLAGS=0x0

Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.icQ3QmExyd/Render

LANG=en_US.UTF-8

TERM=xterm-256color

DISPLAY=/private/tmp/com.apple.launchd.UfJ4VK720X/org.macosforge.xquartz:0

SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.Vu4CN46Ek2/Listeners

SECURITYSESSIONID=186a7

TERM_PROGRAM=Apple_Terminal

XPC_SERVICE_NAME=0

TERM_PROGRAM_VERSION=388

TERM_SESSION_ID=C7E9EF81-1C8B-4A3D-A29D-D72E9B5F8FE8

__CF_USER_TEXT_ENCODING=0x1F8:0x0:0x0

SHELL=/bin/bash

HOME=/Users/pawel

LOGNAME=pawel

USER=pawel

PATH=.:/Users/pawel/anaconda2/bin:/Users/pawel/EMAN2/bin:/Users/pawel/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Developer/usr/bin:/Users/pawel/Desktop/Chimera.app/Contents/MacOS

HOSTTYPE=unknown

VENDOR=apple

OSTYPE=darwin

MACHTYPE=x86_64

SHLVL=1

PWD=/Users/pawel/EMAN2/src/eman2

GROUP=staff

HOST=pawel-Air.attlocal.net

CVSROOT=:ext:pa...@blake.bcm.tmc.edu:/usr/local/CVS/CVS

CVS_RSH=ssh

EMAN2DIR=/Users/pawel/EMAN2

PYTHONPATH=/Users/pawel/EMAN2/lib:/Users/pawel/EMAN2/bin

pawel-Air:/Users/pawel/EMAN2/src/eman2 218> ll /Users/pawel/EMAN2/lib

ls: /Users/pawel/EMAN2/lib: No such file or directory

pawel-Air:/Users/pawel/EMAN2/src/eman2 219> 

[Steve Ludtke]

You are saying it compiled successfully, then you did a 'conda install pyopengl=3.0' and it won't compile any more?  That doesn't make sense...

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Steve Ludtke]

can you do a 'conda list' and check the versions against the ones posted on the wiki?

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Paul Penczek]

No, I did all conda lines, then ccmake, then make, and then it failed on make.

---

From: Steve Ludtke <slud...@gmail.com>
To: em...@googlegroups.com

Sent: Sunday, February 19, 2017 12:26 PM

Subject: Re: [EMAN2] Error in anaconda installer

[Paul Penczek]

pawel-Air:/Users/pawel/EMAN2/src/eman2 220> conda list

# packages in environment at /Users/pawel/anaconda2:

#

_license                  1.1                      py27_1  

alabaster                 0.7.9                    py27_0  

anaconda                  custom                   py27_0  

anaconda-client           1.6.0                    py27_0  

anaconda-navigator        1.2.3                    py27_0  

appnope                   0.1.0                    py27_0  

appscript                 1.0.1                    py27_0  

argcomplete               1.0.0                    py27_1  

astroid                   1.4.9                    py27_0  

astropy                   1.3                 np111py27_0  

babel                     2.3.4                    py27_0  

backports                 1.0                      py27_0  

backports_abc             0.5                      py27_0  

beautifulsoup4            4.5.3                    py27_0  

bitarray                  0.8.1                    py27_0  

blaze                     0.10.1                   py27_0  

bokeh                     0.12.4                   py27_0  

boost                     1.61.0                   py27_0  

boost-cpp                 1.63.0                        2    conda-forge

boto                      2.45.0                   py27_0  

bottleneck                1.2.0               np111py27_0  

bsddb                     1.0                      py27_1  

bzip2                     1.0.6                         3  

cdecimal                  2.3                      py27_2  

cffi                      1.9.1                    py27_0  

chardet                   2.3.0                    py27_0  

chest                     0.2.3                    py27_0  

click                     6.7                      py27_0  

cloudpickle               0.2.2                    py27_0  

clyent                    1.2.2                    py27_0  

cmake                     3.6.3                         0  

colorama                  0.3.7                    py27_0  

conda                     4.2.13                   py27_0    conda-forge

conda-env                 2.6.0                         0    conda-forge

configobj                 5.0.6                    py27_0  

configparser              3.5.0                    py27_0  

contextlib2               0.5.4                    py27_0  

cryptography              1.7.1                    py27_0  

curl                      7.52.1                        0  

cycler                    0.10.0                   py27_0  

cython                    0.25.2                   py27_0  

cytoolz                   0.8.2                    py27_0  

dask                      0.13.0                   py27_0  

datashape                 0.5.4                    py27_0  

db                        5.3.28                        1  

decorator                 4.0.11                   py27_0  

dill                      0.2.5                    py27_0  

docutils                  0.13.1                   py27_0  

entrypoints               0.2.2                    py27_0  

enum34                    1.1.6                    py27_0  

et_xmlfile                1.0.1                    py27_0  

expat                     2.1.0                         0  

fastcache                 1.0.2                    py27_1  

fftw                      3.3.6                         0    conda-forge

flask                     0.12                     py27_0  

flask-cors                3.0.2                    py27_0  

freetype                  2.5.5                         2  

ftgl                      2.1.3                         2    jmbell

funcsigs                  1.0.2                    py27_0  

functools32               3.2.3.2                  py27_0  

futures                   3.0.5                    py27_0  

get_terminal_size         1.0.0                    py27_0  

gevent                    1.2.1                    py27_0  

greenlet                  0.4.11                   py27_0  

grin                      1.2.1                    py27_3  

gsl                       2.2.1                         0  

h5py                      2.6.0               np111py27_2  

hdf5                      1.8.17                        1  

heapdict                  1.0.0                    py27_1  

icu                       58.1                          1    conda-forge

idna                      2.2                      py27_0  

imagesize                 0.7.1                    py27_0  

ipaddress                 1.0.18                   py27_0  

ipykernel                 4.5.2                    py27_0  

ipython                   5.2.2                    py27_0  

ipython_genutils          0.1.0                    py27_0  

ipywidgets                5.2.2                    py27_1  

isort                     4.2.5                    py27_0  

itsdangerous              0.24                     py27_0  

jbig                      2.1                           0  

jdcal                     1.3                      py27_0  

jedi                      0.9.0                    py27_1  

jinja2                    2.9.4                    py27_0  

jpeg                      9b                            0  

jsonschema                2.5.1                    py27_0  

jupyter                   1.0.0                    py27_3  

jupyter_client            4.4.0                    py27_0  

jupyter_console           5.0.0                    py27_0  

jupyter_core              4.2.1                    py27_0  

lazy-object-proxy         1.2.2                    py27_0  

libgcc                    4.8.5                         1  

libgfortran               3.0.0                         0    conda-forge

libiconv                  1.14                          0  

libpng                    1.6.27                        0  

libtiff                   4.0.6                         3  

libxml2                   2.9.4                         0  

libxslt                   1.1.29                        0  

llvmlite                  0.16.0                   py27_0  

locket                    0.2.0                    py27_1  

lxml                      3.7.2                    py27_0  

markupsafe                0.23                     py27_2  

matplotlib                1.5.1               np111py27_0  

mistune                   0.7.3                    py27_1  

mkl                       2017.0.1                      0  

mkl-service               1.1.2                    py27_3  

mpmath                    0.19                     py27_1  

multipledispatch          0.4.9                    py27_0  

nbconvert                 4.2.0                    py27_0  

nbformat                  4.2.0                    py27_0  

ncurses                   5.9                          10  

networkx                  1.11                     py27_0  

nltk                      3.2.2                    py27_0  

nose                      1.3.7                    py27_1  

notebook                  4.3.1                    py27_0  

numba                     0.31.0              np111py27_0  

numexpr                   2.6.2               np111py27_0  

numpy                     1.11.3                   py27_0  

numpydoc                  0.6.0                    py27_0  

odo                       0.5.0                    py27_1  

olefile                   0.44                     py27_0    conda-forge

openmpi                   2.0.2                         0    conda-forge

openpyxl                  2.4.1                    py27_0  

openssl                   1.0.2k                        0  

pandas                    0.19.2              np111py27_1  

partd                     0.3.7                    py27_0  

path.py                   10.0                     py27_0  

pathlib2                  2.2.0                    py27_0  

patsy                     0.4.1                    py27_0  

pep8                      1.7.0                    py27_0  

pexpect                   4.2.1                    py27_0  

pickleshare               0.7.4                    py27_0  

pillow                    4.0.0                    py27_1  

pip                       9.0.1                    py27_1  

ply                       3.9                      py27_0  

prompt_toolkit            1.0.9                    py27_0  

psutil                    5.0.1                    py27_0  

ptyprocess                0.5.1                    py27_0  

py                        1.4.32                   py27_0  

pyasn1                    0.1.9                    py27_0  

pyaudio                   0.2.7                    py27_0  

pycosat                   0.6.1                    py27_1  

pycparser                 2.17                     py27_0  

pycrypto                  2.6.1                    py27_4  

pycurl                    7.43.0                   py27_2  

pyflakes                  1.5.0                    py27_0  

pygments                  2.1.3                    py27_0  

pylint                    1.6.4                    py27_1  

pyopengl                  3.0.2                    py27_0  

pyopenssl                 16.2.0                   py27_0  

pyparsing                 2.1.4                    py27_0  

pyqt                      4.11.4                   py27_4  

pytables                  3.3.0               np111py27_0  

pytest                    3.0.5                    py27_0  

python                    2.7.13                        0  

python-dateutil           2.6.0                    py27_0  

python.app                1.2                      py27_4  

pytz                      2016.10                  py27_0  

pyyaml                    3.12                     py27_0  

pyzmq                     16.0.2                   py27_0  

qt                        4.8.7                         4  

qtawesome                 0.4.3                    py27_0  

qtconsole                 4.2.1                    py27_0  

qtpy                      1.2.1                    py27_0  

readline                  6.2                           2  

redis                     3.2.0                         0  

redis-py                  2.10.5                   py27_0  

requests                  2.12.4                   py27_0  

rope                      0.9.4                    py27_1  

ruamel_yaml               0.11.14                  py27_1  

scandir                   1.4                      py27_0  

scikit-image              0.12.3              np111py27_1  

scikit-learn              0.18.1              np111py27_1  

scipy                     0.18.1              np111py27_1  

seaborn                   0.7.1                    py27_0  

setuptools                27.2.0                   py27_0  

simplegeneric             0.8.1                    py27_1  

singledispatch            3.4.0.3                  py27_0  

sip                       4.18                     py27_0  

six                       1.10.0                   py27_0  

snowballstemmer           1.2.1                    py27_0  

sockjs-tornado            1.0.3                    py27_0  

sphinx                    1.5.1                    py27_0  

spyder                    3.1.2                    py27_0  

sqlalchemy                1.1.5                    py27_0  

sqlite                    3.13.0                        0  

ssl_match_hostname        3.4.0.2                  py27_1  

statsmodels               0.8.0               np111py27_0  

subprocess32              3.2.7                    py27_0  

sympy                     1.0                      py27_0  

terminado                 0.6                      py27_0  

theano                    0.8.2                    py27_0  

tk                        8.5.18                        0  

toolz                     0.8.2                    py27_0  

tornado                   4.4.2                    py27_0  

traitlets                 4.3.1                    py27_0  

unicodecsv                0.14.1                   py27_0  

wcwidth                   0.1.7                    py27_0  

werkzeug                  0.11.15                  py27_0  

wheel                     0.29.0                   py27_0  

widgetsnbextension        1.2.6                    py27_0  

wrapt                     1.10.8                   py27_0  

xlrd                      1.0.0                    py27_0  

xlsxwriter                0.9.6                    py27_0  

xlwings                   0.10.2                   py27_0  

xlwt                      1.2.0                    py27_0  

xz                        5.2.2                         1  

yaml                      0.1.6                         0  

zlib                      1.2.8                         3  

pawel-Air:/Users/pawel/EMAN2/src/eman2 221> 

---

From: Steve Ludtke <slud...@gmail.com>
To: em...@googlegroups.com

Sent: Sunday, February 19, 2017 12:30 PM

Subject: Re: [EMAN2] Error in anaconda installer

[Paul Penczek]

boost is immediately different:

boost                     1.61.0                   py27_0  

boost-cpp                 1.63.0                        2    conda-forge

You have both at 63.

[Paul Penczek]

I should add I also did:

conda install -c conda-forge openmpi

Also different:

ipython                   5.2.2                    py27_0  

numpy                     1.11.3                   py27_0  

scikit-learn              0.18.1              np111py27_1  

[Steve Ludtke]

I would suggest trying to force the specific versions I had. I suspect mixing boost from forge and standard isn't a good idea, and could explain the error...

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Paul Penczek]

OK, I can try to start all over :-(

---

From: Steve Ludtke <slud...@gmail.com>
To: em...@googlegroups.com

Sent: Sunday, February 19, 2017 1:03 PM

Subject: Re: [EMAN2] Error in anaconda installer

[Steve Ludtke]

you don't have to start over. conda install will happily replace one version with another. Syntax is the same as with the pyopengl

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Paul Penczek]

I think I will give up permanently.  It is taking too much time:

pawel-Air:/Users/pawel 203% conda install boost=1.63.0

Fetching package metadata .........

PackageNotFoundError: Package not found: '' Package missing in current osx-64 channels: 

  - boost 1.63.0*

You can search for packages on anaconda.org with

    anaconda search -t conda boost

pawel-Air:/Users/pawel 204% anaconda search -t conda boost

Using Anaconda API: https://api.anaconda.org

Run 'anaconda show <USER/PACKAGE>' to get more details:

Packages:

     Name                      |  Version | Package Types   | Platforms      

     ------------------------- |   ------ | --------------- | ---------------

     ???/boost                 |   1.55.0 | conda           | linux-64       

                                          : http://www.boost.org/

[ERROR] 

Traceback (most recent call last):

  File "/Users/pawel/anaconda2/bin/anaconda", line 6, in <module>

    sys.exit(binstar_client.scripts.cli.main())

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/binstar_client/scripts/cli.py", line 88, in main

    description=__doc__, version=version)

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/binstar_client/scripts/cli.py", line 66, in binstar_main

    return args.main(args)

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/binstar_client/commands/search.py", line 15, in search

    pprint_packages(packages, access=False)

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/binstar_client/utils/pprint.py", line 70, in pprint_packages

    pprint_package(package, access, full_name, revision=revisions)

  File "/Users/pawel/anaconda2/lib/python2.7/site-packages/binstar_client/utils/pprint.py", line 34, in pprint_package

    package['conda_platforms'] = ', '.join(package['conda_platforms'])

TypeError: sequence item 2: expected string or Unicode, NoneType found

---

From: Steve Ludtke <slud...@gmail.com>
To: em...@googlegroups.com

Sent: Sunday, February 19, 2017 1:08 PM

[Steve Ludtke]

As you like. Longer than it took when you did it the other way installing all of the dependencies?  I still think you're just not quite following the instructions precisely. You had:

boost                     1.61.0                   py27_0  

boost-cpp                 1.63.0                        2    conda-forge

but the step in the instructions is:

conda install -c conda-forge boost boost-cpp fftw

which should have given you both boost and boost-cpp from the current conda-forge version. Where 1.61 came from I'm not exactly sure...

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Paul Penczek]

The installation itself is fast and I did it so many times I can do it with closed eyes. 

The problem is it is unsuccessful and I do not know why. I spent three days on it and I think it is enough. 

Regards,

Pawel

[Paul Penczek]

Hi,

facing the prospect of going back to compiled version I gave anaconda another chance and somehow this time it worked.  Outside of openmpi, that is, which still has the incorrect 1.6.3 version, but I am not going to rock the boat and I will ignore it.

The only snag that I detected is that display now block the prompt and I have to kill the the display window to release the prompt.  When repeated, the warning reappears.  Maybe I will leave it for a day hoping it will manage somehow.

However, I lived with worse, so I am prepared to let it go.

Pawel.

In [2]: a=test_image()

In [3]: display(a)

[Paul Penczek]

One more thing,

I also get this warning when I start interactive session:

[Steve Ludtke]

Yes, this is the reason why displaying blocks. ipython changed the way it worked internally, and nobody has figured out how to fix e2.py to work with the new scheme yet, so it goes into fallback mode for Qt windows.

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Jesus Montoya]

Steve, hi

Is CONDA_BUILD_STATE=x still needed?

I thought the nightmare had ended but without reinstalling any of the dependencies or modifying anything in my environment, things were (seemingly) spontaneously broken after updating eman2 today (compiling from source). Last time I used my old iMac to process any data (about a month ago), things were fine. 

After running conda list, I found a few minor differences compared to what is posted on the Wiki. I resolved most of them by installing the specific versions listed for each dependency, as suggested, except the following:

boost                     1.63.0                   py27_4    conda-forge  (my third column says np111py27_6)
boost-cpp                 1.63.0                        1    conda-forge  (my third column says 2)

How do I reinstall boost and boost-cpp so that "py27_4" and "1" appear in the third column of conda list instead of "np111py27_6" and "2"?

The command suggested on the Wiki doesn't do it (conda install -c conda-forge boost boost-cpp)

The specific error I am getting is:

jesuss-imac:~ jgalaz$ useconda2

jesuss-imac:~ jgalaz$ e2spt_boxer.py icon_gpu_prefilt_full_th700_ZSHORT_rotzM33p3yM3x2p4_rotz180_bin4.rec --inmemory

Traceback (most recent call last):

  File "/Users/jgalaz/EMAN2/bin/e2spt_boxer.py", line 41, in <module>

    from EMAN2 import *

  File "/Users/jgalaz/EMAN2/lib/EMAN2.py", line 44, in <module>

    from EMAN2_cppwrap import *

  File "/Users/jgalaz/EMAN2/lib/EMAN2_cppwrap.py", line 33, in <module>

    from libpyAligner2 import *

ImportError: dlopen(/Users/jgalaz/EMAN2/lib/libpyAligner2.so, 2): Library not loaded: @rpath/libboost_python.dylib

  Referenced from: /Users/jgalaz/EMAN2/lib/libpyAligner2.so

  Reason: image not found

The previous solution to this error doesn't seem to help:

cd $EMAN2DIR/lib
for i in *.so
do
install_name_tool $i -change libboost_python.dylib /usr/local/lib/libboost_python.dylib
done

[Steve Ludtke]

Hi Jesus,

I have no idea what CONDA_BUILD_STATE is. It is not mentioned in the mailing list or the Wiki. Someone else must have told you about it. I have never set it or used it on any of my machines.  

Conda will not update anything on its own, so if your conda versions have changed since you installed, you must have done something in the interim to make them change. 

You are correct, however, something seems to have changed recently which breaks the source build on mac. I just did a git pull on a Mac where it was working the other day and I am also getting Boost linker errors, with no other changes. I think Tunay must have changed something recently to make the binary builds work. Will check...

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Steve Ludtke]

Ok, have sorted this out a bit now.  The current instructions were written just as we were getting started with the Anaconda based distribution. That methodology has evolved and the current CMakefile is set up with building EMAN2 for a binary distribution in mind. This will require some alterations to the current build instructions. We're sorting that out now. When done we should have one build system which will produce source-based installs which look pretty much identical to the binary distributions. I think we're probably targeting a week from now for the actual binary release.

Hopefully we will have the source issues resolved sooner than that  :^)

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Steve Ludtke]

After conferring, it appears that the current system is actually fine. If you experience problems (linking problems, path problems, missing file problems, etc.) after doing a 'git pull', you need to do the following:

rm -rf EMAN2    (wherever you have it installed, usually ~/EMAN2)
cd src/eman2     (wherever you have the source code)
rm CMakeCache.txt
make clean
ccmake .
(select options)
c
g
make install

This worked for me, anyway.

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