Installation problem SPRING

[Dario Brack]

Hi,

I am trying o install SPRING on Ubuntu 14.04 but I do have some problems. The first problem was already discussed here (April 10th by Steve Wilson), but the solution suggested did not work for me:

I installed the libssl.so.0.9.8.e and after isntalling and integrating EMAN2 the next step was

./bin/python bootstrap.py

This gives the following error message: 

ERROR:root:code for hash md5 was not found.
Traceback (most recent call last):
  File "/home/dariobrack/Programme/SPRING/parts/EMAN2/Python/lib/python2.7/hashlib.py", line 139, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/home/dariobrack/Programme/SPRING/parts/EMAN2/Python/lib/python2.7/hashlib.py", line 91, in __get_builtin_constructor
    raise ValueError('unsupported hash type %s' % name)
ValueError: unsupported hash type md5
ERROR:root:code for hash sha1 was not found.
Traceback (most recent call last):
  File "/home/dariobrack/Programme/SPRING/parts/EMAN2/Python/lib/python2.7/hashlib.py", line 139, in <module>
    globals()[__func_name] = __get_hash(__func_name)
  File "/home/dariobrack/Programme/SPRING/parts/EMAN2/Python/lib/python2.7/hashlib.py", line 91, in __get_builtin_constructor
    raise ValueError('unsupported hash type %s' % name)
ValueError: unsupported hash type sha1
Traceback (most recent call last):
  File "bootstrap.py", line 167, in <module>
    exec ez_code in ez
  File "<string>", line 67, in <module>
  File "/home/dariobrack/Programme/SPRING/parts/EMAN2/Python/lib/python2.7/md5.py", line 10, in <module>
    from hashlib import md5
ImportError: cannot import name md5



The suggestion to prepend the command 

PYTHONPATH=$PWD/lib/python2.7/site-packages LD_LIBRARY_PATH=$PWD/parts/EMAN2/lib \

did not work but gave the following error message:



PYTHONPATH=$PWD/lib/python2.7/site-packages LD_LIBRARY_PATH=$PWD/parts/EMAN2/lib ./bin/python bootstrap.py

Download error on https://pypi.python.org/simple/zc.buildout/: [Errno 218603680] _ssl.c:553: error:0D07A0A0:asn1 encoding routines:ASN1_mbstring_copy:unknown format -- Some packages may not be found!
Couldn't find index page for 'zc.buildout' (maybe misspelled?)
Download error on https://pypi.python.org/simple/: [Errno 218603680] _ssl.c:553: error:0D07A0A0:asn1 encoding routines:ASN1_mbstring_copy:unknown format -- Some packages may not be found!
Download error on https://pypi.python.org/simple/zc.buildout/: [Errno 218603680] _ssl.c:553: error:0D07A0A0:asn1 encoding routines:ASN1_mbstring_copy:unknown format -- Some packages may not be found!
Couldn't find index page for 'zc.buildout' (maybe misspelled?)
Download error on https://pypi.python.org/simple/: [Errno 218603680] _ssl.c:553: error:0D07A0A0:asn1 encoding routines:ASN1_mbstring_copy:unknown format -- Some packages may not be found!
No local packages or download links found for zc.buildout
error: Could not find suitable distribution for Requirement.parse('zc.buildout')
An error occurred when trying to install zc.buildout. Look above this message for any errors that were output by easy_install.

Could You please help me to fix this problem? Does it maybe not work due to the fact, that I EMANS2 is already installed on my system but at another location?
In order to follow the installation instructions I installed it one more time to the "parts" in the SPRING folder


Thank You in advance 

Best regards


Dario Saczko-Brack

PhD Student
Ludwig-Maximilians-Universität München
Department of Cellular Physiology

[Carsten Sachse]

Dear Dario,

We believe this has to do with certificates that need to be checked. On some network configurations this gives issues. You could try to turn this off.

Could you try this and edit the ez_setup.py in patches.

in line 210:

def download_file_wget(url, target):

    cmd = ['wget', url, '--quiet', '--output-document', target]

    _clean_check(cmd, target)

change to:

    cmd = ['wget', url, '--quiet', '--output-document', '--no-check-certificate', target]

    

You will need to start over and setup again before bootstrapping.

%PYTHONPATH=$PWD/lib/python2.7/site-packages LD_LIBRARY_PATH=$PWD/parts/EMAN2/lib \

./bin/python patches/ez_setup.py

...

Best wishes,

Carsten

[Dario Brack]

Hi Carsten,

thank You for the quick response. It seems like this worked for me, although it worked right now without changing the ez_setup.py.

However, I am having another problem now:

The command
PYTHONPATH=$PWD/lib/python2.7/site-packages LD_LIBRARY_PATH=$PWD/parts/EMAN2/lib ./bin/buildout -v 2>&1 | tee build.log

leads to a lot of outputs but after some time it stops. I can see many error messages. I attached the last part of the output.
One message is for example: SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.
I checked what it means and installed pyhton-dev. python-numpy is also already installed.

Do You have any solution that might solve the problem?

Best

Dario

[Carsten Sachse]

Hi Dario,

As there is a Python.h in 

parts/EMAN2/Python/include/python2.7/Python.h 
there should be no issue.

Are you by any chance not trying to use the local EMAN2 provided from the SPRING website? Please stick to this version as the latest EMAN2 will not work with SPRING.

Best wishes,

Carsten