Leginon

Do a Google search for "scipy clapack" and you will find a couple of solutions and explaination. Depending on the version of linux distribution, the default installation may pick up a bad version.

p.s.

Test this using python command line and

import scipy.linalg

I use nm to check which libclapack or liblapack has clapack_sgesv, found no anylib in atlas has symbols of clapack_sgesv, that mean it is a bad version? and could you please give me details how to debug it in python command line?

Please give details on Linux flavor, version, numpy, scipy versions and how you install them so that we can repeat and come up with ways to deal with it.

Fedora 11, atlas-3.8.3-9.fc11.x86_64, numpy-1.3.0-5.fc11.x86_64, scipy-0.7.0-3.fc11.x86_64. I use rpm to install them if there arenot installed.
Thanks,
Shunming

also in linux machine, the python is python2.6

It is not clear whether you mean that you did or did not use yum to install scipy/numpy. Please find out. We don't have a machine with Fedora 11, so this will be harder for us to repeat.

I use rpm to install all required scipy and numpy. It is the same as yum
Shunming

Here is what is recommended at

http://www.scipy.org/install.html

sudo yum install numpy scipy python-matplotlib ipython python-pandas sympy python-nose

try it if it is not how you did it.

I did a search for "undefined symbol:clapack_sgesv" and this seems to be a known issue: https://bugzilla.redhat.com/show_bug.cgi?id=709782#c5

I suggest modifying LD_LIBRARY_PATH as suggested in that bug report.

I following the above command and it show: numpy, scipy have been installed and it is latest version for fc11(my linux version), it then download and install the other 4 packages except python-pandas( fedora 11 didn't have it).
Then, I tested it and it is the same issue.
Thanks
Shunming

Shunming,

Do you have to use Fedora 11?

Here are comments from Neil Voss who I consult with regarding your problem

Fedora 11 came out in June 2009 went out of service in June 2010. I remember seeing something like this, I think it was an incompatible versions of LAPACK and SCIPY. Maybe it was fixed by moving to Fedora 12. Maybe I even had this problem in 2010, but I forget the details.

I highly recommend that if they do not plan on updating their system often, they should move to CentOS. if they do want to update to the latest, they should install Fedora 19.

This type of compatibility issue is hard to fix without downgrading to the exact version here where we are in general on CentOS. The fact that none of us found specific web posting mentioned Fedora 11 indicates that the problem can likely be resolved by upgrading. I am sorry to say that we will not be able to help with your particular issue with our limited resource.

I restart machine and run start-leginon.py again, now it show I need to configure instruments.cfg. I read documents and didn't find any place saying I should configure instruments.cfg in linux machine. I did configure it in microscope pc
Shunming

If I can not fix this problem, I will consider update my install to latest fedora or centos.
Shunming

When running with Leginon client on microscope, you indeed does not need instruments.cfg on the linux box. If you are just debugging and needing to simulate the scope and camera, you can copy the pyscope/instruments.cfg.template to pyscope/instruments.cfg to avoid this message. However, you should remove it when it is in production use or it might confuse people.

O.K. I was wrong, I apologize. My development machine has too many configurations. You do need instruments.cfg on linux box although it is a bug. I will fix that. Mean while, just use what is in the template even though it does nothing for you.

In fact, there is already an issue open on this. #1311. Instruction for the workaround added.