Leginon

h1. Installation Trouble shooting

h2.  Getting Help

* Once registed for leginon download, the users have access to the " bulletin board":http://emg.nysbc.org/bb.viewforum.php?f=2  where users

and developers post their questions and answers.

* Official bug report and feature request should be entered through  "bugzilla":http://emg.nysbc.org/bugzilla/enter_bug.cgi?product=Leginon .

h2.  Installation/Update problems

* <link linkend="InstT_win_install">Python installer fails on pyScope and numExtension for

Windows</link>

* <link linkend="InstT_bad_update">Not all files are updated</link>

* <link linkend="InstT_1st_Grp">New Group/User added does not show up in the selection

list in Web Leginon Administration Tool</link>.

* <link linkend="Inst_no_tomo">I can't install SciPy/NumPy on SUSE</link>

* <link linkend="InstT_php_display_error">Something is not showing in Web viewer or the

administration tool components</link>

* <link linkend="instlT_updatecom">Stage does not move after a pyScope update on the

computer controlling the microscope</link>

h2. Failed pyScope numExtension Window installation through

python

<title>Why:</title>

*  Specially compiled pyScope and numExtension are needed to comunicate with Gatan

CCD camera. Currently we only have them compiled for python2.5

Solution: Download and use python2.5 and use the window-installer in win-install

folder (start by double-clicking them) not "python setup.py install".

h2. Incomplete Leginon update

This normally happens to files that you have modified in the previous version.

<title>Why:</title>

*  unknown

Solution: Remove the old installation first.

*  Find the location of your Leginon installation. Once you have tried,even

unsuccessfully, to install Leginon. You can use the following command to find

the directory:

<pre>Linux> cd

Linux> start-leginon.py -v</pre>

<pre>Window> Go to \All Programs\Leginon\Leginon Folder from your Start Menu</pre>

*  Go to the directory above it. This is normally the site-package directory

under your python installation

<pre>Linux> rm -r Leginon

Window> drag the Leginon folder to Recycle Bin</pre>

*  Redo Leginon installation.

h2. Installation without a class of nodes

If you encounter a problem with node classes that you don't actually use, you may avoid

loading the codes with the following modification:

*  Fnd the location of your Leginon installation

<pre>Linux> cd

Linux> start-leginon.py -v</pre>

*  go to the subdirectory of noderegistry

<pre>Linux/home> cd leginon_directory/noderegistry</pre>

*  edit the file "default.ncr" to coment out the registry of the class of nodes that

you do not need (Tomography node class in this example):

<pre>#[Tomography]

#module: tomography

#type: Pipeline

#package: tomography</pre>

h2. SciPy Installation failed in SuSE

SciPy may not build properly on some versions of SuSE due to an incompatible LAPACK

package that comes with SuSE. You can get scipy as well as a compatible LAPACK etc. from

http://repos.opensuse.org/science (need to specify your SuSE version and machine etc.

h2. Display errors on webviewer and web

administration tools

To display error and report them to get help for the php, including mysql-php and mrc

extension, do the following:

*  Find your php.ini the following parameters and change them accordingly:

<pre>display_errors = On

error_reporting  =  E_ALL &amp; ~E_NOTICE</pre>

*  Restart your apache server

<pre>> /etc/init.d/apache2 restart</pre>

*  From your webbrowser, refresh the problematic page. If you don't know what to do

with it, report it when you ask for help.

h2.  Administration Tool problems

* <link linkend="InstT_Appl_xml">Application xml files can not be imported</link>.

* <link linkend="InstT_php_display_error">Something is not showing in the administration

tool components</link>

h2. Incomplete xml-imported application

<title>Why:</title>

*  This is a random error that happens ocassionally.

How do you know it is imcomplete? <link linkend="Admin_app_view">view the

application</link> saved in the database in the web admin tool

Solution: Try it again with a new version number in the xml file.

*  check your xml file. It should end with something like this:

<pre>    </sqltable>

<!-- bindingspecdata -->

<!-- launchedapplicationdata -->

<!-- nodespecdata --></pre>

If not, you need to download the correct xml file again.

*  edit the correct xml file. For example, you have MSI-T.xml, then you need

to change

<pre> - Application :MSI-T (1.6)

- Version     :1</pre>

To<pre> - Application :MSI-T (1.6)

- Version     :2</pre>

AND, more importantly,

<pre>  <!-- ApplicationData -->

<sqltable name="ApplicationData" >

<field name="DEF_id" >331</field>

<field name="DEF_timestamp" >2005-05-26 14:16:36</field>

<field name="name" >MSI-T (1.6)</field>

<field name="version" >1</field>

</sqltable></pre>

To<pre>  <!-- ApplicationData -->

<sqltable name="ApplicationData" >

<field name="DEF_id" >331</field>

<field name="DEF_timestamp" >2005-05-26 14:16:36</field>

<field name="name" >MSI-T (1.6)</field>

<field name="version" >2</field>

</sqltable></pre>

*  import this xml file to your dbem again.

*  check the result by refreshing the web browser and then <link

linkend="Admin_app_view">select the new version of the application to view on

screen</link>.

h2.  Test run operation problems

* <link linkend="InstT_test_window_close">When Leginon or Leginon Client is launched,

Python window opens and closes instantaneously on Windows</link>

* <link linkend="InstT_test_no_module">ImportError "No module named xxxx"</link>

* <link linkend="InstT_test_no_tem">Microscope or CCDCamera name does not show up in the

Leginon instrument list in Instrument Node</link>

* <link linkend="InstT_test_no_tem">The Microscope computer where Leginon Client runs does

not show up in the Launcher list of Leginon when opening an application</link>

* <link linkend="no_mag_list">Error message "No Magnification saved for xxx(your

scope)</link>

* <link linkend="instlT_4kfrz">Leginon fails to collect 4kx4k images</link>

h2. Python and Leginon windows do not stay opened on

Windows PC

<title>Why:</title>

*  Windows closes the python process window because an error is detected.

<title>Testing: Start Leginon from a python command window so that the error message can be

read</title>

*  Follow the following menu to open a python command window:

Windows/Start Menu/All Programs/Python2.5/Python (command line)

*  Python> import start

*  Read the error message. Copy it to your bug report when asking NRAMM for

help.

h2. Missing modules

<title>Why:</title>

*  Either the python path is not set up correctly or the module was not installed

properly.

<title>Testing:</title>

* script: <link linkend="inst_syscheck">syscheck.py</link>

If the missing module is not installed under one of the Python module search path

found in the syscheck output, it need to be moved.

h2. "Tecnai" does not show up in instrument list

<title>Why:</title>

*  An error is detected when the instrument is loaded.

<title>Testing: Import the module in pyScope package through a python command window so that

the error message can be read</title>

*  Follow the following menu to open a python command window:

Windows/Start Menu/All Programs/Python2.5/Python (command line)

* *

Follow instruction in pyScope Bulletin Board Thread  ""Testing if pyScope is working

with your TEM or CCD"":http://emg.nysbc.org/bb/viewtopic.php?t=246 .

For example, if "Tecnai" is missing from the instrument list, try

this:<pre>Python>from pyScope import tecnai

Python>myscope = tecnai.Tecnai()

Python>myscope.getMagnification()</pre>

*  Read the error message. Copy it to your bug report when asking for help.

h2. Magnification list not in the database

<title>Why:</title>

*  The first time the TEM is used by leginon and the database, the valid magnification

for the instrument needs to be saved in the database.

Solution: On the scope: Leginon/Instrument> select the microscope to display

parameters and click "Get Magnification" button (The icon is of a calculator) on the

tool bar.

h2. Leginon fails to aquire and save larger images

<title>Why:</title>

* Your computer does not have sufficient memory to acquire and correct the large 4kx4k

images.

Solution:

Put on your computer more memory and more memory swap space.

*  If you file storage system is not on the same computer, there may be problem

transfering large data file. This is known to happen from a Windows machine to disk

storage operated under Linux through Samba.

Solution:

Let us know if you have one.

h2. Leginon fails to move the goniometer after a new

installation or update of pyScope

<title>Why:</title>

* tecnaicom.py, the python wrapper of Tecnai Scripting library, has not been created

in the running pyScope folder on the microscope controlling computer.

Solution:

Double click updatecom.py to run it in the (installed) pyScope folder.

h2. Network problems

* <link linkend="instlT_network">Leginon not seeing the microscope host</link>

h2.  Microscope host that

runs Leginon client does not appear in the Launcher list on the Leginon processing

computer

<title>Possible reasons:</title>

* Host files are not configured properly so that the computers can not commnuicate

by specifying the hostname.

* Connection is refused by one of the computers involved. This might be caused by a

firewall or a inactive server.

<title>Testing and Solutions:</title>

* <link linkend="network_tests">Test network connection</link> with test scripts

test1.py and test2.py as described in the "Start Leginon" chapter.  Various solutions

are listed in the same section.

For more discussion, see leginon bulletin board  "thread on network

problems":http://emg.nysbc.org/bb/viewtopic.php?t=7 .

h2. Troubles with Imaging

* <link linkend="cor_not_read">Reference image from other users not readable( See

Operation Trouble Shooting)</link>

* <link linkend="instlT_updatecom">Navigator does not move the stage after a pyScope

update on the computer controlling the microscope</link>

h2. Troubles with Calibrations

* <link linkend="pixeloff">Available magnification from pixal size calibration is

different from that said on the scope</link>

* <link linkend="instlT_updatecom">Stage does not move after a pyScope update on the

computer controlling the microscope</link>

h2. Magnification list not consistent with that at the

microscope

Commonly Why: Instrument was not selected correctly when Leginon is installed

Solution: Check the parameters of the named instrument in Administration Tool