Installation Troublshooting Guide¶

Troubleshooting the Processing Server:¶

Perform system check¶

In addition to the downloads from our repository, there are several other requirements that you will get either from your OS installation source, or from its respective website. The system check in the Leginon package checks your system to see if you already have these requirements.

cd myami/leginon/ 
python syscheck.py

If python is not installed, this, of course will not run. If you see any lines like "*** Failed...", then you have something missing. Otherwise, everything should result in "OK".

Test Appion¶

• If appion was installed using setup.py you are ready to test out appion.

• Run the following script to test import of Appion libraries and binaries:
  

  cd myami/appion/
  ./check.sh
  

  
  NOTE
  You can ignore EMAN, MATLAB, and UCSF Chimera errors at this point.
   
  What about: raise LeginonConfigError('set IMAGE_PATH in leginonconfig.py')
  leginon.leginonconfig.LeginonConfigError: set IMAGE_PATH in leginonconfig.py

You need to edit leginon.cfg.

• Run the following script to test the installation of 3rd party processing packages:
  

  cd myami/appion/test
  python check3rdPartyPackages.py
  

Troubleshooting the Web Server:¶

Run the web server troubleshooter¶

A web server troubleshooting tool is available at http://YOUR_HOST/myamiweb/test/checkwebserver.php.
You can browse to this page from the Appion and Leginon Tools home page (http://YOUR_HOST/myamiweb) by clicking on [test Dataset] and then [Troubleshoot].

This page will automatically confirm that your configuration file and PHP installation and settings are correct and point you to the appropriate documentation to correct any issues.

Firewall settings¶

You may need to configure your firewall to allow incoming HTTP (port 80) and MySQL (port 3306) traffic:

$ system-config-securitylevel

Security-enhanced linux¶

Security-enhanced linux may be preventing your files from loading. To fix this run the following command:

$ sudo /usr/bin/chcon -R -t httpd_sys_content_t /var/www/html/

see this website for more details on SELinux

Slow image loading¶

If you find that you have many users viewing images, and the images are taking too long to load, there are several ways to address this.

1. Alternative reduxd installation on file server
2. Using imcache to cache mrc images as jpeg images of the default size on myamiweb

Seg fault errors messages in Apache log: Web server does not inform user when login credentials are incorrect¶

If you try to run a job directly from the web gui, and the job fails without providing a message, check to see if it could be due to bad credentials. Test a username or password that you know are incorrect. If you do not receive a clear error message in the GUI, try the following fix.

Install latest version of http://pecl.php.net/package/ssh2:

wget http://pecl.php.net/get/ssh2-0.12.tgz
tar -xzvf ssh2-0.12.tgz 
cd ssh2-0.12
yum install automake make php-devel libtool openssl-devel gcc++ gcc
phpize
yum install gcc php-devel php-pear libssh2 libssh2-devel
./configure 
make
make test
cp modules/ssh2.so   /usr/lib64/php/modules/
service httpd restart

There were Segmentation fault messages in the apache error log and I narrowed it down to Cluster->authenticatedConnection()

It seems that the fix for PHP :: Bug #63192 was needed to fix this bug.