Leginon

Hi Venkata,
My first idea is that this is something related to the privileges settings on the MySQL server, but it could be something else.

Here are some ideas and questions to help identify the problem:

On the microscope computer, start a python command line and run this:

import sinedon
sinedon.getConfig('leginondata')

During your update to 2.2, was any supporting software updated? Python? MySQL-python? Maybe a newer version we have not tested is not working anymore.

Was the host name or IP of the microscope computer or MySQL server changed? Sometimes network communications are sensitive to slight changes. Maybe "cina-t12-01" will work, but not when qualified with the full domain as in "cina-t12-01.ethz.ch". The MySQL privileges may be only accept one or the other.

Was anything changed in the privileges settings of the MySQL server?
On the MySQL server, log into mysql as root to check previleges: "mysql -u root -p mysql"
Then query: "select user, password, host from user;"
Make sure at least one of the rules will allow a connection from the microscope computer using the sinedon.cfg parameters you confirmed above.

Can you connect to the server from another machine using a standard command line MySQL client? For example on a linux system, run "mysql -h ... -u ... -p ..." with the same host name and user parameters that are in your sinedon.cfg.

Hopefully one of those things will help isolate this problem. Let us know what you can find.
Jim

Hi,

Yes the privileges somehow changed in MySQL server or may be I did. With your feedback, it is now working. Thanks for the immediate help.

Even though everything working, I got two errors while upgrade,

1) it at the Microscope computer during install of pyami, which says about a syntax error. The error screenshot is attached to this message.

2) Then in the linux computer, when I run update of database, it prints this two commands

python schema-r16607.py
python log_package_revision.py

when I run the first command, I get this output and didnot update it.The output is like this....

CUSTOM: SELECT value FROM `install` WHERE `key`='revision'
16784 16571
CUSTOM: SELECT value FROM `install` WHERE `key`='revision'
-------------------------------------------
Upgrading leginondb
error ' ' in column name

3) when I run cscheck.py in microscope computer, I get the error as shown in second image attached to this message.

I did not start a new automated run yet,will wait for the feedback to know whether it will be critical to start without avoiding this errors.

regards,
venkata

Hi, Venkata,

Thank you very much for the screen shots and error log. Those make our lives so much easier. It is also really good of you not to start Leginon after having
errors like you had. Now we know the database is mostly intact.

I think I know the reason for only getting 16607 update. It is a bug I've not thought of. I've started an issure #1856 for this and will work on it now. In the
mean time, could you give me what your database says about its version/revision is with a method like this:

mysql -h your_databasehost -u your_mysql_username -p projectdb
mysql> select * from install;
mysql>exit;

I will then know what we need to do to get you back on track.

Thanks.

Anchi

Hi,

Here is the details about the revision and version.

---------------+ | key | value |
---------------+ | settable | 1 | | version | 2.2 | | revision | 16571 |
---------------+

thanks,
venkata

Hi, Venkata,

I've made changes in dbschema in 2.2 branch. If you update your svn check out, you will get them.

Do the following:

1. you will need to find out, if possible what revision your old 2.1 checkout is. Go to where you've checked it out before and type:
   

   svn info
   

   
   You want the number in the line starts with "Revision:" If you've lost it, a good guess is r16197 where we last did bug fixes for you.
2. Run the following script in the new 2.2 branch myami/dbschema/, it will revert your database record in the install table back.
   

   python revertDBinstall.py
   

3. Rerun the deschema_update.py This time you should get more updates. In particular, the reason for your error message before was because schema-r15653.py was not in the list. Then perform the updates as instructed in the wiki page.

If all updates run without error, you should be good to go.

Anchi

Regarding the error in pyami installation with python 2.5 on Windows, Use the workaround for Issue #1857. tifffile.py in question is not used in Leginon operation and only used in Appion if you need to analyze Direct Electron DE camera raw frames.

Anchi

Hi,

Thanks for the reply and update.

we are now having busy sessions of T12 using Leginon. So, when encountered the bugs during the upgrade I switched back to old version 2.1. In one month we are planning to use autoloader and also image analysis on hl preset images. Since I have to test lot of things, the idea is not to touch the previous setup and do a parallel upgrade in a new system.

During the upgrade, as per the requirements of our IT network dept. which they are planning to upgrade all systems to RHEL6.

I want to try to RHEL6 and will get you back about the problems.

Please give your suggestions and also will you support us for RHEl6?.

regards,
venkata

1. The same problem that I replied in http://emg.nysbc.org/boards/6/topics/1125?r=1126#message-1126 still applies to 2.2. Our solution to that php-mrc problem is a new image server, redux, that will become available in 3.0 when we officially support RHEL6. I don't expect that we will release 3.0 before summer ends since it needs to done after Appion testing locally. Other functions needed by Leginon works with standard CentOS 6 installation as far as we know since we have one of our Leginon running computer on CentOS 6 right now and the developers use python 2.6 (come with RHEL/CentOS 6) and up already to develop new code.
2. If you need to use Appion, there is an EMAN 1.9 library problem that creates artifacts in using basic functions like low pass filter on CentOS 6.2. See Issue #1524 and #1827. A solution is posted there but we do not know yet if it is universally adoptable. Our testing on Appion with CentOS 6 is limited until we switch our processing cluster to that.