There was a strange problem with our ensembl server that usually the server becomes “inaccessible” in the morning, but when we tested a few times, the server works extremely well during the day. However, it becomes “inaccessible” again tomorrow morning.
One of our web server response “500 internal server error” occasionally. As this server is used for ensembl, which incurs 20-30 background process for each *view (i.e. contigview, geneview), we figured out a few tunable parameters for better performance.
The background for this issue that our user found local ensembl mirror sometimes inaccessible, but after a few refresh the pages comes out again. I realized the problem was caused by the small default value of max_connections in MySQL server, and the fact the ensembl uses DBI instead of Apache::DBI in the perl.startup script.
In the latest CVS code of ensembl, perl.startup file still uses “DBI” module, soI believe it will have potential performance issues on other mirror sites.
With the unmodified ensembl v37 installation, we got error with DAS tracks:
Can’t locate object method “fetch_all_Features” via package
“Bio::EnsEMBL::ExternalData::DAS::DAS” at
/usr/local/ensembl/site/ensembl/modules/Bio/EnsEMBL/Slice.pm line 2476
Ensembl has new releases every month. The databases names changed, so we have to re-grant all user privileges for all the 30-40 databases. That’s quite tedious.
There are a few development tasks related Ensembl for LSB these
days. After adding zmenu for karyoview, we tried to add pointers to
density karyoview. The original karyoview only shows the tracks, now we
need to add pointers for the cellline information. In addition, these two input should come from different URL option, we prefer “url_file” for tracks and “gene_file” for pointers.
This howto shows our modifications to make links and zmenu works for karyoview in Ensembl (v34).
Yesterday my two concurrent mysqlimport process hangs the production mysql server. The two import process all shows “repair with keycache”. I am not sure why the repair command is issued, but as the “repair with keycache” takes forever and it eventually frozes the entire MySQLs, I have to optimze it.
I have migrated “ensembl + DAS” from Marie’s linux workstation to Kampen and Genesis successfully. Marie has helped me to do everything from scratch (including hacks on ensembl web codes), so that we can track on the changes made. Below is the draft I sent to Ramneek/Neal/Kevin/Tim for review. I also proposed having all these discussed in CMAB meeting when Ramneek is back.
Marie has developed as few DAS service for Ensembl web. Previously the DAS ran on Marie’s own machine and the support team is requried to move this to production. Before I move it, it will be set up on kampen as a testing environment.