Tuesday, April 3, 2007

Database server instabilities...

The machine that is running the database behind the Chemical blogspace is having trouble keeping alive. This is happening since the (scheduled) power outage of this weekend. Now, since the CUBIC has shut down as organization, my postdoc contract has ended too. As a consequence, I will not have frequent access to the machine, and remote SSH access is having hickups too. So far, a (former) collegue (Miguel) is helping me out, by rebooting every now and then, but I will work on a more permanent solution.

The best solution would be to get some permanent hosting somewhere, but without a university position where the machine could run, that is not cheap. Not too expansive either, but for a hobby... In the short term, I am considering moving the database to frontend machine, which has somewhat higher load, but is more stable too.

To be continued...


Rajarshi said...

What type of loads are involved? I'd be happy to host Cb on a machine here at IU.

Joerg Kurt Wegner said...

And I have still the domain.
I will not take an upgrade for more fancy stuff on my own, but if some of you join, we could host it there?


Geoff H said...

It'd be pretty easy for me to host as well. I have a fixed-rate hosting plan (for my personal website), so adding in Cb would be easy.

Antony said...

Take a look at

You will notice we host the Spinneret from David BRadley

I am interested in setting up a ChemSpider Blog shortly.

Maybe you would be interested in joining our server and having us host you. It appears we share similar passions for structures, InChIs, SMILES and so on.

Egon Willighagen said...

All, many thanx for the offers. The load is quite modest, and the realy problem seems to be disk usage by MySQL, while the dumped database is currently less than 40MB large. I guess the indices are not correctly set up. The number of unique visitors is about 80 right now, with page views three times as much. It's mostly HTML with some small images and CML files.

While the CUBIC has shutdown already, the servers can run for somewhat longer, but I guess not really until the end of the year, so if you are serious about hosting it, these are my 'wishes':
- access to the machine
- MySQL daemon (or PostgreSQL)
- Apache with PHP
- access to the log files
- SVN + some other development tools

I would get a URL myself and point it to the server. I would need MySQL to start with, because I need to tune the PHP scripts for accessing a PostgreSQL db.

Joerg Kurt Wegner said...

My provider offers MySQL, PHP and SSH access by upgrading to a solution for 20€/month.

domain is

As said, if some of you join, we can do this, but maybe other solution are cheaper ?


Egon Willighagen said...

I realized some more requirements:
- Perl
- Python
- OpenBabel
- 2GB memory, at least
- fast hard disk

For some reason the MySQL is doing a lot of read/writes, though the database is small. I also noticed all memory consumed, so maybe it's just swapping a lot. The data is <50MB at this moment, but I guess that does not include indexes.

Because I would love to get OPSIN (name2inchi) operational too, Java would be prefered too.

Really, I think a good machine at some uni site is the best option. The PHP frontend seems to be the easy part.