Folding Forum

Head up: Tomorrow morning between 07:30 and 12:00 CEST there will be power maintenance at my place, which will cause some downtime for my servers. My website with qd, FCI, etc will be unavailable during that time and possibly longer if Murphy has its way.

New release of FCI: v1.7.7

Another update to the psummary parser in fci-update-stanford-files.pl, this time to support the space in the contact names for p7620.

The lastest FCI release (and previous releases) can be downloaded from the project website, or you can use the direct link.

New release of FCI: v1.8

I've long sought an interactive molecule viewer for web browser that doesn't use Java, and now I've finally found one: ChemDoodle Web Components by iChemLabs. A really cool chemical toolkit in Javascript using jQuery. It has build in support for PDB files, which FCI already uses for RasMol to generate project images. An interactive project image is now also available for project how provide a current.xyz, which sadly are rare these days. But my FCI server has collected quite some over the years, so it's not as useless as it may seem. See for example: Project 10900 Abeta40_mono_s

Rendering some of the larger molecules such as p2672 IBX in water & p2669 IBX in water will put a bit of a strain on your system, but the smaller molecules such as p3907 & p1584 A7pp2_298K_03 are rendered in a breeze. I think it's worth it for such cool tools.

I'll expect a future release of FCI to use this to render the project images for the v7 client using its protein command, when my FAHClient Remote Interface Perl Implementation is ready. The FCI server can then act as a caching proxy between the web browser and FAHClient, also converting the PyON data to proper JSON to have a realtime feed or cached view of the last protein state that you can interact with. So you wont have to allow direct connections from the Internet to your FAHClient.

My overall development has slowed down quite a bit in pas months, due to busyness at work and elsewhere. But after the new v.7.1.33 and v7.1.38 open beta releases I've picked up development of the remote interface implementation again, but development is still slow.

The lastest FCI release (and previous releases) can be downloaded from the project website, or you can use the direct link.

Looks fine to me. Thanks!

The TPF graphs may be broken, due to a jQuery version conflict between Flot (used for the TPF graphs) and ChemDoodle Web Compontens (used by the Molecule Viewer).

If you experience this problem, edit site.plc and comment out the lines with cdw files.

New release of FCI: v1.8.1

The interactive TPF graphs where boken by the recent introduction of the ChemDoodleWeb Components based interactive molecule viewer.

This has been fixed in this release, which also upgrades the Flot jQuery library from v0.5 to v0.7. You can now also select on the y-axis to zoom in on a graph

The lastest FCI release (and previous releases) can be downloaded from the project website, or you can use the direct link.

New release of FCI: v1.8.2

Featuring only a few minor changes:

* Fixed fci-update-eoc-stats.pl to terminate after failing to download stats for 5 users (it only did that for unsuccessful requests, i.e. not 200 OK). This make the script behave better regarding the recent server load issues EOC has been suffering from.
* ChemDoodle Web Components updated to v4.4.1, mostly for the bugfixes in gl-matrix v1.0.1.
* Updated the installation instructions for FreeBSD 8.2, OpenBSD 5.0, OpenSUSE 12.1 and Arch Linux 2011.08.19.

The lastest FCI release (and previous releases) can be downloaded from the project website, or you can use the direct link.

Install went fine, looks to have quieted some of the noise. Thanks.

What kind of noise is now gone? Did you get many cron emails for failed fci-update-eoc-stats.pl runs?

My FCI server was blocked by Jason as it was among the "worst offenders over-querying the XML" based on a quick look through the logs. When I found out that I was blocked after I checked the site from work, I sent an email to Jason as he requested:

If you have been blocked, but you feel your usage is legitimate, then please email me and we can work things out to figure out what needs to be done.

And he quickly removed my IP from the blacklist the morning after. I described the measures fci-update-eoc-stats.pl takes to play nice with the EOC server (2 second delay between requests, 5 failed requests cause it to quit), which was tweaked back in 2007 when the load issues were a problem too, and were sufficient to be considered a properly behaving script. Looking at the code again made me aware of the bug that only requests that fail with a non-OK HTTP status code were counted and more than 5 requests could fail to return proper XML stats instead giving an HTML warning about the high load letting the script continue to try all users known to FCI.

My FCI servers monitors 61 usernames, which is much more than most other FCI users such as yourself monitor. I didn't think that other FCI users were blacklisted too, but I did a quick round along the other FCI sites I know about and they (including yours) did not seem affected, but your server may still have been blacklisted too. If you got cron mails from fci-update-eoc-stats.pl with connection timeouts, this is most probably the case. So if you get errors such as: Than you should get in touch with Jason at EOC.

The only messages that are expected are the server load warnings like: These warnings can be ignored if they only occur occasionally. If they occur at every run (every 3 hours at XX:42), you can try to reschedule the cronjob some minutes earlier or later. The recommended range is between XX:30 and XX:59, but anything will work as long as the script is done before fci-update-xml-files.pl is run (at XX:30).

Unfortunately I've already deleted the old mails and they have fallen out out of my terminal buffer. I do recall seeing the second message you list, server load high, on occasion.

I got this error on the last run:

The 'Bad hostname' error looks like a DNS issue, probably related to the Stanford Network issues of recent. The same rule of thumb applies, if it only happens occasionally, then don't worry about it. If it happens every time, something needs to be fixed.

The usual advise to solve this lookup problem is to add a record to /etc/hosts, but I don't recommend this approach. DNS was invented because editting /etc/hosts doesn't scale, and you don't get automatic updates when the IP address changes.

Does fci-client.pl have the ability to use a proxy for it's upload?

Thanks.

No, there is no proxy support in FCI client. It currently assumes a direct connection or a transparent proxy.

It shouldn't be too much effort to add proxy support, but my free time is quite limited currently. So I don't have the time to setup a proxy for testing purposes.

Okay, thanks for confirming. I'll wait patiently

New release of FCI: v1.8.3

As has almost become a tradition (3rd year in a row) I get to release a new version of FCI as a Christmas present

This release adds proxy support to FCI client which should have been build in from day one, but I was a bit lazy back then and under the mistaken impression that configuring Squid was hard. That was until I had read the guide (definitive, not hitch hiker one ) a couple of years ago.

I hope to have some more time this X-Mas weekend to hack on the v7 Perl Interface. Because that is long overdue too.

The lastest FCI release (and previous releases) can be downloaded from the project website, or you can use the direct link.