University of Maryland Mike P. Cummings  
Center for Bioinformatics and Computational Biology

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Linux versions of GARLI temporarily deprecated
I have had to temporarily deactivate our Linux versions of GARLI due to a bug preventing all workunits from completing properly under our new phased workunit scheme. Hopefully this bug will be resolved relatively soon; in the meantime, my apologies to our Linux users. 3 Aug 2015, 18:38:25 UTC · Comment

GARLI 2.1 released
I have just released GARLI 2.1 for five platforms (32 and 64 bit Linux, 32 and 64 bit Windows, 64 bit OS X), and have deprecated the 32 bit OS X app version. This version should improve data set load times for large analyses, and may include other improvements that you would notice. Please post if you encounter any problems running the new version. 15 Oct 2014, 17:48:35 UTC · Comment

Server Upgrade
I've just upgraded the server software and web pages, so please let me know if you notice anything amiss. As part of this upgrade, the credit granting should now follow the new BOINC system; hopefully this will address some of the recent complaints about credit granted being erratic and/or too low. As always, your feedback is welcome and your participation much appreciated. 26 Nov 2013, 19:15:07 UTC · Comment

Newest GARLI workunits take some time to show progress
Workunits in the newest batches of GARLI workunits released won't be using a feature that speeds up input file processing since it potentially introduces a bug. So, if your workunit doesn't show signs of progress for the first couple of hours, don't be alarmed and let it continue! Unfortunately, GARLI won't checkpoint during this phase. 18 Jul 2013, 18:12:37 UTC · Comment

GARLI 5.01 released
I have just released GARLI 5.01 for all platforms, which should hopefully fix the checkpointing issue. There should be more work in the system soon, and we'll find out then. 10 Oct 2011, 16:03:20 UTC · Comment

Issue with checkpointing on this first major batch of GARLI 2.0 WUs
It seems that many of the workunits just released error out when attempting to resume from a checkpoint. This is most likely a problem with GARLI 2.0 and the particular specification of these WUs. If you can avoid restarting the BOINC client during these workunits, they should complete properly. We are working to resolve this problem ASAP and we apologize for the inconvenience (and failed WUs). 12 Sep 2011, 15:54:32 UTC · Comment

We have released GARLI-2.0 for the following platforms: Linux (x86), Mac OS X (Intel), and Windows (x86 and x64). These are all version "5.00" -- the executables themselves may have a different name depending on the platform. We have officially dropped PPC/OS X support; apologies to that subset of our participants. The next GARLI job you run via The Lattice Project should be GARLI version 2.0. 2 Aug 2011, 16:33:44 UTC · Comment

Server hardware failure
As many of you may have noticed, our project was down for the last few weeks due to a hardware failure. We have it back up and running now, however, and things should be back to normal. If you notice anything unusual or have questions, feel free to post in the forums about it. 26 Jun 2011, 21:50:00 UTC · Comment

GPU testing
We are beginning some GPU tests. Highly experimental, but not dangerous ;-) At this time it is for Windows users with CUDA GPUs. Please participate! 24 Nov 2010, 3:10:50 UTC · Comment

BOINC Client Activity
Check out our new visualization of BOINC client activity!

(powered by Google Maps)
12 Oct 2010, 18:43:44 UTC · Comment

New Work
Some new work that requires at least 3G of memory (RAM) is slowly becoming available. The runtime on these jobs is uncertain; a lower bound is perhaps 15 hours, an upper bound in the hundreds of hours for slower machines. We'll learn more as we go along, but if the deadline seems too short, don't panic! We're trying to improve our accuracy but have a ways to go yet. 22 Sep 2010, 18:15:51 UTC · Comment

Canceled Workunits
I've canceled the remaining 109 workunits from this troublesome batch of work we've had running since May, since we now have enough results - finally! If you happen to return one of these results from here on out and you don't receive credit because the workunit was canceled, please let me know. 22 Sep 2010, 15:11:05 UTC · Comment

server software upgraded
Just upgraded the server software - let me know if you notice any (unusual) problems. 14 Aug 2010, 18:48:24 UTC · Comment

Upon completion of a workunit from this latest batch of GARLI jobs, you may see a message like the following:

Output file 234594970.40009717460018646.5_0_4 for task 234594970.40009717460018646.5_0 absent

Your result may be temporarily marked as invalid, but never fear - there is code in place on the server that will execute periodically and fix these results and validate them normally. You WILL be granted credit eventually, so please keep crunching!

Thank you! 15 May 2010, 3:04:42 UTC · Comment

Checkpointing and Progress Bar
It has been made clear to me that for long-running GARLI jobs, it is possible for the program to stay in both its initial phase (1-5%) and final phase (95-100%) for an extended period of time. Moreover, these phases can amount to significantly more than 10% of total runtime. During these phases the progress bar will not move and the program will not checkpoint! It is a situation we will work on remedying, but will have to live with for the time being. Thank you for your patience and understanding. 10 May 2010, 16:22:39 UTC · Comment

You may notice some workunits that have potentially hundreds or thousands of results associated with them; these are benchmarks intended to be run once by each host, so please don't be alarmed. 21 Apr 2010, 0:14:05 UTC · Comment

We have recently updated the list of publications from users of the Lattice BOINC Project. For more information about these publications, you may look at our research page. 26 Feb 2010, 0:00:00 UTC · Comment

New GARLI Version
We have just released a long-awaited new version of GARLI that includes improved progress bar updating! No more freezing at 70%! Looking forward to your feedback. 4 Dec 2009, 0:00:00 UTC · Comment

Server Upgrade
Just upgraded the server software, so please let me know if you notice anything out of place. 9 Oct 2009, 0:00:00 UTC · Comment

Workunit Errors
A number of GARLI jobs were accidentally released with an error in the configuration file that caused the job to terminate incorrectly; these jobs have been removed from the system, and we apologize for this. 1 Aug 2009, 0:00:00 UTC · Comment

Web Site Update
The update to the web site is basically done, so if you notice anything wrong, please post about it. Thanks! 11 Jun 2009, 0:00:00 UTC · Comment

Web Site Update
I'm in the progress of updating the project web pages, so please excuse the mess. 10 Jun 2009, 0:00:00 UTC · Comment

Web Site Update
We have switched the server that is hosted on. This will allow us to upgrade the web pages soon! 14 May 2009, 0:00:00 UTC · Comment

GPU Testing
Soon, hopefully this week, we'll be sending out a bunch of GARLI workunits to the entire population -- meaning, each host should get one copy of each workunit, whether you have a GPU or not. This is meant to be a sort of benchmarking, and also a test of the GPU version of GARLI. Update: the tests have commenced! 18 Mar 2009, 0:00:00 UTC · Comment

BOINC News Signature Images
John from has created a service that periodically generates an image of the three latest project news items (including this one, presumably!). Thanks, John! 27 Feb 2009, 0:00:00 UTC · Comment

I upgraded the server software to version 6.7.0, which in limited testing seems to fix the aforementioned memory scheduling bug. 2 Feb 2009, 0:00:00 UTC · Comment

GARLI Failures
As some of you realize, many of the recent GARLI workunits were erroneously sent to hosts without enough memory to crunch them. We're still looking into the cause of this problem. If you were affected, we apologize! 29 Jan 2009, 0:00:00 UTC · Comment

New Work
Despite the fact that we're still waiting on a front end upgrade, we are issuing workunits for a couple of applications, GARLI and MARXAN. Many of the GARLI jobs will be memory intensive, requiring a minimum of 1.2G of RAM. Also, we expect approximately 38,000 MARXAN jobs some time next week. 23 Jan 2009, 0:00:00 UTC · Comment

The server has been upgraded to RHEL5, and the BOINC server software has been upgraded to 6.3.14. Upgrading the web site is on hold until either our main web server is upgraded to RHEL5, or I get the OK to run the frontend on a different host. In any case, it should be soon. 16 Dec 2008, 0:00:00 UTC · Comment

We are upgrading our BOINC server to RHEL5, so the project will be temporarily unavailable for that. Shortly after that work is complete, I will be upgrading the server software, so you can expect still more downtime, so I will keep everyone posted! 1 Dec 2008, 0:00:00 UTC · Comment

Spam Stinks
Attacks by a very persistent spammer have caused us to shut down account creation temporarily. Sorry for the inconvenience! 9 Oct 2008, 0:00:00 UTC · Comment

MARXAN Returns
Completing the trifecta, MARXAN enters the fray... 14 Aug 2008, 0:00:00 UTC · Comment

HMMPfam Returns
In what will be seen as a welcome respite from the recent batch of long-running and otherwise problematic GARLI jobs, we now have HMMPfam flowing into the system! 11 Aug 2008, 0:00:00 UTC · Comment

RAM Upgrade
We are taking a brief downtime to upgrade the RAM in our main BOINC server from 2.5G to 8G! Hope this helps now and down the road. 7 Aug 2008, 0:00:00 UTC · Comment

GARLI Codon Model Runs
The GARLI jobs currently in the system are going to take *much* longer than any we have run previously. Please see this thread for more details. 3 Jul 2008, 0:00:00 UTC · Comment

Unexpected Outage, Part II
We are hopefully back online from an extended and unexpected outage. Many apologies to all those who were wondering what in the world was going on. A couple days turned into a week, and then several weeks as problems kept mounting. In any case, thanks for your patience! 3 Jul 2008, 0:00:00 UTC · Comment

Unexpected Outage
Some days ago we experienced an HVAC failure which caused our main file server to overheat. We have since been working on fixing the problems that resulted, and are still in the process of doing so, but we hope to be back online and fully functional shortly. As for the outstanding work in the system, we'll just have to see how well the system recovers. Sorry for the extended absence! 6 Jun 2008, 0:00:00 UTC · Comment

Results in Progress Dropping?
I've noticed our results in progress continues to drop despite a fair amount of work unsent. I have been unable to find an obvious reason on this end; has anyone running Windows been unable to pull down MARXAN jobs? Please make a post about it. Thanks! Update: Having extended our workunit deadlines, I think this problem is resolved. 15 May 2008, 0:00:00 UTC · Comment

Note about MARXAN
MARXAN is not a native BOINC application and as such doesn't do checkpointing or progress bar updates! Will make a note of this on the applications page. 2 May 2008, 0:00:00 UTC · Comment

Fast CGI Woes
In attempting to upgrade to Fast CGI versions of the cgi/file_upload_handler programs, it seems we've broken file uploads. Update: I'm hoping this issue is resolved. However, please report any errors! (as usual) 26 Apr 2008, 0:00:00 UTC · Comment

HMMPfam Compatibility Problem
A recent re-release of HMMPfam to change the way it reports some errors was not backwards compatible with Intel Macs running 10.4. I've just released a new version which should fix this problem. Sorry to those that were affected! 17 Apr 2008, 0:00:00 UTC · Comment

In case you haven't already noticed, we've started sending some MARXAN jobs through the system. Look for more of these in the days to come! 3 Apr 2008, 0:00:00 UTC · Comment

HMMPfam Jobs
A couple hundred HMMPfam cleanup batches are in the process of being submitted. This will be the first major test of the new file caching code, but hopefully no one notices! 24 Mar 2008, 0:00:00 UTC · Comment

System Enhancements
I am in the process of rolling out some system enhancements, which should have a dramatic impact on the number of simultaneously running HMMPfam jobs we can allow, for example. We will mostly likely scale up this capacity gradually, but if you notice anything odd please don't hesitate to report it. Thanks! 19 Mar 2008, 0:00:00 UTC · Comment

HMMPfam Jobs
It seems that all of the HMMPfam jobs for this massive batch have been submitted, and I will be letting the work trickle out of the system. There are some jobs that need to resubmitted, but I may investigate the results that seem to be stuck in the "Ready to Send" state first. 11 Mar 2008, 0:00:00 UTC · Comment

Technical Difficulties (resolved?)
The problem with the feeder has hopefully been resolved... 10 Feb 2008, 0:00:00 UTC · Comment

Technical Difficulties
Our feeder is mysteriously segfaulting so the project is down until I can get that fixed! 9 Feb 2008, 0:00:00 UTC · Comment

Project Upgrade
I was in the middle of upgrading the server software when I realized that we really (really) need PHP5. I've reverted to what I think is the previous state until we can get PHP upgraded; but let me know if you notice anything odd. 31 Jan 2008, 0:00:00 UTC · Comment

Scheduled Downtime
Due to a scheduled power outage, our BOINC server will be down from Friday afternoon, 1/11, to Saturday afternoon, 1/12, so please don't be alarmed! 9 Jan 2008, 0:00:00 UTC · Comment

Latest HMMPfam Runs
1534 batches of 276 jobs (workunits) x2 results/WU = a whopping 846,768 results to crunch! This should keep us all busy for a while. For more information on HMMPfam, look here. 19 Dec 2007, 0:00:00 UTC · Comment

The Lattice Project Makes The A-List
We are listed under Biology and Medicine, here: Also, see the news item on BOINC's front page. 18 Dec 2007, 0:00:00 UTC · Comment

New GARLI Versions
A new beta version of GARLI is being tested and has been released for our four supported platforms. Please inform us of any problems with the new version, thanks! 28 Nov 2007, 0:00:00 UTC · Comment

HMMPfam Runs
Approximately 500 batches (x133 WUs each) of HMMPfam will be trickling in as they get crunched. We should have more information about this project on the research page soon. 9 Nov 2007, 0:00:00 UTC · Comment

Choosing Applications
Some had asked for the ability to choose which applications they run. Well, now you have that option! If you're logged in, try this link. We hope that if your system meets the minimum requirements to run an application, you will decide to do so, but we provide this option to give our users additional control over the work they receive. 10 Oct 2007, 0:00:00 UTC · Comment

Server Upgrade
The server upgrade is essentially complete, save for one feature. Please report any problems you notice or features that you think are missing. Thanks! 8 Oct 2007, 0:00:00 UTC · Comment

Research Projects
A new page describes types of analyses run on The Lattice BOINC Project, applications used in those analyses, and specific project information. It's a work in progress! Head on over to Research Projects 4 Oct 2007, 0:00:00 UTC · Comment

Server Upgrade
We are in the process of upgrading the server to version 6.1.0, so please report any problems you notice, especially with the web site. I will inform everyone when the upgrade is complete... 3 Oct 2007, 0:00:00 UTC · Comment

Background and Introduction
A note to our faithful crunchers and potential newcomers: we are planning to improve the web site with better information about The Lattice BOINC Project. Hopefully this will serve to both satisfy curiosity and get everyone excited! So check out the new link, Background and Introduction 12 Sep 2007, 0:00:00 UTC · Comment

Native GARLI Version
Finally, the day is at hand... a native version of GARLI has arrived! As a test, I will release the Windows version when the current work in the system finishes up (and I might remove some work prematurely). If all goes well, the other platforms will be right behind. Please let me know if you encounter any problems with the new version of GARLI (which should do checkpointing!) 31 Aug 2007, 0:00:00 UTC · Comment

GARLI Update
The developer of GARLI is hard at work on a new version, which will include checkpointing. We hope to have this released next week! Thanks to everyone crunching for us... 22 Aug 2007, 0:00:00 UTC · Comment

Native HMMPfam Version
A native BOINC version of HMMPfam has been released which does checkpointing and status bar updates. Hopefully it will improve throughput and user satisfaction! A native GARLI version is soon to follow, by the way... 31 Jul 2007, 0:00:00 UTC · Comment

GARLI Trials
The deadline for these workunits has been made 5 days, and this should be enforced on any new workunits that are created. 9 Jul 2007, 0:00:00 UTC · Comment

GARLI Trials
Soon we will be releasing some GARLI workunits into the wild. We have an experiment outlined that will require several thousand workunits crunched, in due time. Initially, HR will be turned off for GARLI. 5 Jul 2007, 0:00:00 UTC · Comment

Turning On HR Once Again
Regretfully, we are turning on homogeneous redundancy for HMMPfam once again because there are simply too many inconsistencies, numerical and otherwise, that are causing results to be marked as invalid. Plans to release a native BOINC version are on hold pending developer time to work on a Windows version. 28 Jun 2007, 0:00:00 UTC · Comment

Turning off HR
A new Windows version has been released which should correct some formatting differences in the output. Therefore, homogeneous redundancy has been turned off, but we will be monitoring any validation errors that occur. It's also worth mentioning that we are working on a wrapper-less, native BOINC version of HMMPfam that will do checkpointing. Stay tuned! 26 Jun 2007, 0:00:00 UTC · Comment

Faster HMMPfam Versions Released
The 3x faster version of HMMPfam has been released for Windows. We are continuing to modify the source so that we may be able to turn off HR for this application eventually. We are approximately 40% of the way through this batch of work, but we are cutting off the flow of work into the system for a short time. Thanks for your continued interest in the project! 23 Jun 2007, 0:00:00 UTC · Comment

Faster HMMPfam Versions Released
Versions of HMMPfam approximately 3x faster have been released for all platforms except Windows, which is soon to come. 23 Jun 2007, 0:00:00 UTC · Comment

Settings Modified to Work Better with HR
I have increased the number of results available in the feeder's shared memory segment from 384 to 3840, so you should see the "there was work, but it was committed to other platforms" message more less frequently! 21 Jun 2007, 0:00:00 UTC · Comment

Settings Modified to Work Better with HR
I have increased the number of results available in the feeder's shared memory segment from 100 to 384, and I've set it to purge stale WUs every ten minutes instead of every thirty. You should hopefully see the "there was work, but it was committed to other platforms" message less frequently now. 15 Jun 2007, 0:00:00 UTC · Comment

Small Mishap
I just released a few workunits which contain an error that causes the HMMPfam application to terminate immediately, quite probably putting some of your clients into an endless loop. If you're affected, just reset your project, and my apologies. 15 Jun 2007, 0:00:00 UTC · Comment

More HMMPfam On the Way
We have word that a batch of HMMPfam six times larger than the most recent batch is on its way. Look for it in the next couple of days! 13 Jun 2007, 0:00:00 UTC · Comment

Latest News
All of the work for this batch is in the system. The output from the newly released Windows version differs slightly from the other platforms, unfortunately, so I'm going to turn homogeneous redundancy for HMMPfam back on at some point. For those whose results were marked invalid recently, we're sorry. 13 Jun 2007, 0:00:00 UTC · Comment

Initial HMMPfam Tests
To all who participated in our first test, thanks. I also appreciate the feedback on the message boards. We have a second wave of work going in now that is approximately 16 times bigger than the first one, so it should keep everyone busy for a while! For information on this research, look here. 9 Jun 2007, 0:00:00 UTC · Comment

Project URL Activated!
All, you should now point your clients to We will have a small to moderate amount of work in the system shortly. This will be our first test with public clients since the project was re-launched, so we'll see what happens. However, this is real data, not test data! Good luck, everybody. 7 Jun 2007, 0:00:00 UTC · Comment

Account Creation Enabled
I didn't see a reason not to allow new accounts to be created at this point, so go right ahead, and post something if you encounter problems. However, do not try to attach to the project - it won't work just yet! I'll send another notice when the project URL is activated. 4 Jun 2007, 0:00:00 UTC · Comment

Testing, testing...
We're currently trying out the new HMMPfam application. Hopefully within a couple of weeks we'll be ready to turn it loose on everyone. As the day draws near, we'll open up account creation again so all can get ready. Thanks for your patience and continued interest! 31 May 2007, 0:00:00 UTC · Comment

There's Work in the Pipeline
Within a few weeks, we'll probably open up the project again in some limited capacity in order to test a new application, which is a part of the HMMER suite. This should give everyone something to look forward to! 11 May 2007, 0:00:00 UTC · Comment

Hello, Everybody!
We've noticed you found the site. We are currently working on polishing up the site's features, so expect changes and things to break. We've disabled account creation and client connections for the time being. We may or may not reply to message board posts. And it's uncertain when real work will be flowing through the system again, but we'll keep you posted... Sincerely, The Lattice Project Team 17 Apr 2007, 0:00:00 UTC · Comment

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