Posted 2 May 2023 by
valterc
Yes, I noticed it, some script error probably because the percentage is more than 100%.
Anyway, the FANTOM-1 exp is now finished. I will double check that script when the new experiment will start.
Posted 28 Apr 2023 by
valterc
Right now that our queue is empty it is the perfect time to switch our filesystem to the new one and to upgrade the operating system of the server. This will probably happen the 2nd of May, for a couple of days. During this period the server may be down for awhile. After that, if everything will go smoothly, we plan to start distributing work again.
Posted 21 Apr 2023 by
valterc
We don't have plans, right now, for the future of the "mouse" experiment. In the next week we will probably start an experiment on Vitis vinifera. In the meanwhile people are working on the human single-cell data based on Tabula Sapiens.
Posted 17 Apr 2023 by
valterc
As you may see from the server status page we are waiting for a very small number of workunits before the complete end of the FANTOM-1 project (right now there are still 37 genes/isoforms to be completed).
In the meantime I will distribute another small batch of "mouse" related workunits, biologists seem happy with the preliminary results.
Posted 7 Apr 2023 by
valterc
At our current pace the remaining workunits related to the very long and computational intensive OneGenE FANTOM-1 experiment (started in March 2018) will be distributed in more or less two days. This will be the end of this job.
For the future of the gene@home project please look at this thread
https://gene.disi.unitn.it/test/forum_thread.php?id=366
Posted 4 Apr 2023 by
valterc
Can you accelerate "gene_work_generator" anyhow ?
The amount of tasks up for grabs is always zero, meaning that people have more workers than your TN-GRID servers can generate.
This is especially important now, where WCG project is down and Rosetta is out-of-work-units (again).
At this time, with our hardware resources, this is the best we can do...
Posted 30 Mar 2023 by
valterc
The number of queued is rising (it's 88856 now), so we may reach 102% in the end :)
Yes, this counts also the "other" genes, it would be rather complicated to fix it now, that 2% more should be considered as a "necessary overhead" ;)
Posted 30 Mar 2023 by
valterc
Yep, there is obviously something wrong in the table. Some genes, in the past, were "expanded" with different parameters (so there are duplicates in the gene list), other ones were expansions with no real gene inside (no gene seed, we call them "empties"). The overhead should be something around 1000.
Anyway the situation right now is that ALL the genes were put into the queue and yes, the order is lexicographical descending, the last one will be A2LD1
Posted 21 Mar 2023 by
valterc
Why is the number of Queued genes/isoforms greater than the number of genes/isoforms? Was something added to the project? Source: science status page
Well, there is something wrong with it.... I will check this out.
Posted 21 Mar 2023 by
valterc
I am curious as to how the project currently foresees its future regarding the approaching finalization of the gene expansion of the OneGenE FANTOM-1 set. At the moment we should be finishing up the current work on 31st of March 2023. On the website you do list other data sets currently on hold or on testing. Any chance you could elaborate on the future work envisioned for TN Grid? What about a possible timeline for the continuation of the project? What will happen with the finished work? Are you targeting a publication?
Best
Very briefly, after the end of the FANTOM experiment we will collect all the data, do some statistical and biological analysis. The targets will be one (or more) publication and a web service to make the results available to the scientific community.
For the future: we are playing with a brand new Vitis vinifera dataset and will probably continue to do something related to the mouse. The main new task should be related to single-cell data (still working on this).
I may guess that after the end of FANTOM there may be a period with shortage of workunits but I hope that it will not last long.
Posted 14 Mar 2023 by
valterc
The University have bought a new one and they planned the moving procedure. The HPC cluster should be moved this Monday (March, 6th), the other resources will follow.
I will reasonably shut down the server when needed, I will tell you when as soon as I know the date. Meanwhile the work generator will be active just a few hours a day, so very few workunits will be available.
Any news??
Not really, The University should have finished moving the HPC-related storage. That's probably why the old storage "seems" to be much more reliable than before (I let the work generator run continuously).
We are still waiting to our turn to move.
Posted 7 Mar 2023 by
valterc
I also noticed these "ghost" tasks.
I don't exactly know the reason behind this but, when the file system is acting bad everything on the server is painfully slow, also at the lower level (kernel, locks, sockets). Probably the server is trying to send out a workunit, flags this on the DB but timeouts getting it from the HD, or sending it via http.
These kind of workunits will have the effect of delaying the computation until the deadline (and yes, will be flagged "timeout error"). I know it's annoying but actually, at least, it's not a waste of computation.
Posted 2 Mar 2023 by
valterc
As all of you already know we are constantly struggling with our problematic storage. The University have bought a new one and they planned the moving procedure. The HPC cluster should be moved this Monday (March, 6th), the other resources will follow.
I will reasonably shut down the server when needed, I will tell you when as soon as I know the date. Meanwhile the work generator will be active just a few hours a day, so very few workunits will be available.
Thank you all for your understanding and patience.
Posted 18 Feb 2023 by
valterc
Yes, now it's working. I will try to check the "unable to upload" problem as soon as possible. Unfortunately it's Saturday:)
Posted 16 Feb 2023 by
valterc
I recently got a MacBook Air with the M1 processor. I thought that, maybe, the gene@home application running on generic ARM x64 processor (a static built) could run on this hardware, so I modified the cc_config.xml file by adding
<alt_platform>aarch64-openwrt-linux-musl</alt_platform>
Yep, the client got the "Intel 64-bit Mac OS 10.5 or later" version of the application and it is running, surprisingly for me, maybe Rosetta2 kicked in (I'm not a Mac expert...)
The computer is this one https://gene.disi.unitn.it/test/show_host_detail.php?hostid=84395 (50% cpu dedicated to BOINC)
Posted 2 Feb 2023 by
valterc
Some "mouse" related workunits will be available in the next days
Posted 12 Jan 2023 by
valterc
The "usual" file system issues... Will try tomorrow to look at it.
Posted 22 Dec 2022 by
valterc
If you are running Windows just enable test applications from your preferences page.
Posted 20 Dec 2022 by
valterc
https://gene.disi.unitn.it/test/forum_thread.php?id=355
Nothing I can do but wait for the problem to be solved by the University's staff.
Posted 15 Dec 2022 by
valterc
They were just a few hundreds, very fast.. The students are working with the results.