Posted 6 Jun 2022 by
valterc
server side I got something like (apache cgi:error)
(104)Connection reset by peer: [client x.x.x.x:40986] AH01225: Error reading request entity data
BTW I also have one unable to upload task... Can't figure out why...
Posted 6 Jun 2022 by
valterc
OK, I stopped and restarted the server, checked the databases with mysqlcheck, did a consistency check on the file system, deleted a bunch of zero bytes files inside the upload directory and looked for weird errors inside the logs.
I didn't find something looking particularly "strange", however.
Will monitor the situation and try something else tomorrow
Posted 5 Jun 2022 by
valterc
Sure I've seen a number that ran around an hour. Right now I have plenty that are running around 2.5 hours.
I have 31 completed WUs that won't upload. They're all files under 10 kb and Retrying never sends them up. At some point they do seem to have gone up but the list has been growing longer each day for the last week.
My Validation Pending has grown to over 5000 when normally it's well under 2000 which seems odd since they finish faster.
Just curious.
On the server status page there is a higher than usual number of "tasks in progress". Will check tomorrow, while back in the office, if there is something strange on the server.
Posted 5 Jun 2022 by
valterc
I haven't had any in a while but occasionally I will receive a task that runs for under 1 hour (Ryzen 9 3900X). I am guessing these are just shorter tasks. Has anybody else noticed the shorter tasks?
The last workunit of every gene expansion batch is shorter than the others, it is the one containing "wu-294" in its name
Posted 5 May 2022 by
valterc
See we are back to no work available. Work generator not running.
What's up?
The mysql server crashed overnight for unknown reasons, back to normal right now.
Posted 26 Apr 2022 by
valterc
We actually do have a mysterious bug, from the very beginning of the project, that may invalidate the result in some cases. We figured out that it is related with the check-pointing but usually it may happens if a task is stopped and restarted at the very beginning, i.e. before the first checkpoint. So, both of your cases are strange. The second one particularly; any workunit of the current type is made up by 294 chunks and checkpoints are written on the disk only when one chunk has been computed: so there shouldn't be checkpoint #600.
For the second question, there is not any BOINC built-in way to handle checkpoints, only some suggestions. While writing the applications you should figure out if it is possible (in some cases it isn't, depends on the algorithm) and write the checkpoint code (saving and restoring the computational "state")
Posted 8 Apr 2022 by
valterc
The main goal right now is to finish the FANTOM-1 experiment. Alongside there will be another dataset of Vitis vinifera. We are planning to do new experiments, either with other datasets or organisms. We are also evaluating the feasibility to do something with Single-cell transcriptomics data.
Posted 7 Apr 2022 by
valterc
Your host statistics seem normal. You may have a RAC drop because you are not able to get enough workunits to fill up your processor. This is also normal here right now because of the huge number of requests. In this case I suggest you to set up a backup project.
Posted 28 Mar 2022 by
valterc
Time to create the next badge :-)
Done ;)
Posted 28 Feb 2022 by
valterc
The issue here is not about the server itself, which, by the way, is not very powerful but is working. The problem is the *big* University storage system that we heavily use (I don't know the technical specs of it)
The complete expansion of a single human gene (input file, output files etc.) is ~385Mb (compressed). Just for the human genome dataset we have already expanded around 57000 of them. I let you do the math ;)
Most of the disk storage that we use is obviously just for keeping the history. The needed "live" storage for running the server is about 4-8 terabytes.
So, what we need in order to be independent of the University's storage system is something like, at minimum, 2x 4TB (Raid 0), for example two 3.84TB SSD SAS Read Intensive 12Gbps 2.5in Hot-plug. Please check the prices https://www.dell.com/en-us/shop/384tb-ssd-sas-read-intensive-12gbps-512e-25in-pm6-hot-plug/apd/345-bbxy/storage-drives-media
We simply don't have that money....
Posted 26 Feb 2022 by
valterc
The court process is related to a new storage system. The old one, that we currently use, has (and had) some serious problems, simply speaking it's painfully slow, sometimes. There are two possible scenarios:
- The IT crew will fix the problem in a few hours or days (as happened in the past) and I will restart everything.
- The problem is not fixable. I already managed to find another disk, although not so big. In this case I have to wait until the current queue becomes almost empty (you may look at the numbers in the project status), transfer everything to that disk and start again.
[EDIT} now it "seems" that everything is working at full speed, will check again in a few hours.
Posted 26 Feb 2022 by
valterc
While buying expensive things we have to issue a government tender, open to any company in the EU. Someone won the contract, an excluded one did not agree and started a legal issue, so everything was frozen. Unfortunately this kind of legal issue is very slow to resolve here in Italy.
Posted 26 Feb 2022 by
valterc
The "storage" problem is here again.... I stopped the work generator to lighten the load of the system, I will check again the server in a few (a dozen) hours.
Posted 19 Feb 2022 by
valterc
Please read this https://boinc.berkeley.edu/teams/
And yes, you need to create the team here.
Posted 26 Jan 2022 by
valterc
Did you change something?
Now my Task uploaded.
As you can see 2 of the other Pcs could now upload it too
http://gene.disi.unitn.it/test/workunit.php?wuid=32282024
One could upload it after 2 weeks
The last time I was able to check the system and try something (including stopping and restarting the server) was two days ago... Mysterious things happen...
The only idea I have is that it was something related with the external storage system we use, anyway, very strange indeed.
Posted 24 Jan 2022 by
valterc
I checked the server logs, the db and the file system, did not find any clue about this problem... The tasks are present in the database, you may check them using the web interface. No ideas what to do next...
Posted 23 Jan 2022 by
valterc
Will check again tomorrow, back at the office. Did you try to stop and start the boinc client? (Sometimes it helps)
Posted 23 Jan 2022 by
valterc
The upload should be possible now, I think.
Posted 17 Jan 2022 by
valterc
Well, eventually. Talking about Vitis vinifera, the biologists are working on a new gene expression dataset, an improved version of the last one that we plan to expand in the next months.
Posted 8 Jan 2022 by
valterc
Don't know very well how BAM works but I guess that the problem is that you need to create the account first using the web form and the invitation code.