They are much larger molecules so they were crashing on the QM queue cause they ran out of scratch space. I have seen them use up to 18GB scratch space so at the moment I don't know yet how to run these on GPUGRID as it seems to be an issue with many users.

The most recent Betas have worked OK for me. But I have 32 GB memory, which may help.
http://www.gpugrid.net/results.php?hostid=334241&offset=0&show_names=0&state=0&appid=35

You could set up a special sub-project for the large molecules if you want to.

We are using QC beta to test large molcules and how much disk space they take. I think they can (temporarily of course) go up to 20 GB of space (!). I am not sure about RAM - they should be < 4 GB.

We'll need to think whether to split the app in large and small.

Regarding conda: it's an "internal" installation. So no, you can't update, and you shouldn't. That message is unfortunate.

Best

We are using QC beta to test large molcules and how much disk space they take. I think they can (temporarily of course) go up to 20 GB of space (!). I am not sure about RAM - they should be < 4 GB.

We'll need to think whether to split the app in large and small.

Regarding conda: it's an "internal" installation. So no, you can't update, and you shouldn't. That message is unfortunate.

Best

Well... So my Threadripper could need up to 160GB of space?! It has just 32GB...

Well... So my Threadripper could need up to 160GB of space?! It has just 32GB...

We are talking about DISK space. Only a few WUs will be that big - unless we make a "big" queue.

T
[/quote]

As far as I know virtualization is almost native speed these days, especially for computing.

Yes, if you are using "hard" virtualization like Esx and Hyper-v.
"Soft" virtualization like VirtualBox or VmPlayer may suffer bottlenecks

We are using QC beta to test large molcules and how much disk space they take.

Toni, if I may ask you, what molecule size are we (roughly) talking about? As you know, because of my son I have personal interest in HCF1 research, and I would like to get a feel how far science is still away from handling that large molecules. Thanks in advance and my apologies for coming up with my personal issues once in a while.

---

I would love to see HCF1 protein folding and interaction simulations to help my little boy... someday.

I have a degree in Theoretical physics obtained in 1967, but that was related to elementary particle physics. Then in the Nineties, while at Trieste Area Science Park as manager of a UNIX BULL Laboratory I attended a few lectures in the UN Center for Genetic Engineering and Biotechnology on the Density Functional Theory. Since retirement, I have run a few BOINC projects including one on Monte Carlo Method applied to Quantum Chemistry but it no longer exists. This is the first time I am running a project which uses Neural Networks.
Tullio

Well... So my Threadripper could need up to 160GB of space?! It has just 32GB...

We are talking about DISK space. Only a few WUs will be that big - unless we make a "big" queue.

T

[/quote]

I'm also talking about disk space. I'm using 32GB Optane module as boot drive. It's time to change it for something bigger.

@kain: the disk space is used in the directory BOINC is running. Usually (if you use the distribution installers) it is the in the disk used at the root of the file system, indeed.

I had to enlarge the root partition to accommodate the QC beta 3.31 since boinc from the Fedora distro by default installs in /var/lib/boinc and runs as a daemon under systemctl. After that, the WU's seemed to run fine but they sure ate up a lot of RAM. Both my 8 core's have 16 GB RAM and I was running them 2 concurrent with 4 cores each. I think only two errored out and the rest completed and validated. Guess I'll have to max my 8 core machines with 32 GB RAM to run the bigger molecules.

---

Crunching since Feb 2003 (United Devices, Find-a-Drug)

Are you able to set the disk limit in the boinc preferences to prevent too many WUs from running?

Easier and more precise simply to set max_concurrent in app_config.xml

Great to know, thanks. Actually I was also wondering if boinc respects the disk limits .

Worth it to perform the experiment, certainly. Possibly depends whether it respects the declared space needed (<rsc_disk_bound>), or the actual space used. If the latter, there might be a problem if the actual usage increases gradually during the run - BOINC might only check it when deciding whether to start a(nother) new task. Lots of fun to be had with those possibilities...

@Toni, Yes boinc does appear to respect the client disk settings as it lets one know if disk space is too low to run certain projects in the event log. I usually set a high arbitrary GB size but the client appears to react to the real amount available in the execution partition and uses the percentage limits to notify user when disk space is too low. I had to readjust the percent limits higher (in the client settings) a few days ago to run the 3.30 app on one of my machines. Probably due to the project directory getting too full. I hate to reset the project and loose WU's but I suppose I will have to eventually.

We are using QC beta to test large molcules and how much disk space they take.

Toni, if I may ask you, what molecule size are we (roughly) talking about? As you know, because of my son I have personal interest in HCF1 research, and I would like to get a feel how far science is still away from handling that large molecules. Thanks in advance and my apologies for coming up with my personal issues once in a while.

I get it. Thank you so much for your help.

---

I would love to see HCF1 protein folding and interaction simulations to help my little boy... someday.

Toni, if I may ask you, what molecule size are we (roughly) talking about?

The molecules for QM are max 50 atoms or so. The size is however not very indicative. This is a specific "chemistry-oriented" type of calculations.

Toni, if I may ask you, what molecule size are we (roughly) talking about?

The molecules for QM are max 50 atoms or so. The size is however not very indicative. This is a specific "chemistry-oriented" type of calculations.

Thank you VERY much for that line, I really appreciate that. I was already afraid of being a constant bother. Of course I understand that we are still years or even decades away from handling huge proteins like HCF1 and I don't want to be obtrusive. Having said that, I would like to keep sight of those long term targets.

Thanks again... if I may, I will get back to you with this question in a couple of years. But I am glad that Gpugrid and its team is more than just being "exclusively academic". There actually is a vision of the future we can believe in.

---

I would love to see HCF1 protein folding and interaction simulations to help my little boy... someday.

On an EDX online course on quantum computers which I followed recently there was a professor at Dartmouth University who uses a quantum computer to do quantum chemistry calculations.
Tullio

Hey JoergF, while we are not doing proteins with QM yet, (some other groups are trying to do that with networks), what we are calculating is directly related to drug design so I think it is very relevant.
To do whole proteins at QM level accuracy I think will take quite a few more years.