Basically: at the end of each chunk the task decides whether it thinks it has time to complete another one without going over the target run time.

This is really interesting. So what happens in the event that a task ends early and has a chunk left over? Does it get added to a different task? It seems like, at some time or another, you would have a task which is mainly composed of "orphan" chunks.

Basically: at the end of each chunk the task decides whether it thinks it has time to complete another one without going over the target run time.

This is really interesting. So what happens in the event that a task ends early and has a chunk left over? Does it get added to a different task? It seems like, at some time or another, you would have a task which is mainly composed of "orphan" chunks.

My understanding is that Work units consist of a protein chain in an initial state. Each task within the work unit then takes a random seed value which determines where and how to start folding that protein in the search for the lowest energy configuration so there are effectively a near infinite number of tasks that can be performed.

When the work unit is returned any promising configurations found can be used as the starting point for another work unit or a particularly good configuration can be accepted as a working model for the protein.

I would be interested in any corrections to this understanding from those that know.

It doesn’t matter. The aim is not to examine every possibility: given the unfathomably large search space, it cannot be. With hundreds of thousands of work units in each batch, it is statistically insignificant whether any individual task completes N or N⁠+⁠1 models. The probability that the ‘orphan’ is the one that will cure all the world’s ills is negligible.

What I imagine does happen is that if any regions of the search space look ‘interesting’ they will be studied more closely in a subsequent batch of work. That is one of the reasons the task deadlines are so short: the results of one batch are analysed rapidly to guide the choice of parameters for the next.

[snip]

My understanding is that Work units consist of a protein chain in an initial state. Each task within the work unit then takes a random seed value which determines where and how to start folding that protein in the search for the lowest energy configuration so there are effectively a near infinite number of tasks that can be performed.

When the work unit is returned any promising configurations found can be used as the starting point for another work unit or a particularly good configuration can be accepted as a working model for the protein.

I would be interested in any corrections to this understanding from those that know.

Some of them are like that. Some are, instead, one step each from a list of starting points.

Some are two proteins, to see if these two will bind together.

I'm sure that there are more varieties I don't yet know about.

[snip]

My understanding is that Work units consist of a protein chain in an initial state. Each task within the work unit then takes a random seed value which determines where and how to start folding that protein in the search for the lowest energy configuration so there are effectively a near infinite number of tasks that can be performed.

When the work unit is returned any promising configurations found can be used as the starting point for another work unit or a particularly good configuration can be accepted as a working model for the protein.

I would be interested in any corrections to this understanding from those that know.

Some of them are like that. Some are, instead, one step each from a list of starting points.

Some are two proteins, to see if these two will bind together.

I'm sure that there are more varieties I don't yet know about.

Thanks, I’m learning slowly :-)

given the unfathomably large search space

Okay, scratch the infinite monkey approach then.

Where does the excess potential energy go?

I am getting a little sick of the "waiting for memory" practice of suspending computation of a task when there is no shortage of available memory

I am getting a little sick of the "waiting for memory" practice of suspending computation of a task when there is no shortage of available memory

Is it restricted to certain computer(s) and / or certain project(s)?

Is this happening when BOINC is trying to switch between projects to satisfy resource share settings? Rosetta tasks allocate hundreds of megabytes each; if they’re being kept in memory when something else is trying to run, there may well be a shortage. Try deselecting Computing preferences » Leave non-GPU tasks in memory while suspended.

Aside: Running the benchmarks on this 3900X will get it earning the right amount of credit. (There may be other machines that need it too; I didn’t go through them all…)

Is this happening when BOINC is trying to switch between projects to satisfy resource share settings?

I see it, on multiple machines, and I'm only running Rosetta.

It's peculiar. There's clearly enough free main memory to run a project, not to mention the swap. Diddling with the values in preferences doesn't seem to wake it up, either. It just goes away on its own.

I've written it off to a cost of doing business, but if there is a fix for it I wouldn't mind at all.

I see it, on multiple machines, and I'm only running Rosetta.

It's peculiar. There's clearly enough free main memory to run a project, not to mention the swap.

Several of your machines have only 8 GB memory. This isn't enough for 12 cores.
You need at least 1 GB/core to run Rosetta (I usually have 32 GB on my 12-core machines, and more on the larger ones).
Just looking at the "free" memory doesn't do it. Rosetta (and all other BOINC projects too) need to reserve a certain amount to run.
They won't leave home without it.

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I see it, on multiple machines, and I'm only running Rosetta.

It's peculiar. There's clearly enough free main memory to run a project, not to mention the swap.

Several of your machines have only 8 GB memory. This isn't enough for 12 cores.
You need at least 1 GB/core to run Rosetta (I usually have 32 GB on my 12-core machines, and more on the larger ones).

And 32GB for 24 cores isn't enough either if you want to use all of them to do Rosetta work.
I generally allow 1.3GB of RAM per Task- you need to leave enough for the Operating System & and any other programmes that might be running as well (with huge core/thread count systems (32+), you'd probably be OK with 800MB or even less per core as you don't often get many high RAM requirement Tasks (2GB+) at any given time).

I've written it off to a cost of doing business, but if there is a fix for it I wouldn't mind at all.

Just adding more RAM won't necessarily fix it- you need to allow BOINC to actually use what is there.
In your Account settings, Computing preferences, Memory

    When computer is in use, use at most 95 %
When computer is not in use, use at most 95 %
Leave non-GPU tasks in memory while suspended

Make sure Leave non-GPU.. is Not selected.
Works for me.

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Grant
Darwin NT

FWIW

Scheduler down
Project down for maintenance

Just got a 1hr delay after an update attempt

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Several of your machines have only 8 GB memory. This isn't enough for 12 cores.

You need at least 1 GB/core to run Rosetta

I had noticed that the 12 core host was lagging, so I have ordered another 8gb stick for that one. That's the only 12 core machine. There's one other machine with 4 cores and 4gb (nominally) of memory, but that one can't be expanded; just have to live with it as it is.

Make sure Leave non-GPU.. is Not selected.
Works for me.

Heh. I had it on Not Selected, then Selected per the advice of someone else in another thread, now it is back to Not Selected again. Let's see if that helps.

Several of your machines have only 8 GB memory. This isn't enough for 12 cores.

You need at least 1 GB/core to run Rosetta

I had noticed that the 12 core host was lagging, so I have ordered another 8gb stick for that one. That's the only 12 core machine. There's one other machine with 4 cores and 4gb (nominally) of memory, but that one can't be expanded; just have to live with it as it is.

There are lots of other Boinc Projects that have much smaller ram requirements and would love your help too!!

There are lots of other Boinc Projects that have much smaller ram requirements and would love your help too!!

I'm sure that all of them would love my help, cuzz. But if there's one thing that you learn as an American living in the Philippines, it's that there is always a lot more love of help than there is of you.

There are lots of other Boinc Projects that have much smaller ram requirements and would love your help too!!

I'm sure that all of them would love my help, cuzz. But if there's one thing that you learn as an American living in the Philippines, it's that there is always a lot more love of help than there is of you.

I totally agree with that statement!! My though was about you being able to use all of your cpu cores at another project instead of just one or two here at Rosetta.

My though was about you being able to use all of your cpu cores at another project instead of just one or two here at Rosetta.

Rosetta is a nice little hobby for me right now. I'm learning new things and the subject matter is congruent with my son's PhD project, so there's that. At some point I suppose those benefits will plateau and, when it does, I will look for new roses to smell. Is there one project that stands out for you as a recommendation?

Is there one project that stands out for you as a recommendation?

The new trRosetta should be even better.

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