[Tom Bair]

Sven,

Just out of curiosity how much memory on your 32 cores? How long to process a standard Ti run (rough order of magnitude)? Just wondering about cpu vs memory. We have 8 cores and 32G and run about 11 hours.

Tom

[sklages]

Tom,

this machine has 128G memory.
A standard run takes about 7h using 30 cores. But the difference when using less cores is
marginal. There seems not too be a huge difference in processing time when using 20-30
cores. Less than 20 cores increases run time.

But this may also be dependent on how many other processes are producing I/O on
that local disks ...

I had runs processed on 10 cores taking more than 13h ... (for testing).

The Roche processing software scales terribly bad ..

Sven

[Tom Bair]

Sven,

Just wondering, from your posts it sounds like you are getting stuff in the GS_CACHEDIR, but it looks like you have enough memory that your jobs should just be in memory. I see "Using memory-only storage for flowgrams." in the gs log and don't see any files forming in the GS_CACHEDIR. I know I had to set ulimit as unlimited for this to happen though. I probably just misunderstood your post. Memory-only storage is something to check for as it considerably speeds (less i/o) the process at least on our system (which is probably atypical)

Tom

[sklages]

Tom,

when running the first tests on automating the signalprocessing stuff, I wasn't aware of
GS_CACHEDIR and as a consequence /tmp got filled up by gsRunProcessor. Our tmp
is somewhat around 10G.

In my latest processing job last night I was looking in GS_CACHEDIR from time to time
to see what kind of files are generated ... I couldn't find any cache file at all .. good.
And, yes, I also see "Using memory-only storage for flowgrams." in the gs log ..

I have no idea what blew up my tmp the first time :-(

I should have a closer look on memory consumption.

Nevertheless, Roche should work on better parallelisation and thus on better
scalablity .. :-)

cheers,
Sven