[gpfsug-discuss] alphafold and mmap performance

[Stuart Barkley]

Over the years there have been several discussions about performance
problems with mmap() on GPFS/Spectrum Scale.

We are currently having problems with mmap() performance on our
systems with new alphafold <https://github.com/deepmind/alphafold>
protein folding software.  Things look similar to previous times we
have had mmap() problems.

The software component "hhblits" appears to mmap a large file with
genomic data and then does random reads throughout the file.  GPFS
appears to be doing 4K reads for each block limiting the performance.

The first run takes 20+ hours to run.  Subsequent identical runs
complete in just 1-2 hours.  After clearing the linux system cache
(echo 3 > /proc/sys/vm/drop_caches) the slow performance returns for
the next run.

GPFS Server is 4.2.3-5 running on DDN hardware.  CentOS 7.3
Default GPFS Client is 4.2.3-22. CentOS 7.9

We have tried a number of things including Spectrum Scale client
version 5.0.5-9 which should have Sven's recent mmap performance
improvements. Are the recent mmap performance improvements in the
client code or the server code?

Only now do I notice a suggestion:
    mmchconfig prefetchAggressivenessRead=0 -i
I did not use this.  Would a performance change be expected?

Would the pagepool size be involved in this?

Stuart Barkley
-- 
I've never been lost; I was once bewildered for three days, but never lost!
                                        --  Daniel Boone