The latest release of GenBank has put SRSbuild here into a slow
crawl. It has been trying to index this release for over 48 hours.
It makes progress, but at a snail's pace. My guess is that
this is a memory-limit problem. The previous GenBank build on this
machine took probably less than 6 hours.
The machine that is indexing has (merely) 32MB of real memory, and
about 100mb of virtual memory. Is this slowness likely due to
srs having to use virtual memory extensively? Or might this indicate
some other problem? There are some machines here w/ more memory,
but it will be harder for me to run srsindex on them.
Another question: if I index just genbank on a different machine,
is it likely that I will run into similar problems if I run srsbuild
to do the cross-indexing on this original server?
I'm using version 4.02 of srs on this server.
Thanks for any tips -- Don
Here is the current 'ps' output for this process:
USER PID %CPU %MEM SZ RSS TT STAT START TIME COMMAND
molbio 24676 0.8 47.4 60144 13396 ? D Jun 12 294:20 srsbuild GENBANK
and here is current virtual memory stats output on this server:
fly% vmstat 5
procs memory page disk faults cpu
r b w avm fre re at pi po fr de sr d0 d1 d2 d3 in sy cs us sy id
0 5 0 0 1920 0 51 1 2 0 0 93 8 0 5 2 171 497 109 8 5 87
1 1 0 0 1932 3 14 588 8 612 0 264 46 0 29 2 532 500 262 18 8 74
0 1 0 0 1952 3 13 640 0 664 0 355 39 0 36 0 552 502 280 6 7 87
0 3 0 0 1908 2 8 564 12 660 16 378 49 0 16 0 493 667 220 7 11 81
0 2 0 0 1964 2 22 828 28 724 0 475 36 0 38 0 555 557 239 6 14 80
1 2 0 0 1876 3 21 792 52 896 0 589 53 0 33 7 647 603 254 10 16 74
The above in my limited experience suggests this machine is paging virtual
memory too much (page pi/po are kilobytes paged in/out per second)
--
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu
