new Genbank slows srs indexer to crawl

Don Gilbert gilbertd at sunflower.bio.indiana.edu
Wed Jun 14 15:39:15 EST 1995



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




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