AMBER Archive (2001)

Subject: ISTAR option and performance

From: Anton B. Guliaev (anton_at_vostok.lbl.gov)
Date: Tue Oct 09 2001 - 12:39:10 CDT

Dear Amber users,

we are running sander (Amber 6.0) for rather large systems (over 30000 atoms) at NERSC facility at LBL
using IBM SP. We had to recompile sander without ISTAR2 option to accommodate such a large system.
After that we observed significant drop in performance (almost 3 times) when we used sander without ISTAR
option (4 nodes 16 processors each). Any feedback would be appreciated. Without istar we collected 100000
steps in 6.7 hours (200ps). It dropped to 35000 steps using the sander without ISTAR option... thanks a lot --
Anton
        *******************************
        * Anton B. Guliaev, Ph.D *
        * Life Sciences Division *
      _ * LBNL, Berkeley CA 94720 * _
     / )* abguliaev_at_lbl.gov *( \
    / / * F:(510)-486-6488 * \ \
  _( (_ * T: 510-486-5773 * ) )_
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