On Wed, Jan 02, 2013, Kirill Nuzhdin wrote:
> Does anyone know if I'm using sander.LES.MPI in a correct way?
> >>
> >> gf_Hqspcfw.pimd:
> >> =============================
> >> -O -i Hqspcfw.pimd.in -p Hqspcfw.pimd.prmtop -c spcfw.pimd.rst.1 -o
> >> bead.pimd1.out -r bead.pimd1.rst -x bead.pimd1.crd -v bead.pimd1.vel
> >> -inf bead.pimd1.info -pimdout rpmd.pimd.out
> >> -O -i Hqspcfw.pimd.in -p Hqspcfw.pimd.prmtop -c spcfw.pimd.rst.2 -o
> >> bead.pimd2.out -r bead.pimd2.rst -x bead.pimd2.crd -v bead.pimd2.vel
> >> -inf bead.pimd2.info -pimdout rpmd.pimd.out
> >> -O -i Hqspcfw.pimd.in -p Hqspcfw.pimd.prmtop -c spcfw.pimd.rst.3 -o
> >> bead.pimd3.out -r bead.pimd3.rst -x bead.pimd3.crd -v bead.pimd3.vel
> >> -inf bead.pimd3.info -pimdout rpmd.pimd.out
> >> -O -i Hqspcfw.pimd.in -p Hqspcfw.pimd.prmtop -c spcfw.pimd.rst.4 -o
> >> bead.pimd4.out -r bead.pimd4.rst -x bead.pimd4.crd -v bead.pimd4.vel
> >> -inf bead.pimd4.info -pimdout rpmd.pimd.out
> >> =============================
> >>
> >>
> >> Hqspcfw.pimd.in:
> >> =============================
> >> &cntrl
> >> ipimd = 4
> >> ntx = 1, irest = 0
> >> ntt = 0
> >> jfastw = 4
> >> nscm = 0
> >> temp0 = 300.0, temp0les = -1.
> >> dt = 0.0002, nstlim = 10
> >> cut = 7.0
> >> ntpr = 1, ntwr = 5, ntwx = 1, ntwv = 1
> >> /
> >> =============================
> >>
> >>
> >> non-MPI, LES version running with Hqspcfw.pimd.in, Hqspcfw.pimd.prmtop
> >> and spcfw.pimd.rst.* is fine!
> >>
> >> while sander.LES.MPI (as soon as any of the four tasks from the group
> >> file is done) is crashing with the following error:
I'm a bit lost here: if you are running PIMD using the LES scheme (i.e. so
that only a part of the system is quantized) you would not have a group file.
If you want the entire system to be quantized, then you would not use LES, but
rather run sander.MPI *with* a group file. You seem(?) to be trying to run
LES and having a group file, and I don't think that will work.
Look at the examples in $AMBERHOME/test/pimd, where the distinction between
"full" and "partial" rpmd can be seen. Make sure these tests run OK, and then
look for the differences between what the tests are doing and what your jobs
are (trying to) do.
...good luck...dac
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Received on Wed Jan 02 2013 - 10:00:12 PST
