Re: Compile NAMD on Bluegene

From: Dong Luo (us917_at_yahoo.com)
Date: Fri Jun 16 2006 - 13:56:46 CDT

It works! The Apoa1 benchmark run at 0.132721s/step
with 128 cpus. I failed to run before simplely because
the login node is another computer and compiled NAMD
is not for running on it. I guess charm++ failed the
test due to the same reason since it also used the xlc
comiler which is for parrellel running on bgl. Thanks
for help.

--- Dong Luo <us917_at_yahoo.com> wrote:

> When I type charmrun, it says:
> you must set BL_HOME environment variable.
> Setting BL_HOME to any value including
> /bgl/BlueLight/ppcfloor/, the result changed to:
> charmrun: line 39: [: -nt: unary operator expected
> Running on 1 processors:
> charmrun: line 47: /BlueLight/bin/CIORUN: No such
> file
> or directory
> charmrun: line 47: /BlueLight/bin/CIORUN: cannot
> execute: No such file or directory
>
> I googled CIORUN, it seems belong to BGLsim. Since I
> am running program on real BG/L, why should it still
> try to use CIORUN?
>
> NAMD compilation is finished after removing -ldl
> from
> BlueGeneL.tcl and using fftw within machine. (Newly
> compiled fftw gives an error: undefined reference
> to
> `__ctype_b_loc') Howerver, when I test with just
> typing namd2, it tells me: illegal instruction.
>
> Will this comilation be really useable?
>
> --- Gengbin Zheng <gzheng_at_ks.uiuc.edu> wrote:
>
> >
> > I don't remember we used BGL_HOME, I thought it
> > should be BL_INSTALL
> > it should be the path prefix that has
> bglsys/include
> > and bglsys/lib,
> > typically it is /bgl/BlueLight/ppcfloor/
> >
> > Gengbin
> >
> > Dong Luo wrote:
> >
> > >This Blue Gene machine is located at Boston
> > >University. As far as I know, NAMD is not
> > installed.
> > >Since NAMD requires single precision fftw to do
> the
> > >PME calculation and I found the preinstalled fftw
> > with
> > >the machine has this version, I will use that
> fftw
> > >first. It it failed again, I will try to compile
> it
> > as
> > >Gengbin suggested.
> > >I have another question as mentioned in previous
> > post,
> > >ie, what BL_HOME variable should I define to be
> > able
> > >to use charm++?
> > >
> > >--- Gengbin Zheng <gzheng_at_ks.uiuc.edu> wrote:
> > >
> > >
> > >
> > >>I think most Blue Gene machines already have
> NAMD
> > >>installed, you may
> > >>want to find out.
> > >>
> > >>To compile your own version, please check out
> the
> > >>following web site for
> > >>how to compile fftw for NAMD
> > >>
> > >>
> > >>
> >
>
>http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdCompile
> > >
> > >
> > >>Gengbin
> > >>
> > >>Mgr. Lubos Vrbka wrote:
> > >>
> > >>
> > >>>hi,
> > >>>
> > >>>
> > >>>
> > >>>>This time, after compiled for a while, the new
> > >>>>
> > >>>>
> > >>problem
> > >>
> > >>
> > >>>>came out as:
> > >>>>"src/ComputePme.C", line 8.10: 1540-0836 (S)
> The
> > >>>>#include file <sfftw.h> is not found.
> > >>>>"src/ComputePme.C", line 9.10: 1540-0836 (S)
> The
> > >>>>#include file <srfftw.h> is not found.
> > >>>>I checked the fftw directory and find out
> there
> > >>>>
> > >>>>
> > >>are
> > >>
> > >>
> > >>>>only fftw.h and rfftw.h in the include
> > directory.
> > >>>>As the fftw libary are downloaded from the
> > >>>>
> > >>>>
> > >>website as
> > >>
> > >>
> > >>>>suggested (I downloaded the file
> > >>>>fftw-bluegene.tar.gz), I now have no idea how
> to
> > >>>>
> > >>>>
> > >>fix
> > >>
> > >>
> > >>>>this problem.
> > >>>>Please give some hints. Thanks.
> > >>>>
> > >>>>
> > >>>i don't have any experience with namd
> > compilation,
> > >>>
> > >>>
> > >>but this error
> > >>
> > >>
> > >>>means that you are trying to use single
> precision
> > >>>
> > >>>
> > >>version of the fftw
> > >>
> > >>
> > >>>binary that is apparently missing on your
> > >>>
> > >>>
> > >>computer. maybe there is
> > >>
> > >>
> > >>>some switch you can use to specify that you
> want
> > >>>
> > >>>
> > >>to use double
> > >>
> > >>
> > >>>precision fftw instead of single precision (in
> > >>>
> > >>>
> > >>configure scripts the
> > >>
> > >>
> > >>>switch is usually --enable-float/--disable
> > float).
> > >>>
> > >>>
> > >>i don't know what
> > >>
> > >>
> > >>>is the situation for namd, though...
> > >>>
> > >>>regards,
> > >>>lubos
> > >>>
> > >>>
> > >>>
> > >
> > >
> >
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> >
> >
>
>
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