[gmx-users] execution of water tutorial files on BG/L

[Florian Haberl]

hi,

On Monday 25 September 2006 16:52, Hiroshi Fujisaki wrote:
> Dear David,
>
> THanks for your reply.
> I noticed what you said, and actually our system at
> Boston University has a frontend (linux) and a backend (BG/L).
> http://scv.bu.edu/SCV/Archive/IBM/BGL/GettingStarted.html#COMPILE
>
> I seemed to compile gromacs on linux and tried to
> run it on BG/L (or vice versa?). So my next question is
> how to solve this problem? Is this a question only
> administrators can solve?

You have to crosscompile as your link say, or easier solution you submit an 
interactive job (don t know if this works with ibm tool but should be) and 
than you can compile on one node.

Else you have to choose correct architecture and compiler as the howto say:

with tcsh shell you can try

setenv CC  blrts_xlc
setenv F77  blrts_xlf
setenv CXX  blrts_xlC

all other is an extension from the example:

setenv CCFLAGS  -O3 -qarch=440 -qtune=440
setenv F77FLAGS  -O3 -qarch=440 -qtune=440
setenv CXXFLAGS -O3 -qarch=440 -qtune=440
..


C_LIBS = $(YOUR_C_LIBS) \
	-L/bgl/BlueLight/ppcfloor/bglsys/lib \
	-lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts

C_INCLUDES = -I/bgl/BlueLight/ppcfloor/bglsys/include \
	$(YOUR_C_INCLUDES)

F77_LIBS = $(YOUR_F77_LIBS) \
	-L/bgl/BlueLight/ppcfloor/bglsys/lib \
	-lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts

F77_INCLUDES = -I/bgl/BlueLight/ppcfloor/bglsys/include \
	$(YOUR_F77_INCLUDES)

CXX_LIBS = $(YOUR_CXX_LIBS) \
	-L/bgl/BlueLight/ppcfloor/bglsys/lib \
	-lcxxmpich.rts -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts

CXX_INCLUDES = -I/bgl/BlueLight/ppcfloor/bglsys/include \
	$(YOUR_CXX_INCLUDES)


Normally it should work, you also have to compile fftw on this architecture.


Greetings,

Florian 


>
> Best wishes,
>
> > Hiroshi Fujisaki wrote:
> > > Dear Gromacs users,
> > >
> > > After installing fftw-3.1.2 and gromacs itself on our
> > > BlueGene facility, I am testing the tutorial
> > > files, but I fail when I try all of them. For example,
> > > for the water case (.../share/gromacs/tutor/water),
> > > "grompp -v" seems to work, but "mdrun -v" suddenly
> > > stops with the following message
> > > "Illegal instruction"
> >
> > Most likely you have compiled for the wrong architecture.
> >
> > > I've never experienced this when I use gromacs in
> > > a linux machine. Could you suggest something?
> > > The gromacs was compiled with a single precision
> > > and single CPU version.
> > >
> > > I appreciate your help.
> > >
> > > Best wishes,
> >
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> > phone:	46 18 471 4205		fax: 46 18 511 755
> > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > _______________________________________________
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-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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