[gmx-users] execution of water tutorial files on BG/L
Hiroshi Fujisaki
fujisaki at bu.edu
Tue Sep 26 00:48:21 CEST 2006
Dear Florian,
Our administrator is now trying to compile gromacs
on BlueGene, but he now fails.
I attach the error make log below.
I appreciate your comments.
##############################################################
Making all in include
make[1]: Entering directory
`/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/incl
ude'
Making all in .
make[2]: Entering directory
`/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/incl
ude'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory
`/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/inclu
de'
Making all in types
make[2]: Entering directory
`/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/incl
ude/types'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory
`/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/inclu
de/types'
make[1]: Leaving directory
`/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/inclu
de'
Making all in src
make[1]: Entering directory
`/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src'
make all-recursive
make[2]: Entering directory
`/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src'
Making all in gmxlib
make[3]: Entering directory
`/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src/
gmxlib'
Making all in nonbonded
make[4]: Entering directory
`/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src/
gmxlib/nonbonded'
Making all in nb_kernel
make[5]: Entering directory
`/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src/
gmxlib/nonbonded/nb_kernel'
blrts_xlc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o mknb.o mknb.c
blrts_xlc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o
mknb_metacode.o mknb_m
etacode.c
blrts_xlc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o mknb_common.o
mknb_com
mon.c
blrts_xlc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o
mknb_declarations.o mk
nb_declarations.c
blrts_xlc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o
mknb_outerloop.o mknb_
outerloop.c
blrts_xlc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o
mknb_innerloop.o mknb_
innerloop.c
blrts_xlc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o
mknb_interactions.o mk
nb_interactions.c
blrts_xlc -DHAVE_CONFIG_H -I. -I. -I../../../../src -o mknb mknb.o
mknb_metacode
.o mknb_common.o mknb_declarations.o mknb_outerloop.o mknb_innerloop.o
mknb_inte
ractions.o
rm -f kernel-stamp
./mknb -double -software_invsqrt
>>> Gromacs nonbonded kernel generator (-h for help)
>>> Generating double precision functions in C.
>>> Using Gromacs software version of 1/sqrt(x).
Error: Cannot open nb_kernel010_c.c for writing.
make[5]: *** [kernel-stamp] Error 1
make[5]: Leaving directory
`/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src/g
mxlib/nonbonded/nb_kernel'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory
`/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src/g
mxlib/nonbonded'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src/g
mxlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
`/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory
`/project2/scv/sondak/gromacs/bgl/gromacs-3.3.1/src'
make: *** [all-recursive] Error 1
#############################################################
> 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
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
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>
> --
> -------------------------------------------------------------------------------
> Florian Haberl
> Computer-Chemie-Centrum
> Universitaet Erlangen/ Nuernberg
> Naegelsbachstr 25
> D-91052 Erlangen
> Telephone: +49(0) $BchC(B9131 $BchC(B85 26581
> Mailto: florian.haberl AT chemie.uni-erlangen.de
> -------------------------------------------------------------------------------
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--
Hiroshi Fujisaki <fujisaki at bu.edu>
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