Re: Compile NAMD on Bluegene

From: Dong Luo (us917_at_yahoo.com)
Date: Thu Jun 15 2006 - 11:35:18 CDT

I just tried both the fftw in machine and newly
compiled fftw, the NAMD compilation stopped at the
same place (seems the last step):
......
/bgl/BlueLight/ppcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/bin/ld:
cannot find -ldl
Fatal Error by charmc in directory
/scratch/dong/NAMD_2.6b1_Source/BlueGeneL-MPI-xlC
   Command /opt/ibmcmp/vacpp/7.0/bin/blrts_xlC
-L/usr3/graduate/dongluo/tcl/lib
-L/usr3/graduate/dongluo/fftw/lib
-L/bgl/BlueLight/ppcfloor/bglsys/lib
-I/scratch/dong/charm/mpi-bluegenel-xlc/include
-DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -qstrict
 -Q -qarch=440d -qtune=440 -qfloat=rsqrt:fltint -o
namd2
-L/scratch/dong/charm/mpi-bluegenel-xlc/bin/../lib
-I/scratch/dong/charm/mpi-bluegenel-xlc/bin/../include
/scratch/dong/charm/mpi-bluegenel-xlc/bin/../lib/libldb-rand.o
obj/buildinfo.o obj/common.o obj/dcdlib.o obj/erf.o
obj/main.o obj/mainfunc.o obj/memusage.o obj/strlib.o
......
obj/WorkDistrib.o obj/pub3dfft.o obj/vmdsock.o
obj/parm.o obj/imd.o obj/dcdplugin.o moduleinit19381.o
-lmod
uleNeighborLB -lmodulecommlib
/scratch/dong/charm/mpi-bluegenel-xlc/bin/../lib/libmemory-default.o
/scratch/dong/charm/mpi-bluegenel-xlc/bin/../lib/libthreads-default.o
-lck -lconv-cplus-y -lconv-core -lconv-util -lckqt
-lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts
-lrts.rts -ltcl8.3 -ldl -lsrfftw -lsfftw -lm
-lmoduleNeighborLB -lmodulecommlib -lm returned error
code 1
charmc exiting...
rm -f moduleinit19381.C moduleinit19381.o
make: *** [namd2] Error 1

I checked that the file:
/bgl/BlueLight/ppcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/bin/ld
is there, but don't know what -ldl means.

--- 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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