Re: building namd on CRAY-XT3

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Nov 05 2008 - 02:10:32 CST

On Tue, 4 Nov 2008, BIN ZHANG wrote:

BZ> Hi, Axel:
BZ> Thanks a lot for your suggestion. I just tried your idea, and got the
BZ> following error:
BZ>

[...]

BZ> child process exit status 1: /scratch/local/usr/bin/ld
BZ> Fatal Error by charmc in directory
BZ> /u0/b/bingo/DEISA_BENCH/applications/NAMD/tmp/namd_Cray-XT4-HECToR_apoa1_i000006/n32p2t1_t001_i01/src/NAMD_2.6_Source/CRAY-XT3
BZ>
BZ> I guess "strtoul.o" is too important to be deleted. :-)

no. this is a different issue. i would be _very_ surprised if
the definition of errno is part of strtoul.

most likely, the hacked tcl that you are using was compiled against
a different version of the c-library (i.e. there is a high chance
that you'll get a non-working executable anyways), but a hack to
get around this error would be to do:

cat > my_errno.c <<EOF

int errno;

EOF

gcc -c my_errno.c

ar rsv /<insert_path_here>/libtcl8.3.a my_errno.o

good luck,
   axel.

BZ> Bin
BZ>
BZ>
BZ> On Nov 4, 2008, at 10:49 PM, Axel Kohlmeyer wrote:
BZ>
BZ> >On Tue, 4 Nov 2008, BIN ZHANG wrote:
BZ> >
BZ> > BZ> Hi,
BZ> > BZ> While compiling with the "hacked" version of TCL, I still got
BZ> > BZ> errors(a
BZ> > BZ> different one)
BZ> > BZ>
BZ> > BZ> /usr/lib64/libc.a(strtoul.o)(.text+0x0): In function `strtoul':
BZ> > BZ> ./sysdeps/generic/strtol.c:110: multiple definition of `strtoul'
BZ> > BZ> /u0/b/bingo/tcl/tcl-crayxt3/lib/libtcl8.3.a(strtoul.o)(.text+0x0):
BZ> > BZ> first
BZ> > BZ> defined here
BZ> > BZ> /usr/bin/ld: Warning: size of symbol `strtoul' changed from 521 in
BZ> >
BZ> >[...]
BZ> >
BZ> >BZ> Any ideas?
BZ> >
BZ> >obviously the strtoul.o in the tcl lib conflict with the OS provided
BZ> >one. why not try to get rid of one? since you cannot manipulate the
BZ> >OS, how about?
BZ> >
BZ> >ar d /u0/b/bingo/tcl/tcl-crayxt3/lib/libtcl8.3.a strtoul.o
BZ> >
BZ> >axel.
BZ> >
BZ> > BZ> Thanks a lot.
BZ> > BZ>
BZ> > BZ> Bin
BZ> > BZ>
BZ> > BZ>
BZ> > BZ>
BZ> > BZ> On Nov 4, 2008, at 1:38 PM, Giacomo Fiorin wrote:
BZ> > BZ>
BZ> > BZ> >Hi Bin, I think you probably need unfortunately a specially modified
BZ> > BZ> >Tcl library for Cray XT3:
BZ> > BZ> >
BZ> > BZ> >http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdOnCrayXT3
BZ> > BZ> >
BZ> > BZ> >---- -----
BZ> > BZ> >Giacomo Fiorin
BZ> > BZ> > Center for Molecular Modeling at
BZ> > BZ> > University of Pennsylvania
BZ> > BZ> > 231 S 34th Street, Philadelphia, PA 19104-6323
BZ> > BZ> >phone: (+1)-215-573-4773
BZ> > BZ> >fax: (+1)-215-573-6233
BZ> > BZ> >mobile: (+1)-267-324-7676
BZ> > BZ> >mail: giacomo.fiorin_<at>_gmail.com
BZ> > BZ> >web: http://www.cmm.upenn.edu/
BZ> > BZ> >---- ----
BZ> > BZ> >
BZ> > BZ> >
BZ> > BZ> >
BZ> > BZ> >On Tue, Nov 4, 2008 at 2:38 PM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
BZ> > BZ> > >Hi, there:
BZ> > BZ> > >
BZ> > BZ> > > I wonder whether anyone has the experience of building NAMD on
BZ> > BZ> > >CRAY-XT3
BZ> > BZ> > >system?
BZ> > BZ> > > I have compiled charm++ successfully using jube
BZ> > BZ> > >(http://www.deisa.eu/science/benchmarking), but I was having
BZ> > BZ> > >problem with
BZ> > BZ> > >the NAMD part. Since I want to build TCL supported version, I have
BZ> > BZ> > >to
BZ> > BZ> > >install tcl myself.(As far as I know, tcl is not provided on CRAY.
BZ> > BZ> > >correct?)
BZ> > BZ> > > Then, at the last step of compiling, I got the error:
BZ> > BZ> > >
BZ> > BZ> > >/usr/bin/ld: cannot find -ltcl8.4
BZ> > BZ> > >child process exit status 1: /usr/bin/ld
BZ> > BZ> > >Fatal Error by charmc in directory
BZ> > BZ> > >/u0/b/bingo/DEISA_BENCH/applications/NAMD/tmp/namd_Cray-XT4-HECToR_apoa1_i000006/n32p2t1_t001_i01/src/NAMD_2.6_Source/CRAY-XT3
BZ> > BZ> > >
BZ> > BZ> > > But I did install TCL, and provided the directory in
BZ> > BZ> > > cray-xt3.tcl.
BZ> > BZ> > >
BZ> > BZ> > > Any idea what's going on?
BZ> > BZ> > > Any suggestion is greatly appreciated.
BZ> > BZ> > > Thanks a lot.
BZ> > BZ> > >
BZ> > BZ> > >Bin
BZ> > BZ> > >
BZ> > BZ> > >
BZ> > BZ> > >
BZ> > BZ> > >
BZ> > BZ> > >
BZ> > BZ> > >
BZ> > BZ> > >
BZ> > BZ> > >
BZ> > BZ> > >-------------------------------------------------------------
BZ> > BZ> > >The tree of liberty must be refreshed from time to time with the
BZ> > BZ> > >blood of
BZ> > BZ> > >patriots and tyrants.
BZ> > BZ> > >
BZ> > BZ> > >
BZ> > BZ>
BZ> > BZ>
BZ> > BZ>
BZ> > BZ>
BZ> > BZ>
BZ> > BZ>
BZ> > BZ>
BZ> > BZ>
BZ> > BZ>
BZ> > BZ> -------------------------------------------------------------
BZ> > BZ> The tree of liberty must be refreshed from time to time with the blood
BZ> > BZ> of
BZ> > BZ> patriots and tyrants.
BZ> > BZ>
BZ> >
BZ> >--
BZ> >=======================================================================
BZ> >Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
BZ> > Center for Molecular Modeling -- University of Pennsylvania
BZ> >Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
BZ> >tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
BZ> >=======================================================================
BZ> >If you make something idiot-proof, the universe creates a better idiot.
BZ>
BZ>
BZ>
BZ>
BZ>
BZ>
BZ>
BZ>
BZ>
BZ> -------------------------------------------------------------
BZ> The tree of liberty must be refreshed from time to time with the blood of
BZ> patriots and tyrants.
BZ>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

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