Re: building namd on CRAY-XT3

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Nov 05 2008 - 00:49:51 CST

On Tue, 4 Nov 2008, BIN ZHANG wrote:

BZ> Hi,
BZ> While compiling with the "hacked" version of TCL, I still got errors(a
BZ> different one)
BZ>
BZ> /usr/lib64/libc.a(strtoul.o)(.text+0x0): In function `strtoul':
BZ> ./sysdeps/generic/strtol.c:110: multiple definition of `strtoul'
BZ> /u0/b/bingo/tcl/tcl-crayxt3/lib/libtcl8.3.a(strtoul.o)(.text+0x0): first
BZ> defined here
BZ> /usr/bin/ld: Warning: size of symbol `strtoul' changed from 521 in

[...]

BZ> Any ideas?

obviously the strtoul.o in the tcl lib conflict with the OS provided
one. why not try to get rid of one? since you cannot manipulate the
OS, how about?

ar d /u0/b/bingo/tcl/tcl-crayxt3/lib/libtcl8.3.a strtoul.o

axel.

BZ> Thanks a lot.
BZ>
BZ> Bin
BZ>
BZ>
BZ>
BZ> On Nov 4, 2008, at 1:38 PM, Giacomo Fiorin wrote:
BZ>
BZ> >Hi Bin, I think you probably need unfortunately a specially modified
BZ> >Tcl library for Cray XT3:
BZ> >
BZ> >http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdOnCrayXT3
BZ> >
BZ> >---- -----
BZ> >Giacomo Fiorin
BZ> > Center for Molecular Modeling at
BZ> > University of Pennsylvania
BZ> > 231 S 34th Street, Philadelphia, PA 19104-6323
BZ> >phone: (+1)-215-573-4773
BZ> >fax: (+1)-215-573-6233
BZ> >mobile: (+1)-267-324-7676
BZ> >mail: giacomo.fiorin_<at>_gmail.com
BZ> >web: http://www.cmm.upenn.edu/
BZ> >---- ----
BZ> >
BZ> >
BZ> >
BZ> >On Tue, Nov 4, 2008 at 2:38 PM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
BZ> > >Hi, there:
BZ> > >
BZ> > > I wonder whether anyone has the experience of building NAMD on CRAY-XT3
BZ> > >system?
BZ> > > I have compiled charm++ successfully using jube
BZ> > >(http://www.deisa.eu/science/benchmarking), but I was having problem with
BZ> > >the NAMD part. Since I want to build TCL supported version, I have to
BZ> > >install tcl myself.(As far as I know, tcl is not provided on CRAY.
BZ> > >correct?)
BZ> > > Then, at the last step of compiling, I got the error:
BZ> > >
BZ> > >/usr/bin/ld: cannot find -ltcl8.4
BZ> > >child process exit status 1: /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> > > But I did install TCL, and provided the directory in cray-xt3.tcl.
BZ> > >
BZ> > > Any idea what's going on?
BZ> > > Any suggestion is greatly appreciated.
BZ> > > Thanks a lot.
BZ> > >
BZ> > >Bin
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> > >
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 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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