Re: building namd on CRAY-XT3

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Wed Nov 05 2008 - 01:19:37 CST

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

/u0/b/bingo/tcl/tcl-crayxt3/lib/libtcl8.3.a(tclUnixFile.o)(.text
+0xab7): In function `TclpGetCwd':
: warning: the `getwd' function is dangerous and should not be used.
/u0/b/bingo/tcl/tcl-crayxt3/lib/libtcl8.3.a(tclCmdMZ.o)(.text+0x21a4):
In function `Tcl_StringObjCmd':
: undefined reference to `errno'
/u0/b/bingo/tcl/tcl-crayxt3/lib/libtcl8.3.a(tclCmdMZ.o)(.text+0x21c5):
In function `Tcl_StringObjCmd':
: undefined reference to `errno'
/u0/b/bingo/tcl/tcl-crayxt3/lib/libtcl8.3.a(tclCmdMZ.o)(.text+0x21f2):
In function `Tcl_StringObjCmd':
: undefined reference to `errno'
/u0/b/bingo/tcl/tcl-crayxt3/lib/libtcl8.3.a(tclCmdMZ.o)(.text+0x2208):
In function `Tcl_StringObjCmd':
: undefined reference to `errno'
/u0/b/bingo/tcl/tcl-crayxt3/lib/libtcl8.3.a(tclCmdMZ.o)(.text+0x22b9):
In function `Tcl_StringObjCmd':
: undefined reference to `errno'
/u0/b/bingo/tcl/tcl-crayxt3/lib/libtcl8.3.a(tclCmdMZ.o)(.text+0x22d1):
more undefined references to `errno' follow
child process exit status 1: /scratch/local/usr/bin/ld
Fatal Error by charmc in directory /u0/b/bingo/DEISA_BENCH/
applications/NAMD/tmp/namd_Cray-XT4-HECToR_apoa1_i000006/
n32p2t1_t001_i01/src/NAMD_2.6_Source/CRAY-XT3

       I guess "strtoul.o" is too important to be deleted. :-)
Bin

On Nov 4, 2008, at 10:49 PM, Axel Kohlmeyer wrote:

> 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.

-------------------------------------------------------------
The tree of liberty must be refreshed from time to time with the blood
of patriots and tyrants.

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