Re: building namd on CRAY-XT3

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Wed Nov 05 2008 - 00:16:34 CST

Hi,
     While compiling with the "hacked" version of TCL, I still got
errors(a different one)

/usr/lib64/libc.a(strtoul.o)(.text+0x0): In function `strtoul':
./sysdeps/generic/strtol.c:110: multiple definition of `strtoul'
/u0/b/bingo/tcl/tcl-crayxt3/lib/libtcl8.3.a(strtoul.o)(.text+0x0):
first defined here
/usr/bin/ld: Warning: size of symbol `strtoul' changed from 521 in /u0/
b/bingo/tcl/tcl-crayxt3/lib/libtcl8.3.a(strtoul.o) to 92 in
/u0/b/bingo/tcl/tcl-crayxt3/lib/libtcl8.3.a(tclUnixPipe.o)(.text
+0x104): In function `TclpCreateTempFile':
: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
/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.
child process exit status 1: /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

       Any ideas?
       Thanks a lot.

Bin

On Nov 4, 2008, at 1:38 PM, Giacomo Fiorin wrote:

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

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

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