Re: NAMD related

From: Anilkumar Naik (anilkumar.j.naik_at_gmail.com)
Date: Tue Jun 11 2013 - 02:14:17 CDT

Hi,

I did testing with a small program:
test.c:
nt main(int argc, char **argv)
{
    Tcl_Main(argc, argv, 0);
    return 0;
}

1)
xlc test.c -L/usr/lib64 -ltcl8.5 -ldl

/usr/bin/ld: skipping incompatible /usr/lib64/libtcl8.5.so when searching
for -ltcl8.5
/usr/bin/ld: skipping incompatible /usr/lib64/libtcl8.5.so when searching
for -ltcl8.5
/usr/bin/ld: cannot find -ltcl8.5

2)
$cc test.c -L/usr/lib64 -ltcl8.5 -ldl
$ls
a.out

3)
gcc test.c -L/usr/lib64 -ltcl8.5 -ldl
$ls
a.out

May be xlc is skipping incompatible libtcl8.5.so?

Regards,
Anilkumar

On Tue, Jun 11, 2013 at 12:13 PM, Anilkumar Naik <anilkumar.j.naik_at_gmail.com
> wrote:

> Hi,
>
> Sorry for repeated query. But this is necessary to inform all of you the
> problem. So can experts rectify our mistakes.
>
> TCL installaed packages:
> rpm -qa | grep tcl
> tcl-8.5.7-6.el6.ppc64
> tcl-devel-8.5.7-6.el6.ppc64
> tcl-pgtcl-1.6.2-3.el6.ppc64
>
>
> Below error at psfgen.o:
> =============================
> xlc -q64 -Isb/src -Iplugins/include -DSTATIC_PLUGIN -DPSFGEN_USEPLUGINS
> -I/usr/include -DNAMD_TCL -O3 -DNAMD_VERSION=\"CVS-2013-06-10\"
> -DNAMD_PLATFORM=\"Linux-PPC-smp\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY
> -DNODEAWARE_PROXY_SPANNINGTREE -DUSE_NODEPATCHMGR -o psfgen obj/tcl_main.o
> obj/tcl_psfgen.o obj/charmm_file.o obj/charmm_parse_topo_defs.o
> obj/extract_alias.o obj/hash.o obj/hasharray.o obj/memarena.o
> obj/pdb_file.o obj/pdb_file_extract.o obj/psf_file.o obj/psf_file_extract.o
> obj/topo_defs.o obj/topo_mol.o obj/topo_mol_output.o
> obj/topo_mol_pluginio.o obj/stringhash.o obj/dcdplugin.o obj/jsplugin.o
> obj/namdbinplugin.o obj/pdbplugin.o obj/psfplugin.o -L/usr/lib64/
> libtcl8.5.so -ldl -lm^M
> obj/tcl_main.o:(.text+0x14): undefined reference to `Tcl_Main'^M
> obj/tcl_psfgen.o:(.text+0x38): undefined reference to `Tcl_Merge'^M
> ==============================
>
> Regards,
> Anilkumar
>
>
> On Tue, Jun 11, 2013 at 10:46 AM, Anilkumar Naik <
> anilkumar.j.naik_at_gmail.com> wrote:
>
>> Thanks for reply.
>>
>> TCL installed and LD_LIBRARY_PATH is set. But still having these errors.
>>
>> $echo $LD_LIBRARY_PATH
>> /users/home/anilkumar/NAMD_CVS-2013-06-10_Source/fftw/lib:/usr/lib64
>>
>> $ls /usr/lib64/libtcl8.5.so
>> /usr/lib64/libtcl8.5.so
>>
>> No binary found for IBM power7 arch. That's the reason for source
>> compilation.
>>
>> charm++ runs very smooth. NAMD is having little issues. I will give one
>> more attempt by installing TCL in $home/tcl area.
>>
>> Regards,
>> Anilkumar
>>
>>
>>
>> On Mon, Jun 10, 2013 at 8:54 PM, Norman Geist <
>> norman.geist_at_uni-greifswald.de> wrote:
>>
>>> Hi,****
>>>
>>> ** **
>>>
>>> you just seem to not have TCL installed, or not the directory containing
>>> it, is not in your LD_LIBRARY_PATH. These are linux basics and not related
>>> to namd. Why donít you use a precompiled version of namd?****
>>>
>>> ** **
>>>
>>> Norman Geist.****
>>>
>>> ** **
>>>
>>> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
>>> Auftrag von *Anilkumar Naik
>>> *Gesendet:* Montag, 10. Juni 2013 13:35
>>> *An:* Namd Mailing List
>>> *Betreff:* namd-l: NAMD related****
>>>
>>> ** **
>>>
>>> Dear All,****
>>>
>>> ** **
>>>
>>> I am trying to run NAMD as non root user. So may be missing some path or
>>> linking that causing below errors. Sorry for asking simple question. ***
>>> *
>>>
>>> ** **
>>>
>>> Using charm as:****
>>>
>>> ./build charm++ mpi-linux-ppc mpicxx -j8 --with-production****
>>>
>>> ** **
>>>
>>> Using NAMD_2.9_Source as:****
>>>
>>> /config Linux-PPC-MX64-xlc64.arch --charm-base ./charm-6.4.0
>>> --charm-arch mpi-linux-ppc-mpicxx --arch-suffix ppc64****
>>>
>>> ** **
>>>
>>> Attached NAMD make config, NAMD arch and PATH setting files.****
>>>
>>> ** **
>>>
>>> Pl give some help to understand below errors. This is will very helpful
>>> for us to start using NAMD on IBM Linux-Power 7 arch. Looking forward for
>>> some reply. ****
>>>
>>> ** **
>>>
>>> =================****
>>>
>>> obj/tcl_psfgen.o:(.text+0x7814): undefined reference to
>>> `Tcl_NewStringObj'****
>>>
>>> obj/tcl_psfgen.o:(.text+0x7828): undefined reference to
>>> `Tcl_ListObjAppendElement'****
>>>
>>> obj/tcl_psfgen.o:(.text+0x7894): undefined reference to
>>> `Tcl_AppendResult'****
>>>
>>> obj/tcl_psfgen.o:(.text+0x7920): undefined reference to `Tcl_Merge'****
>>>
>>> obj/tcl_psfgen.o:(.text+0x7938): undefined reference to `Tcl_Eval'****
>>>
>>> obj/tcl_psfgen.o:(.text+0x7944): undefined reference to `Tcl_Free'****
>>>
>>> obj/tcl_psfgen.o:(.text+0x7958): undefined reference to `Tcl_Merge'****
>>>
>>> obj/tcl_psfgen.o:(.text+0x7970): undefined reference to `Tcl_Eval'****
>>>
>>> obj/tcl_psfgen.o:(.text+0x797c): undefined reference to `Tcl_Free'****
>>>
>>> obj/tcl_psfgen.o:(.text+0x7a9c): undefined reference to `Tcl_SetResult'*
>>> ***
>>>
>>> obj/tcl_psfgen.o:(.text+0x7ae8): undefined reference to
>>> `Tcl_AppendResult'****
>>>
>>> obj/tcl_psfgen.o:(.text+0x7b1c): undefined reference to
>>> `Tcl_AppendResult'****
>>>
>>> obj/tcl_psfgen.o:(.text+0x80fc): undefined reference to `Tcl_NewIntObj'*
>>> ***
>>>
>>> obj/tcl_psfgen.o:(.text+0x810c): undefined reference to
>>> `Tcl_SetObjResult'****
>>>
>>> obj/tcl_psfgen.o:(.text+0x8150): undefined reference to
>>> `Tcl_AppendResult'****
>>>
>>> obj/tcl_psfgen.o:(.text+0x8178): undefined reference to
>>> `Tcl_AppendResult'****
>>>
>>> obj/tcl_psfgen.o:(.text+0x81b8): undefined reference to
>>> `Tcl_AppendResult'****
>>>
>>> gmake: *** [psfgen] Error 1****
>>>
>>> gmake: *** Waiting for unfinished jobs....****
>>>
>>> 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the
>>> potential to alter the semantics of a program. Please refer to
>>> documentation on the STRICT/NOSTRICT option for more information.****
>>>
>>> 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the
>>> potential to alter the semantics of a program. Please refer to
>>> documentation on the STRICT/NOSTRICT option for more information.****
>>>
>>> 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the
>>> potential to alter the semantics of a program. Please refer to
>>> documentation on the STRICT/NOSTRICT option for more information.****
>>>
>>> 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the
>>> potential to alter the semantics of a program. Please refer to
>>> documentation on the STRICT/NOSTRICT option for more information.****
>>>
>>> 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the
>>> potential to alter the semantics of a program. Please refer to
>>> documentation on the STRICT/NOSTRICT option for more information.****
>>>
>>> 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the
>>> potential to alter the semantics of a program. Please refer to
>>> documentation on the STRICT/NOSTRICT option for more information.****
>>>
>>> 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the
>>> potential to alter the semantics of a program. Please refer to
>>> documentation on the STRICT/NOSTRICT option for more information.****
>>>
>>> 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the
>>> potential to alter the semantics of a program. Please refer to
>>> documentation on the STRICT/NOSTRICT option for more information.****
>>>
>>> 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the
>>> potential to alter the semantics of a program. Please refer to
>>> documentation on the STRICT/NOSTRICT option for more information.****
>>>
>>> 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the
>>> potential to alter the semantics of a program. Please refer to
>>> documentation on the STRICT/NOSTRICT option for more information.****
>>>
>>> =================****
>>>
>>> ** **
>>>
>>> Regards,****
>>>
>>> Anilkumar****
>>>
>>
>>
>

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