Re: NAMD related

From: Anilkumar Naik (anilkumar.j.naik_at_gmail.com)
Date: Tue Jun 11 2013 - 01:43:30 CDT

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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