AW: NAMD/VMD installation on Linux Clusters with InfiniBand

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu May 30 2013 - 05:14:55 CDT

The error messages at the beginning of the file could indicate that you
havn’t used the -DARCH_POWERPC flag during compile stage and therefore the
object files are incompatible at link stage. Make sure you have the required
flags set and remember to “make clean” to recomplile from scratch, so that
the new settings can take effect at all.

 

Norman Geist.

 

Von: anilkumar.j.naik_at_gmail.com [mailto:anilkumar.j.naik_at_gmail.com] Im
Auftrag von Anilkumar Naik
Gesendet: Donnerstag, 30. Mai 2013 09:50
An: Andrew Emerson
Cc: Axel Kohlmeyer; owner-namd-l_at_ks.uiuc.edu; Norman Geist; Namd Mailing
List
Betreff: Re: namd-l: NAMD/VMD installation on Linux Clusters with InfiniBand

 

Dear All,

 

TCL error I fixed by giving absolute path at Make.config, its worked. But
now struck with new set of errors. Pl have a look at attached file which
gives error details. Pl feel free to correct me if anything wrong steps used
to compile NAMD.

 

Thanks for help.

 

Regards,

Anilkumar

 

On Thu, May 30, 2013 at 12:08 PM, Anilkumar Naik <anilkumar_at_tifr.res.in>
wrote:

Dear All,

 

I get this below "Unresolved reference to symbol" message when tried to
make namd. I really not getting any hint to remove these messages. TCL is
installed by a RPM and its working fine. Don't know why below messages.

 

Pl some expert look into the problem and help to first time install namd on
power 7 machine.

 

xlc_r -w -Isb/src -Iplugins/include -DSTATIC_PLUGIN -DPSFGEN_USEPLUGINS
-I/usr/include -DNAMD_TCL -O4 -qarch=auto -qtune=auto -DNAMD_VERSION=\"2.9\"
-DNAMD_PLATFORM=\"Linux-POWER-MPI-ppc64\" -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

1586-206 (S) Unresolved reference to symbol "Tcl_Main".

1586-206 (S) Unresolved reference to symbol "Tcl_Merge".

1586-206 (S) Unresolved reference to symbol "Tcl_Eval".

1586-206 (S) Unresolved reference to symbol "Tcl_Free".

1586-206 (S) Unresolved reference to symbol "Tcl_AppendResult".

1586-206 (S) Unresolved reference to symbol "Tcl_GetAssocData".

1586-206 (S) Unresolved reference to symbol "Tcl_SetAssocData".

1586-206 (S) Unresolved reference to symbol "Tcl_CreateCommand".

1586-206 (S) Unresolved reference to symbol "Tcl_PkgProvide".

1586-206 (S) Unresolved reference to symbol "Tcl_GetInt".

1586-206 (S) Unresolved reference to symbol "Tcl_SetResult".

1586-206 (S) Unresolved reference to symbol "Tcl_DeleteAssocData".

1586-206 (S) Unresolved reference to symbol "Tcl_AppendElement".

1586-206 (S) Unresolved reference to symbol "Tcl_Alloc".

1586-206 (S) Unresolved reference to symbol "Tcl_NewIntObj".

1586-206 (S) Unresolved reference to symbol "Tcl_SetObjResult".

1586-206 (S) Unresolved reference to symbol "Tcl_NewListObj".

1586-206 (S) Unresolved reference to symbol "Tcl_ListObjAppendElement".

1586-206 (S) Unresolved reference to symbol "Tcl_NewStringObj".

1586-204 (S) Unresolved references to objects are detected.

1586-341 (U) Code generation was not performed due to previously detected
errors. Object file not created.

gmake: *** [psfgen] Error 1

gmake: *** Waiting for unfinished jobs....

 

 

Regards,

Anilkumar

 

On Mon, May 27, 2013 at 5:55 PM, Andrew Emerson <a.emerson_at_cineca.it> wrote:

Hi
Well, in fact as Anilkumar Naik has discovered, they stop the compilation.
The solution is to make sure that the -DARCH_POWERPC option is present in
all the compiler flag variables in the .arch file, such as CXXOPTS and
COPTS.

regards
Andy Emerson

On 25/05/2013 05:42, Axel Kohlmeyer wrote:

These don't look like errors to me.

--
Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.
  _____  
From: Anilkumar Naik  <mailto:anilkumar_at_tifr.res.in> <anilkumar_at_tifr.res.in>
Sender: owner-namd-l_at_ks.uiuc.edu
Date: Fri, 24 May 2013 15:25:02 +0530
To: Norman Geist <mailto:norman.geist_at_uni-greifswald.de>
<norman.geist_at_uni-greifswald.de>
Cc: Namd Mailing List <mailto:namd-l_at_ks.uiuc.edu> <namd-l_at_ks.uiuc.edu>
Subject: Re: namd-l: NAMD/VMD installation on Linux Clusters with InfiniBand
 
Hi, 
 
Having following errors while installing "NAMD_2.9_Source" from source. How
to fix below error?
 
"src/ComputeNonbondedBase2.h", line 32.9: 1540-1401 (I) An unknown "pragma
ivdep" is specified.
"src/ComputeNonbondedBase.h", line 1930.9: 1540-1401 (I) An unknown "pragma
ivdep" is specified.
"src/ComputeNonbondedBase2.h", line 32.9: 1540-1401 (I) An unknown "pragma
ivdep" is specified.
"src/ComputeNonbondedBase2.h", line 32.9: 1540-1401 (I) An unknown "pragma
ivdep" is specified.
 
Regards,
Anilkumar
 
On Thu, May 23, 2013 at 11:54 AM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:
Hello Anilkumar,
 
I’m afraid you will have to build namd for this special architecture on your
own, there’s no precompiled build. The available builds are incompatible as
they can’t use bigendian binary numbers like the IBM uses. But fortunately,
building namd is not that difficult.
You will find the required information on how to do it, at least in some
README files shipped with the namd source. You will not need any special
compilers else than the usual GNU ones. If you are lucky, the IT service,
managing the cluster, will help you. Inform yourself about the infiniband
installation, if not the OFED driver is used or IPoIB is not installed, you
will have to build namd against a separate MPI instead of simply using
charm++.
Feel free to ask if you get stucked somewhere. 
 
Mit freundlichen Grüßen
 
Norman Geist.
 
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Anilkumar Naik
Gesendet: Mittwoch, 22. Mai 2013 18:18
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: NAMD/VMD installation on Linux Clusters with InfiniBand
 
Dear All,
 
Any binary or RPM for installing NAMD/VMD on below machine? how to check
system configuration for compatible for NAMD/VMD?
 
Pl help to get installed NAMD. Thanks for help.
 
OS:
====================
LSB Version:
:core-4.0-noarch:core-4.0-ppc64:graphics-4.0-noarch:graphics-4.0-ppc64:print
ing-4.0-noarch:printing-4.0-ppc64
Distributor ID: RedHatEnterpriseServer
Description:    Red Hat Enterprise Linux Server release 6.0 (Santiago)
Release:        6.0
Codename:       Santiago
=====================
 
Architecture: IBM Power 7
File system: General Parallel File System (GPFS)
Network: Infiniband and Host Bus Adaptor interfaces
 
Software installed
================================
Operating System - RHEL 6.0 with 2.6.32-220.el6.ppc64 kernel 
Job scheduler LoadLeveler 4.1.1
Parallel Operating Environment 5.2.2.0
IBM compiler suite for ANSI C89, ISO C99 and Fortran 77, 90, 95 and 2003
GCC Compiler
Gaussian 09c.01
TCP Linda
OpenMP
MPI
============
 
Regards,
Anilkumar
 
 
-- 
Dr. Andrew Emerson
Supercomputing Applications and Innovation Dept (SCAI)
CINECA
Via Magnanelli, 6/3 40033 Casalecchio di Reno (BO), Italy.
a.emerson_at_cineca.it
0039-0516171653
skype: aem01966
http://hpc.cineca.it
 
 

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