Re: NAMD/VMD installation on Linux Clusters with InfiniBand

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun May 26 2013 - 02:08:46 CDT

On Sun, May 26, 2013 at 7:46 AM, Anilkumar Naik <anilkumar_at_tifr.res.in> wrote:
> Dear Dr.Axel,
>
> Thanks for help.fftw error was solved.
>
> tcl8.5 is installed at namd directory. struck with below error. Pl suggest.

apparently, you didn't install tcl properly, or didn't adapt the
configuration correctly. the error message is self-explanatory.

> ====
> xlc -q64 -Isb/src -Iplugins/include -DSTATIC_PLUGIN -DPSFGEN_USEPLUGINS
> -I/shared/namd/NAMD_2.9_Source/tcl/include -DNAMD_TCL -O3
> -DNAMD_VERSION=\"2.9\" -DNAMD_PLATFORM=\"Linux-PPC-MPI-ppc64\"
> -DREMOVE_PROXYRESULTMSG_EXTRACOPY -DNODEAWARE_PROXY_SPANNINGTREE
> -DUSE_NODEPATCHMGR -o sortreplicas obj/sortreplicas.o obj/dcdplugin.o
> obj/jsplugin.o obj/namdbinplugin.o obj/pdbplugin.o obj/psfplugin.o -lm
> xlC -q64 -D_NO_MALLOC_H
> -I.rootdir/./charm-6.4.0/mpi-linux-ppc-mpicxx/include -DCMK_OPTIMIZE=1 -Isrc
> -Iinc -Iplugins/include -DSTATIC_PLUGIN
> -I/shared/namd/NAMD_2.9_Source/tcl/include -DNAMD_TCL
> -I/shared/namd/NAMD_2.9_Source/fftw/include -DNAMD_FFTW
> -DNAMD_VERSION=\"2.9\" -DNAMD_PLATFORM=\"Linux-PPC-MPI-ppc64\"
> -DREMOVE_PROXYRESULTMSG_EXTRACOPY -DNODEAWARE_PROXY_SPANNINGTREE
> -DUSE_NODEPATCHMGR -O3 -qnohot -DCMK_OPTIMIZE -o obj/ComputeMoa.o -c
> src/ComputeMoa.C
> /usr/bin/ld: cannot find -lnamdtcl8.3
> 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.
> ===
>
> Regards,
> Anilkumar
>
>
>
> On Fri, May 24, 2013 at 7:25 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Fri, May 24, 2013 at 3:25 PM, Anilkumar Naik <anilkumar_at_tifr.res.in>
>> wrote:
>> > Dear All,
>> >
>> > Need your help to understand below errors.
>>
>> you should try this first:
>>
>> http://lmgtfy.com/?q=sfftw.h+namd
>>
>> axel.
>>
>>
>> > ====================
>> > "src/SimParameters.C", line 42.10: 1540-0836 (S) The #include file
>> > <sfftw.h>
>> > is not found.
>> > "src/SimParameters.C", line 43.10: 1540-0836 (S) The #include file
>> > <srfftw.h> is not found.
>> > gmake: *** [obj/SimParameters.o] 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.
>> > ==============
>> >
>> > Regards,
>> > anilkumar
>> >
>> >
>> > On Fri, May 24, 2013 at 3:25 PM, Anilkumar Naik <anilkumar_at_tifr.res.in>
>> > wrote:
>> >>
>> >> 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,
>> >>>
>> >>>
>> >>>
>> >>> Iím afraid you will have to build namd for this special architecture
>> >>> on
>> >>> your own, thereís no precompiled build. The available builds are
>> >>> incompatible as they canít 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 GrŁŖen
>> >>>
>> >>>
>> >>>
>> >>> 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:printing-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. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

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