Re: NAMD/VMD installation on Linux Clusters with InfiniBand

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri May 24 2013 - 08:55:42 CDT

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.

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