Re: NAMD/VMD installation on Linux Clusters with InfiniBand

From: Anilkumar Naik (anilkumar_at_tifr.res.in)
Date: Fri May 24 2013 - 08:25:10 CDT

Dear All,

Need your help to understand below errors.

====================
"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****
>>
>
>

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