Re: NAMD/VMD installation on Linux Clusters with InfiniBand

From: Andrew Emerson (a.emerson_at_cineca.it)
Date: Mon May 27 2013 - 07:25:19 CDT

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 <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<norman.geist_at_uni-greifswald.de>
> *Cc: *Namd Mailing List<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
> <mailto: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>
> [mailto: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 <mailto: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. 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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