Re: NAMD/VMD installation on Linux Clusters with InfiniBand

From: Anilkumar Naik (anilkumar_at_tifr.res.in)
Date: Fri May 24 2013 - 04:55:02 CDT

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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