AW: installing namd on ibm cluster (powerpc)

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Dec 05 2011 - 00:29:43 CST

The script cannot be the problem at this point because its already tried to
execute the namd binary. Are you sure that you have AIX machines?? Please
tell me what hardware/machines you have and what operating system you are
running, I think you just have a wrong binary ;) because the message comes
from your shell and tell you that it cannot execute this binary, surely
because itís a wrong one. Just tell me what machines you have, and we see
then ;)

 

Good luck

Norman Geist.

 

Von: Gurunath Katagi [mailto:gurukatagi_at_gmail.com]
Gesendet: Freitag, 2. Dezember 2011 17:03
An: Norman Geist
Betreff: Re: namd-l: installing namd on ibm cluster (powerpc)

 

Hello sir,
as u said , i am trying with precompiled version,
but when i try to run the job, i as getting the following error in the error
file :

ATTENTION: 0031-408 4 tasks allocated by LoadLeveler, continuing...
/home/staff/sec/secdpal/gurunath/namd-sp2/NAMD_2.7_AIX-POWER-MPI/namd2:
/home/staff/sec/secdpal/gurunath/namd-sp2/NAMD_2.7_AIX-POWER-MPI/namd2:
cannot execute binary file
/home/staff/sec/secdpal/gurunath/namd-sp2/NAMD_2.7_AIX-POWER-MPI/namd2:
/home/staff/sec/secdpal/gurunath/namd-sp2/NAMD_2.7_AIX-POWER-MPI/namd2:
cannot execute binary file
/home/staff/sec/secdpal/gurunath/namd-sp2/NAMD_2.7_AIX-POWER-MPI/namd2:
/home/staff/sec/secdpal/gurunath/namd-sp2/NAMD_2.7_AIX-POWER-MPI/namd2:
cannot execute binary file
/home/staff/sec/secdpal/gurunath/namd-sp2/NAMD_2.7_AIX-POWER-MPI/namd2:
/home/staff/sec/secdpal/gurunath/namd-sp2/NAMD_2.7_AIX-POWER-MPI/namd2:
cannot execute binary file

and the out file gives the message like :
Running> poe
/home/staff/sec/secdpal/gurunath/namd-sp2/NAMD_2.7_AIX-POWER-MPI/namd2
md1.conf -nodes 16 -tasks_per_node 4 -rmpool 1

which seems ok ...

my submission script goes like the following:

#!/bin/sh
# @ error = job1.$(Host).$(Cluster).$(Process).err
# @ output = job1.$(Host).$(Cluster).$(Process).out
# @ class = ptask64
# @ job_type = parallel
# @ total_tasks = 4
# @ blocking = unlimited
# @ wall_clock_limit=01:00:00
# @ queue
/home/staff/sec/secdpal/gurunath/namd-sp2/NAMD_2.7_AIX-POWER-MPI/charmrun
+p64 /home/staff/sec/secdpal/gurunath/namd-sp2/NAMD_2.7_AIX-POWER-MPI/namd2
'md1.conf'

Can u please tell me any modification to this script, so that it runs
successfully ...
or let me how do u run ..

and the kind of network that we have is "Dual Gigabit network with Nortel
5510 Gigabit switches"

Thank you
Gurunath

On Thu, Dec 1, 2011 at 7:20 PM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:

Hi,

 

another question just for my interest. Why do you want to compile namd
yourself? The precompiled versions from namd homepage work nice. What kind
of network do you have?

 

regards

 

Norman Geist.

 

Von: Gurunath Katagi [mailto:gurukatagi_at_gmail.com]

Gesendet: Donnerstag, 1. Dezember 2011 13:38

An: Norman Geist
Betreff: Re: namd-l: installing namd on ibm cluster (powerpc)

 

Dear sir ..

sorry for late response ..
still it complains the same thing about C++ compiler not working ..
it is possible for u come one gmail chat sometimes, so that i can do it more
thoroughly ..

Thank you
Gurunath

On Tue, Nov 1, 2011 at 11:54 AM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:

Hi,

 

charm++ is a objective parallel framework which has ist own mpi
implementation. If you donít want to use these internals, you can build
charmrun on top of your own mpi. So you must have an mpi installed, like
openmpi for example. Then these mpi installation will have a C wrapper
compiler mpicc. This is only a wrapper and will call another C compiler (the
one you build this mpi with) with the right options and files needed for an
working mpi executable. In openmpi you can change the compiler which will be
called by the wrappers with the environment variables OMPI_MPICC OMPI_MPIF90
etc.

Also if you want that mpi you must have the wrappers in your PATH
environment variable so that

 

MPICC=mpicc can be looked up to MPICC=/absolute/path/to/mpicc #

 

This is done with

 

export PATH=$PATH:/my/path/to/mpi

 

And check with

 

which mpicc

 

This should pouint to the right wrapper then.

 

If you do not want to have an own mpi, which is not really needed, just use
a precompiled binary of namd or build charm with the internals, this has the
best performance especially on gigabit because it can run on udp while it
has its own checking built in.

 

Feel free to ask ;)

 

Norman Geist.

 

Von: Gurunath Katagi [mailto:gurukatagi_at_gmail.com]
Gesendet: Montag, 31. Oktober 2011 07:59
An: Norman Geist
Betreff: Re: namd-l: installing namd on ibm cluster (powerpc)

 

hi ..
could u please elaborate ..

because, when i try to build, it asks us that ' u have mpicc enabled on ur
path, do u want to build charm++ on this MPI' ..

and one more thing is..
if u compile without mpi, how to runt the jobs using poe ..?

Thank u
Gurunath

On Sat, Oct 29, 2011 at 11:23 PM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:

If you do not have mpi, dont use it, use the charm++ internal

 

Mit freundlichen GrŁŖen

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Gurunath Katagi
Gesendet: Freitag, 28. Oktober 2011 22:14
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: installing namd on ibm cluster (powerpc)

 

Dear all,
I was trying to install NAMD 2.8 version on IBM clsuter from source code

$uname -a
Linux cnode39 2.6.5-7.244-pseries64 #1 SMP Mon Dec 12 18:32:25 UTC 2005
ppc64 ppc64 ppc64 GNU/Linux

when i try to build the charm++ using the command ,
$env MPICXX=mpicc ./build charm++ mpi-linux-ppc mpicc --no-build-shared
--with-production

it gives the error saying mpicxx compiler doesnt work and i have tried with
mpicc also, its giving the error .. i have pasted part of the output ..

configure: WARNING: unrecognized options: --with-productio
Setting load balancing timer type as 'double'
checking machine name... mpi-linux-ppc
checking "cp command as"... cp -p
checking "C++ compiler as"... "mpicxx "
checking "whether C++ compiler works"... "no"
Cannot compile C++ programs with mpicxx
 (check your charm++ version)
-----------..................

Can anybody suggest compilers and other things need to be taken care of
during installation on this machine ..
or is there a precompiled vaersion of NAMD avaibale for this ibm cluster( i
have tried using AIX-power-lapi, but doesn't seem to work ) ..?

Thank u
Gurunath

 

 

 

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