From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Feb 19 2004 - 14:06:20 CST
hello,
I was able to overcome the problems posed below by compiling (namd,
fftw,tcl, charm++ )and adding the isomalloc workaround described
on the namdOnAIX wiki page.
However, my job dies in the fft optimization with the following error:
Info: VELOCITY REASSIGNMENT FREQ 100
Info: VELOCITY REASSIGNMENT TEMP 0
Info: VELOCITY REASSIGNMENT INCR 2
Info: VELOCITY REASSIGNMENT HOLD 298
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.312341
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 80 80 60
Info: Attempting to read FFTW data from FFTW_NAMD_2.5_IBM-SP.txt
Info: Optimizing 6 FFT steps. 1...
frost067{bennion1}663: less test.e
ERROR: 0031-250 task 0: Illegal instruction
It doesn't matter how many nodes have been allocated.
The core file isn't very informative as the debug symbols are not
included.
Has this been seen before?
Brian
On Wed, 18 Feb 2004, Gengbin Zheng wrote:
>
> Hi,
>
> I believe the AIX machine we used to compile the binary is not
> compatible with the one you are using. You may have to compile NAMD
> from source code to get it working.
>
> Gengbin
>
>
> On Tue, 17 Feb 2004, Hansang Bae wrote:
>
> > Did somebody solve this problem?
> > I have the same problem.
> >
> > Thanks,
> > Hansang Bae
> >
> > On Wed, 4 Feb 2004 aida_at_mit.edu wrote:
> >
> > > Hi all,
> > >
> > > I want to run simulations on an IBM cluster and have the NAMD Version 2.5 for
> > > AIX-RS6000 installed on my home directory. When I try submitting a parallel job
> > > (using Load Leveler), I get the following error message. Am I supposed to
> > > independently obtain this missing module from somewhere? Or am I running it
> > > wrongly?
> > >
> > > Thanks in advance for your help.
> > >
> > > Aida
> > >
> > > ****************************************
> > >
> > > error message:
> > >
> > > exec (): 0509-036 Cannot load program /home/wi1/aida/NAMD_2.5_AIX-RS6000/namd2
> > > because of the following errors:
> > >
> > > 0509-150 Dependent module /u/ac/jphillip/fftw/lib/libhC.a(shr.o) could
> > > not be loaded
> > >
> > > 0509-022 Cannot load module /u/ac/jphillip/fftw/lib/libhC.a(shr.o)
> > >
> > > *****************
> > >
> > > Command file sent to Load Leveler:
> > >
> > > |--------------------------------------------------------------------------|
> > > | |
> > > | # @ job_type = parallel |
> > > | # @ executable = /usr/bin/poe |
> > > | # @ arguments = ~/NAMD_2.5_AIX-RS6000/namd2 ~/Simulation/file.conf > |
> > > | ~/Simulation/file.log |
> > > | # @ output = out/ll_parallel.$(host).$(jobid).$(stepid).out |
> > > | # @ error = out/ll_parallel.$(host).$(jobid).$(stepid).err |
> > > | # @ notification = error |
> > > | # @ wall_clock_limit = 10:00:00 |
> > > | # @ class = grid |
> > > | # @ total_tasks = 8 |
> > > | # @ blocking = unlimited |
> > > | # @ resources = ConsumableCpus(1) ConsumableMemory(1000mb) |
> > > | # @ queue |
> > > | |
> > > | |
> > > |--------------------------------------------------------------------------|
> > >
> >
>
>
*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************
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