Re: Problems compiling NAMD

From: Jesper Soerensen (jes_at_chem.au.dk)
Date: Mon Oct 06 2008 - 09:54:25 CDT

Hi Alexander,

I'm running CentOS 4.3. I've tried using both OpenMPI and MPICH but both
fail. I've tried:
OpenMPI version 1.2.6
MPICH version 1.2.7
Using Intel compilers (icc & ifort) version 10.1.017

I ran the megatest set from charm++ and I get a failure in test14:

> ./mpirun ./pgm
> ...
> test 14: initiated [tempotest (fang)]
> p0_29927: p4_error: interrupt SIGSEGV: 11

> mpirun -np 4 -all-local ./pgm
> Megatest is running on 4 processors.
> ...
> test 14: initiated [tempotest (fang)]
> p2_30323: p4_error: interrupt SIGSEGV: 11
> p3_30346: p4_error: Found a dead connection while looking for
messages: 0
> [jesper_at_fe1 megatest]$ p1_30297: p4_error: interrupt SIGx: 13
> rm_l_2_30324: (10.011719) net_send: could not write to fd=5, errno =
32
> rm_l_3_30347: (7.667969) net_send: could not write to fd=5, errno = 32
> p2_30323: (12.027344) net_send: could not write to fd=5, errno = 32
> p3_30346: (13.675781) net_send: could not write to fd=5, errno = 32
> p1_30297: (18.843750) net_send: could not write to fd=5, errno = 32

Does anybody recognize this?

Kind regards,

Jesper

On Fri, 2008-10-03 at 22:44 +0500, Alexander A. Vakhrushev wrote:
> Hi Jesper!
>
> What is platform of your cluster?
>
> 2008/10/3 Jesper Soerensen <jes_at_chem.au.dk>:
> > Hi,
> >
> > I've just compiled NAMD on our cluster and this runs through fine, but
> > when I start a job I get the following error in the log file:
> >>Info: Entering startup phase 8 with 134856 kB of memory in use.
> >>Info: Finished startup with 143120 kB of memory in use.
> >>1 additional process aborted (not shown)
> >
> > And the cluster job-error log says:
> >>mpirun noticed that job rank 0 with PID 25232 on node s07n06 exited on
> >>signal 11 (Segmentation fault).
> >
> > I am running a Linux-amd64-MPI-icc-ifort version if this helps. Also, let
> > me know if there is more information I can give to help solve the
> > problem. I'm just wondering if anybody has seen this type of error
> > before.
> >
> > Kind regards,
> >
> > Jesper Soerensen
> >
> >
> > --
> > Jesper Sørensen, M.Sc.
> > Ph.D.-student
> > Biomodelling Group, inSPIN and iNANO centers
> > Department of Chemistry
> > University of Aarhus
> > Langelandsgade 140
> > 8000 Aarhus C
> > Office: 1510-419
> > Tlf. 89423385
> > email: jes_at_chem.au.dk
> > www: www.chem.au.dk/~biomodelling
> >
> >
>
>
>

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