Hi everyone,
I have been encountering a weird (considering my poor MPI knowledge)
problem with sander.MPI of Amber12.
As the subject says, after updating CentOS from the release 6.5 to
the 6.6 one (command: yum update), I get in a totally random fashion
the MPI error reported below. By totally random I mean that this error
sometimes occurs and sometimes does not.
It must be added that the problem has been happening on 7 out of 9 blades,
all with
identical installation of Amber12 and MPICH 3.1 (with regard to the
remaining 2 blades,
I have not yet checked if this issue appears, but I am quite sure it would).
Any suggestion/comment to get this problem sorted out is very welcome.
Thanks in advance,
Massimiliano
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(467)..............:
MPID_Init(177).....................: channel initialization failed
MPIDI_CH3_Init(70).................:
MPID_nem_init(319).................:
MPID_nem_tcp_init(171).............:
MPID_nem_tcp_get_business_card(418):
MPID_nem_tcp_init(377).............: gethostbyname failed, vg02 (errno 1)
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 7942 RUNNING AT vg02
= EXIT CODE: 1
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
Error opening unit 30: File "../Dynamics_3/substate81_dyn3.rst" is
missing or unreadable
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 7962 RUNNING AT vg02
= EXIT CODE: 1
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
Error opening unit 30: File "../Dynamics_4/substate81_dyn4.rst" is
missing or unreadable
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 7988 RUNNING AT vg02
= EXIT CODE: 1
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
--
Dr Massimiliano Porrini
Valérie Gabelica Team
U869 ARNA - Inserm / Bordeaux University
Institut Européen de Chimie et Biologie (IECB)
2, rue Robert Escarpit
33607 Pessac Cedex
FRANCE
Tel : 33 (0)5 40 00 63 31
http://www.iecb.u-bordeaux.fr/teams/GABELICA
Emails: massimiliano.porrini.inserm.fr
m.porrini.iecb.u-bordeaux.fr <m.porrini.iecb.u-bordeaux.fr>
mozz76.gmail.com
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Received on Mon Nov 03 2014 - 03:00:03 PST
