From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 11 2009 - 12:08:02 CST
On Wed, 2009-11-11 at 17:17 +0100, Yogesh Aher wrote:
> Dear NAMD users,
>
> I compiled NAMD using openmpi for 32-bit and 64-bit machines
> separately (keeping them on individual machines with same names) and
> now when I would like to run both executables simultaneously in
> parallel mode, it gives me following error:
yogesh,
forget about the complications of running mixed
architecture and just run the 32-bit binaries throughout.
using a 64-bit binary does not automatically imply
that it runs faster(!). it is only on x86 architectures
(due to limitations of the number of general purpose
registers in 32-bit mode) that 64-bit binaries are at
all competitive. on "proper" cpu architectures, the
64-bit version often has of the order of 10-20% overhead
due to having to use twice as large pointer variables
and thus using the CPU cache less efficiently.
cheers,
axel.
>
> user_at_studpcxx:~$ mpirun -hostfile machines namd namd.conf
>
> Charm++> Running on MPI version: 2.1 multi-thread support:
> MPI_THREAD_SINGLE (max supported: MPI_THREAD_SINGLE)
> Charm++> cpu topology info is being gathered.
> Charm++> 2 unique compute nodes detected.
> ------------- Processor 2 Exiting: Called CmiAbort ------------
> Reason: Internal Error: Unknown-msg-type. Contact Developers.
>
> ------------- Processor 3 Exiting: Called CmiAbort ------------
> Reason: Internal Error: Unknown-msg-type. Contact Developers.
>
> [2] Stack Traceback:
> [0] CmiAbort+0x25 [0x8366f3e]
> [1] namd [0x830d4cd]
> [2] CmiHandleMessage+0x22 [0x8367c20]
> [3] CsdScheduleForever+0x67 [0x8367dd2]
> [4] CsdScheduler+0x12 [0x8367d4c]
> [5] _Z10slave_initiPPc+0x21 [0x80fa09d]
> [6] _ZN7BackEnd4initEiPPc+0x53 [0x80fa0f5]
> [7] main+0x2e [0x80f65b6]
> [3] Stack Traceback:
> [0] CmiAbort+0x25 [0x8366f3e]
> [1] namd [0x830d4cd]
> [2] CmiHandleMessage+0x22 [0x8367c20]
> [3] CsdScheduleForever+0x67 [0x8367dd2]
> [4] CsdScheduler+0x12 [0x8367d4c]
> [5] _Z10slave_initiPPc+0x21 [0x80fa09d]
> [6] _ZN7BackEnd4initEiPPc+0x53 [0x80fa0f5]
> [7] main+0x2e [0x80f65b6]
> [8] __libc_start_main+0xd3 [0x88fde3]
> [9] __gxx_personality_v0+0x101 [0x80f3405]
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> [8] __libc_start_main+0xd3 [0x31cde3]
> [9] __gxx_personality_v0+0x101 [0x80f3405]
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 2 with PID 16227 on
> node sibar exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> --------------------------------------------------------------------------
> [studpcxx.xxx.xxx.xx][[7575,1],0][btl_tcp_frag.c:124:mca_btl_tcp_frag_send] mca_btl_tcp_frag_send: writev failed: Connection reset by peer (104)
> Info: NAMD 2.6 for Linux-amd64-MPI
> Info:
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
> Info:
> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 60102 for mpi-linux-x86_64
> [studpcxx.xxx.xxx.xx:27457] 1 more process has sent help message
> help-mpi-api.txt / mpi-abort
> [studpcxx.xxx.xxx.xx:27457] Set MCA parameter
> "orte_base_help_aggregate" to 0 to see all help / error messages
>
> Has anybody tried to work with such mixed environment of 32-bit &
> 64-bit machines..
>
> Look forward to hear about the solution..
>
> Thanking you,
> Sincerely,
> Yogesh
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com Institute for Computational Molecular Science College of Science and Technology Temple University, Philadelphia PA, USA.
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