AMBER Archive (2009)

Subject: 回复： 回复： [AMBER] parallel error

From: 廖青华 (fantastic_0919_at_yahoo.com.cn)
Date: Mon Jun 15 2009 - 08:13:56 CDT

Yes, it shows that it can't open *.rst file, but the *.rst file is the output file. I am confused. The following lines is the information of the error when I run " /usr/local/mpich2/bin/mpirun -np 4 sander.MPI -O -i heat.in -o heat.out -p com_solvated.prmtop -c min3.rst -r heat.rst -x heat.mdcrd -ref min3.rst"

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Fatal error in MPI_Allreduce: Other MPI error, error stack:
MPI_Allreduce(707)........................: MPI_Allreduce(sbuf=0x87372e0, rbuf=0x8737300, count=3, MPI_DOUBLE_PRECISION, MPI_SUM, MPI_COMM_WORLD) failed
MPIR_Allreduce(289).......................:
MPIC_Sendrecv(126)........................:
MPIC_Wait(270)............................:
MPIDI_CH3i_Progress_wait(214).............: an error occurred while handling an event returned by MPIDU_Sock_Wait()
MPIDI_CH3I_Progress_handle_sock_event(420):
MPIDU_Socki_handle_read(637)..............: connection failure (set=0,sock=3,errno=104:Connection reset by peer)[cli_2]: aborting job:
Fatal error in MPI_Allreduce: Other MPI error, error stack:
MPI_Allreduce(707)........................: MPI_Allreduce(sbuf=0x87372e0, rbuf=0x8737300, count=3, MPI_DOUBLE_PRECISION, MPI_SUM, MPI_COMM_WORLD) failed
MPIR_Allreduce(289).......................:
MPIC_Sendrecv(126)........................:
MPIC_Wait(270)............................:
MPIDI_CH3i_Progress_wait(214)...rank 0 in job 1  localhost.localdomain_48125   caused collective abort of all ranks
  exit status of rank 0: killed by signal 9
..........: an error occurred while handling an event returned by MPIDU_Sock_Wait()
MPIDI_CH3I_Progress_handle_sock_event(420):
MPIDU_Socki_handle_read(637)..............: connection failure (set=0,sock=3,errno=104:Connection reset by peer)

Could you help me? Thanks very much!

Best wishes,

Qinghua Liao

 fantastic_0919_at_yahoo.com.cn or fantasticqhl_at_yahoo.com

________________________________
发件人： Tom Joseph <ttjoseph_at_gmail.com>
收件人： AMBER Mailing List <amber_at_ambermd.org>
已发送： 2009/6/15(周一), 下午8:51:49
主题： Re: 回复： [AMBER] parallel error

What does your output file (that you specified with -o) look like?
Often there will be an error message in that in addition to the MPI
abort message.

--Tom

On Mon, Jun 15, 2009 at 8:08 AM, 廖青华<fantastic_0919_at_yahoo.com.cn> wrote:
> Dear Tom Joseph,
> Thanks very much for your reply. I know what you mean. But problem is that after specify my input and output files correcly, I will still get the error.I am just confused. Could you help me figure it out? Thanks very much!
>
> Best wishes
>
> Qinghua Liao
>
>  fantastic_0919_at_yahoo.com.cn or fantasticqhl_at_yahoo.com
>
>
>
>
> ________________________________
> 发件人： Tom Joseph <ttjoseph_at_gmail.com>
> 收件人： AMBER Mailing List <amber_at_ambermd.org>
> 已发送： 2009/6/15(周一), 下午7:54:19
> 主题： Re: [AMBER] parallel error
>
> Did you run sander.MPI without any input files? If you don't specify
> any it will do an MPI abort.
>
> --Tom
>
> On Mon, Jun 15, 2009 at 3:31 AM, 廖青华<fantastic_0919_at_yahoo.com.cn> wrote:
>> Hi amber users,
>>
>> I encountered the error of parallel calculations. I use the ifort compiler to compile amber, and also using mpich2 as parallel software. After compiling parallel vertion of amber, I run sander.MPI, but I got the error like this:
>>
>>  application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0[unset]: aborting job:
>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>
>> I don't know what's the problem, can someone help me to figure it out? Any response will be appreciated.
>>
>> All the best,
>>
>> Qinghua Liao
>>  fantastic_0919_at_yahoo.com.cn or fantasticqhl_at_yahoo.com
>>
>>
>>      ___________________________________________________________
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