AMBER Archive (2009)

Subject: [AMBER] multisander error

From: Justine Condo (j-shaw_at_northwestern.edu)
Date: Mon Jan 12 2009 - 16:03:37 CST

Dear AMBER-list,
I am trying to do a thermodynamic integration calculation following the
online tutorial example for AMBER 9. I have created my .group files and
all their respective dependencies and a script file. When I submit the job
I receive the following error message:

-catch_rsh
/opt/gridengine/default/spool/compute-0-19/active_jobs/4596.1/pe_hostfile
compute-0-19
compute-0-19
compute-0-19
compute-0-19
Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.

  Running multisander version of sander amber9
     Total processors = 4
     Number of groups = 2

     Looping over processors:
        WorldRank is the global PE rank
        NodeID is the local PE rank in current group

        Group = 0
        WorldRank = 0
        NodeID = 0

        WorldRank = 1
        NodeID = 1

        Group = 1
        WorldRank = 2
        NodeID = 0

        WorldRank = 3
        NodeID = 1

rank 2 in job 1 compute-0-19_48554 caused collective abort of all ranks
  exit status of rank 2: killed by signal 9
...
...
...

I have no idea what is wrong and am hoping someone can assist me in this
detective work!

Thanks in advance,
Justine 

-- 
-*****************************
Justine Shaw-Condo -Ph.D. Candidate
Ratner and Meade Groups
Department of Chemistry
Northwestern University
Office: 4039 Nano
Phone: 847 467 4991
Email: j-shaw_at_northwestern.edu
*************************************
"Great minds discuss ideas; Average minds discuss events; Small minds
discuss people. "-Eleanor Roosevelt
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