AMBER Archive (2007)

Subject: RE: AMBER: problem with starting REM on amber9

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Wed Jun 06 2007 - 02:07:14 CDT

thanks for the reply, it is working now.
Regards
priya

Ross Walker <ross_at_rosswalker.co.uk> wrote: Dear Priya,
  
 Are you certain that all nodes can see and have permission to read each input file in the same path? Are you certain the code runs in the directory you expect it to? I.e. is the working directory correct? I assume you can submit regular parallel jobs to your cluster and they run okay?
  
 All the best
 Ross
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---------------------------------
   From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of priya priya
Sent: Tuesday, June 05, 2007 07:21
To: amber_at_scripps.edu
Subject: Re: AMBER: problem with starting REM on amber9

   
group file is as follows, and with this groupfile it gives :

#
# multisander or replica exchange group file
#
-O -i am25_rem.in.000.rep1 -o test_rem.out.rep1 -c test_heat.rst.000.rep1 -r test_rem.rst.rep1 -x test_rem.mdcrd.rep1
-O -i am25_rem.in.001.rep2 -o test_rem.out.rep2 -c test_heat.rst.001.rep2 -r test_rem.rst.rep2 -x test_rem.mdcrd.rep2
-O -i am25_rem.in.002.rep3 -o test_rem.out.rep3 -c test_heat.rst.002.rep3 -r test_rem.rst.rep3 -x test_rem.mdcrd.rep3
-O -i am25_rem.in.003.rep4 -o test_rem.out.rep4 -c test_heat.rst.003.rep4 -r test_rem.rst.rep4 -x test_rem.mdcrd.rep4
-O -i am25_rem.in.004.rep5 -o test_rem.out.rep5 -c test_heat.rst.004.rep5 -r test_rem.rst.rep5 -x test_rem.mdcrd.rep5
-O -i am25_rem.in.005.rep6 -o test_rem.out.rep6 -c test_heat.rst.005.rep6 -r test_rem.rst.rep6 -x test_rem.mdcrd.rep6
-O -i am25_rem.in.006.rep7 -o test_rem.out.rep7 -c test_heat.rst.006.rep7 -r test_rem.rst.rep7 -x test_rem.mdcrd.rep7
-O -i am25_rem.in.007.rep8 -o test_rem.out.rep8 -c test_heat.rst.007.rep8 -r test_rem.rst.rep8 -x test_rem.mdcrd.rep8

ERROR:
Unit 5 Error on OPEN: am25_rem.in.005.rep6

[5] MPI Abort by user aborting program !
PSE: [5(24970)] Aborting program
PSE: [5]: Killing all processes, reason: Abort

  Unit 5 Error on OPEN: am25_rem.in.000.rep1

[0] MPI Abort by user aborting program !
PSE: [0(24098)] Aborting program

  Unit 5 Error on OPEN: am25_rem.in.004.rep5

[4] MPI Abort by user aborting program !

  Unit 5 Error on OPEN: am25_rem.in.007.rep8

[7] MPI Abort by user aborting program !

Unit 5 Error on OPEN: am25_rem.in.004.rep5

[4] MPI Abort by user aborting program !

  Unit 5 Error on OPEN: am25_rem.in.007.rep8

[7] MPI Abort by user aborting program !
PSE: [7(24974)] Aborting program
PSE: [7]: Killing all processes, reason: Abort
PSE: [4(24968)] Aborting program
PSE: [4]: Killing all processes, reason: Abort

  Unit 5 Error on OPEN: am25_rem.in.006.rep7

[6] MPI Abort by user aborting program !
PSE: [6(24972)] Aborting program
PSE: [6]: Killing all processes, reason: Abort

and yes i am trying for 50ps first.
Regards
Priya
Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote: iles what is your groupfile?
also nstlim of 25000 seems long, this is 50ps between exchanges.
is that what you want?

     On 6/5/07, priya priya < priyaanand_27_at_yahoo.co.in> wrote:
hi
 
Im trying to run REMD using AMBER9 on Linux cluster.

              I did this as follows:

       Step1 - First I did initial minimization

       Step2 - The system was heated up to 300K for 100 ps

       Step3 - Equilibration was carried out at 300K for 1000ps.

       Step4 -. Each replica was independently equilibrated at its own
temperature, input file for rem is as follows:

          am.in - igb = 0
 &cntrl
     imin = 0, nstlim = 25000, dt = 0.002,
    ntx = 5, temp0 = 250.0,
    ntt = 1, tol = 0.000001, saltcon = 0.2,
    ntc = 2, ntf = 1, ntb = 0, nsnb = 20,
    ntwx = 500, ntwe = 500, ntwr = 500, ntpr = 500,
    scee = 1.2, cut = 99.0,
           ntr = 0, tautp = 0.1, offset = 0.09,
    nscm = 500, igb = 1, numexchg = 40000,
    irest = 1, ntave = 0,
 /

  but when i try to submit my job on AMBER9 parallel using script it gives:
 
Unit 15 Error on OPEN:
 
 
 
  Unit 15 Error on OPEN:

 
 
[0] MPI Abort by user aborting program !
PSE: [0(29570)] Aborting program
PSE: [0]: Killing all processes, reason: Abort
[11] MPI Abort by user aborting program !
PSE: [11(19281)] Aborting program

PSE: [11]: Killing all processes, reason: Abort
forrtl: error (78): process killed (SIGTERM)
 
  Unit 15 Error on OPEN:
 
 
[1] MPI Abort by user aborting program !
PSE: [1(29572)] Aborting program

PSE: [1]: Killing all processes, reason:
 Abort
forrtl: error (78): process killed (SIGTERM)
 
could antbody please suggest me what the error is.
 
Regards
       
       
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