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.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.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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Received on Wed Jun 06 2007 - 06:07:32 PDT
