Dear AMBER creators,
I'm trying to run the following script to simulate a heating step of my protein:
#!/bin/bash --login
#PBS -N PLP_heating
#PBS -l walltime=24:00:00
#PBS -l select=2
#PBS -j oe
#PBS -A e280-Croft
module load amber
cd /work/e280/e280/enxds6/PLP
export MPICH_FAST_MEMCPY=1
export MPI_COL_OPT_ON=1
aprun -n 48 pmemd.MPI -O -i LAMPLP_heat1.in -o LAMPLP_heat1.out -p LAMPLP.prmtop -c LAMPLP_min2.rst -r LAMPLP_heat1.rst -ref LAMPLP.inpcrd -x LAMPLP_heat1.mdcrd
echo "DONE"
...but it stopped after 20 seconds with the text:
ModuleCmd_Load.c(226):ERROR:105: Unable to locate a modulefile for 'null'
ModuleCmd_Load.c(226):ERROR:105: Unable to locate a modulefile for 'null'
Rank 0 [Thu Sep 3 03:44:01 2015] [c2-1c1s4n0] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0 0x8ABA6D in _gfortran_backtrace at backtrace.c:258
#1 0x8947E0 in _gfortrani_backtrace_handler at compile_options.c:129
#2 0x90C01F in raise
#3 0x90BFDB in raise at pt-raise.c:41
#4 0x91C5D0 in abort at abort.c:92
#5 0x7DED71 in MPID_Abort
#6 0x7BFBD2 in MPI_Abort
#7 0x797BB4 in pmpi_abort
#8 0x4A2156 in __pmemd_lib_mod_MOD_mexit
#9 0x4854CE in __shake_mod_MOD_shake
#10 0x47E2B7 in __runmd_mod_MOD_runmd
#11 0x4B6543 in MAIN__ at pmemd.F90:0
_pmiu_daemon(SIGCHLD): [NID 02000] [c2-1c1s4n0] [Thu Sep 3 03:44:02 2015] PE RANK 0 exit signal Aborted
[NID 02000] 2015-09-03 03:44:02 Apid 17270990: initiated application termination
Application 17270990 exit codes: 134
Application 17270990 exit signals: Killed
Application 17270990 resources: utime ~9s, stime ~3s, Rss ~63044, inblocks ~137873, outblocks ~60547
DONE
--------------------------------------------------------------------------------
Attached there is the produced output file (400 steps and then it stopped).
-it was supposed to be a 3 steps heating production stage, but with three commands the error text was quite the same (error open LAMPLP_heat2.rst, so I tried with just one step but looks like doesn't want to work); it has worked for two stage minimization so I guess it is not a problem of topology and coordinate files.
What might it be?
Thanks
Damiano
________________________________________
From: David A Case [david.case.rutgers.edu]
Sent: 28 August 2015 13:20
To: AMBER Mailing List
Subject: Re: [AMBER] hpc error
On Fri, Aug 28, 2015, Damiano Spadoni wrote:
>
> following your suggests, I tried to run my simulation using many less
> cores and processors and increase them little by little, but a new
> problem occurrs, the hpc facility is writing weird output files (here I
> report my last try on 64 nodes, but the problem is the same even on 2)
> where the same step is repeated more than once and make it impossible to
> finish any jobs. Here I report the error message and some other files
> are attached:
Here is at least one key problem with your script:
aprun -n 768 pmemd -O -i S4F4_md_200ps.in -o S4F4_md200ps32.out -p
SF4.prmtop -c S4F4_heat.rst -r S4F4_md200ps32.rst -x S4F4_md200ps32.mdcrd
You need to be running pmemd.MPI *not* pmemd. You are essentially running the
same (serial) program on every core, and the output is being intermingled.
And, while you are trying to get things working, why not run a much shorter
job? (Set nstlim to 100 or so, with a small value of ntpr.)
Even the correct program (pmemd.MPI) will probably never scale to 768 cores.
Be sure to try a variety of values to optimize this.
....dac
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Received on Thu Sep 03 2015 - 03:30:03 PDT
