AMBER Archive (2006)

Subject: Re: AMBER: 'lastrst' error for amber8

From: Arvind Marathe (arvind_at_mbu.iisc.ernet.in)
Date: Fri Sep 15 2006 - 15:01:43 CDT

Thanks David,
you are right. test.parallel gives the same 'lastrst' error at
./Run.tip4p. So i recompiled whole of amber serial and parallel. Tests for
amber serial run fine, parallel gets compiled without problem but
test.parallel gets stuck up at ./Run.tip4p again. I have pasted below the
entire test.parallel run. So what could have gone wrong with the
OS/hardware or with anything else? And what is the way out?

Output for make test.parallel

...........................................................................

 make test
cd dmp; ./Run.dmp
This test not set up for parallel
 cannot run in parallel with #residues < #pes
cd adenine; ./Run.adenine
This test not set up for parallel
 cannot run in parallel with #residues < #pes
==============================================================
cd cytosine; ./Run.cytosine
diffing cytosine.out.save with cytosine.out
PASSED
==============================================================
cd nonper; ./Run.nonper
diffing mdout.nonper.save with mdout.nonper
PASSED
==============================================================
cd nonper; ./Run.nonper.belly
diffing mdout.belly.save with mdout.belly
PASSED
==============================================================
cd nonper; ./Run.nonper.belly.mask
diffing mdout.belly.mask.save with mdout.belly.mask
PASSED
==============================================================
cd nonper; ./Run.nonper.min
diffing mdout.min.save with mdout.min
PASSED
==============================================================
cd nonper; ./Run.cap
diffing mdout.cap.save with mdout.cap
PASSED
==============================================================
cd nonper; ./Run.nonper.nocut
diffing mdout.nocut.save with mdout.nocut
PASSED
==============================================================
cd tip4p; ./Run.tip4p
MPI: Program /software/amber8/exe/sander, Rank 0, Process 16385 called
MPI_Abort(<communicator>, 1)

MPI: --------stack traceback-------
sh: idb: command not found
***** Processor 3
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
 In this slab, Atoms found: 864 Allocated: 512

 Exceeding lastrst in get_stack
   lastrst = 29400
   top_stk= 27096
   isize = 4608
   request= 31704
  Increase lastrst in the &cntrl namelist

MPI: -----stack traceback ends-----
MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
MPI: aborting job
  ./Run.tip4p: Program error
make: *** [test.sander.no_lmod] Error 1

............................................................................

> On Thu, Sep 14, 2006, Arvind Marathe wrote:
>
>> I did check out the density and it is very stable at 1.05 throughout the
>> simulation,....
>
>> Secondly it does run with single processor as you predicted so i suppose
>> it might be a problem with the biological system and not the
>> software/hardware.
>
>> Using the restart file of equilibration run, i ran 6 production runs
>> upto
>> 5 ns without any problem. Only when i analysed those results and tried
>> to
>> extend my simulations, i ran into the problem of 'lastrst'. (and i am
>> not
>> able to extend any of the 6 simulations.) So today just to crosscheck, i
>> tried to start a production run 'fresh' from the end of equilibration
>> stage i.e. by using the restart file of equilibration run and again, i
>> got
>> the 'lastrst' error.
>
> This sounds like something has changed with the executable you are using,
> or
> with the computer environment you are running on. If I read this
> correctly,
> you cannot reproduce runs that you made earlier (i.e. starting from the
> same
> input files). You might try recompiling the codes; also, you didn't
> mention
> whether you have run the parallel test cases since this problem surfaced,
> but
> you should do that if you haven't already done so. It could be a bug in
> Amber, but this smells more like a problem of file corruption or changes
> in
> the underlying OS or hardware, such that jobs that used to run no longer
> work.
>
> ...good luck...dac
>
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