no log or dump when using -in

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1

Hello All,

When I use the -in command line option I don’t get a log or dump file, however, when I use “<” I do get all my dump and log files. I’m using a pbs script to submit my job:

#PBS -l walltime=15:00:00
#PBS -l nodes=1:ppn=12:comp
#PBS -N Polymer
#PBS -o stdout
#PBS -j oe
#PBS -M helstreak@…8…
#PBS -m be

module load lammps
module load openmpi

pbsdcp -s $PBS_O_WORKDIR/* $TMPDIR

cd $TMPDIR

mpiexec -np 12 lmp-2011 -sf opt -in TAD.in

pbsdcp -g ‘*’ $PBS_O_WORKDIR
cd $PBS_O_WORKDIR

I’m not sure if that helps but I appreciate any help (or none helpful) comments. Thanks

2

-in and file input has nothing to do with output.
I don't see how this could influence it.

Steve

3

Hi Steve,

Thanks for the reply.

If I submit my job like:

mpiexec -np 12 lmp-2011 -sf opt -in TAD.in

I don’t get any type of output besides stdout. But if I submit the job like:

mpiexec -np 12 lmp-2011 -sf opt -in TAD.in < TAD.in

Then I get log files and dumps.

Thanks for the help.

4

Hi Steve,

Thanks for the reply.

If I submit my job like:

mpiexec \-np 12 lmp\-2011 \-sf opt \-in TAD\.in

I don't get any type of output besides stdout. But if I submit the job
like:

mpiexec \-np 12 lmp\-2011 \-sf opt \-in TAD\.in &lt; TAD\.in

Then I get log files and dumps.

Thanks for the help.

that seems more like you are having a problem with
your MPI installation or your machine setup.

the file that you pass in through redirection will not
be read. you can pass in anything, e.g. use < /dev/null

i remember way back when the OSC mpiexec launcher
for MPICH had problems of this kind. in any case, i suggest
you contact the system manager/administrator and/or
check out the user documentation. this is definitely
not a problem of LAMMPS.

axel.

5

a) You can't run TAD without using partitions in your command line,
    so I don't see how what you are doing would work
b) you shouldn't use both -in in.foo and < in.foo - that is like

6

sorry - message got sent early

b) you shouldn't use both -in in.foo and < in.foo - that is like
doing input twice

I repeat my earlier Q - can you run examples/tad/in.tad the
way the README in that dir says to run it?

Note that you should get files like log.lammps.* and screen.*
b/c you are running in multipartition mode

Steve

7

I copied the wrong command in the last email. I put:

mpiexec -np 12 lmp-2011 -sf opt -in TAD.in < TAD.in

But I meant:

mpiexec -np 12 lmp-2011 -partition 12x1 -sf opt -in TAD.in < TAD.in

I cannot run the examples unless I use “<” to supply the input. Simply using “-in” does not work. As Axel said, this is probably something with the cluster.

8

Can you run a simple LAMMPS examples on a single processor, like bench/in.lj
using -in in.lj instead of < in.lj? Can you do it on
one processor? Can you do it with a compiled "make serial"
version of LAMMPS which doesn't use a real MPI library?

Steve