[slurm-users] siesta jobs with slurm, an issue

[Mahmood Naderan]

I am able to directly run the command on the node. Please note in the
following output that I have pressed ^C after some minutes. So, the errors
are related to ^C.


[mahmood at compute-0-3 ~]$ mpirun -np 4
/share/apps/chem/siesta-4.0.2/spar/siesta dimer1prime.fdf dimer1prime.out
Siesta Version  : v4.0.2
Architecture    : x86_64-unknown-linux-gnu--unknown
Compiler version: GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
Compiler flags  : mpifort -g -O2
PP flags        : -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT
PARALLEL version

* Running on    4 nodes in parallel
>> Start of run:  22-JUL-2018  21:39:41

                           ***********************
                           *  WELCOME TO SIESTA  *
                           ***********************

reinit: Reading from standard input
************************** Dump of input data file
****************************
^C--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
No species found!!!
Stopping Program from Node:    0
************************** End of input data file
*****************************

reinit:
-----------------------------------------------------------------------
reinit: System Name:
reinit:
-----------------------------------------------------------------------
reinit: System Label: siesta
reinit:
-----------------------------------------------------------------------

initatom: Reading input for the pseudopotentials and atomic orbitals
----------
No species found!!!
Stopping Program from Node:    0


Regards,
Mahmood



On Sun, Jul 22, 2018 at 8:44 PM, Bill Barth <bbarth at tacc.utexas.edu> wrote:

> That doesn't look like a slurm problem to me necessarily. Looks like
> SIESTA quit of its own volition (thus the call to MPI_ABORT()). I suggest
> you ask your local site support to take a look or go to the SIESTA
> developers. I doubt you'll find any SIESTA experts here to help you.
>
> All I can suggest is to check that all the paths you have provided SIESTA
> are correct (the path to the executable is clearly fine b/c SIESTA starts,
> but can it fine prime.fdf?). Otherwise start with your local support team.
>
> Best,
> Bill.
>
> --
> Bill Barth, Ph.D., Director, HPC
> bbarth at tacc.utexas.edu        |   Phone: (512) 232-7069
> Office: ROC 1.435            |   Fax:   (512) 475-9445
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.schedmd.com/pipermail/slurm-users/attachments/20180722/a1796316/attachment.html>