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

[John Hearns]

Are you very sure that the filesystem with the input file is mounted on the
compute nodes?
Try to cat the file.

On 22 July 2018 at 19:11, Mahmood Naderan <mahmood.nt at gmail.com> wrote:

> 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
>>
>>
>
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