Thanks for the hint. In fact the siesta user wasted my time too!!
:/
Regards,
Mahmood
On Sun, Jul 22, 2018 at 11:13 PM, Renfro, Michael wrote:
> You’re getting the same fundamental error in both the interactive and
> batch version, though.
>
> The ‘reinit: Reading from standard input’ line se
You’re getting the same fundamental error in both the interactive and batch
version, though.
The ‘reinit: Reading from standard input’ line seemed off, since you were
providing an argument for the input file. But all the references I find to
running Siesta in their manual (section 3 and section
Yes. Since with my user account, I can not login to nodes, I first ssh to
the node via root and the su there.
[root@rocks7 ~]# ssh compute-0-3
Warning: untrusted X11 forwarding setup failed: xauth key data not generated
Last login: Sun Jul 22 21:40:09 2018 from rocks7.local
Rocks Compute Node
Rock
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 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. S
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@compute-0-3 ~]$ mpirun -np 4
/share/apps/chem/siesta-4.0.2/spar/siesta dimer1prime.fdf dimer1prime.out
Siesta Version : v4.
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 sugge
Hi,
I don't know why siesta jobs are aborted by the slurm.
[mahmood@rocks7 sie]$ cat slurm_script.sh
#!/bin/bash
#SBATCH --output=siesta.out
#SBATCH --job-name=siesta
#SBATCH --ntasks=8
#SBATCH --mem=4G
#SBATCH --account=z3
#SBATCH --partition=EMERALD
mpirun /share/apps/chem/siesta-4.0.2/spar/sies
