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...@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@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 <bba...@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 >> bba...@tacc.utexas.edu | Phone: (512) 232-7069 >> Office: ROC 1.435 | Fax: (512) 475-9445 >> >> >
