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 16) show something more like: mpirun -np 4 /share/apps/chem/siesta-4.0.2/spar/siesta < dimer1prime.fdf > dimer1prime.out and those examples line up with the idea that Siesta reads its commands from standard input, not by literally opening an input file specified as a command-line argument. If the version of the command using < and > works correctly, then it’s definitely not a Slurm issue, it’s an issue with how you invoked Siesta. > On Jul 22, 2018, at 12:11 PM, 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 >
