<div dir="ltr"><div class="gmail_default" style="font-family:tahoma,sans-serif">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.</div><div class="gmail_default" style="font-family:tahoma,sans-serif"><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif"><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif">[mahmood@compute-0-3 ~]$ mpirun -np 4 /share/apps/chem/siesta-4.0.2/spar/siesta dimer1prime.fdf dimer1prime.out<br>Siesta Version : v4.0.2<br>Architecture : x86_64-unknown-linux-gnu--unknown<br>Compiler version: GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)<br>Compiler flags : mpifort -g -O2<br>PP flags : -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT<br>PARALLEL version<br><br>* Running on 4 nodes in parallel<br>>> Start of run: 22-JUL-2018 21:39:41<br><br> ***********************<br> * WELCOME TO SIESTA *<br> ***********************<br><br>reinit: Reading from standard input<br>************************** Dump of input data file ****************************<br>^C--------------------------------------------------------------------------<br>MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD<br>with errorcode 1.<br><br>NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br>You may or may not see output from other processes, depending on<br>exactly when Open MPI kills them.<br>--------------------------------------------------------------------------<br>No species found!!!<br>Stopping Program from Node: 0<br>************************** End of input data file *****************************<br><br>reinit: -----------------------------------------------------------------------<br>reinit: System Name:<br>reinit: -----------------------------------------------------------------------<br>reinit: System Label: siesta<br>reinit: -----------------------------------------------------------------------<br><br>initatom: Reading input for the pseudopotentials and atomic orbitals ----------<br>No species found!!!<br>Stopping Program from Node: 0<br><br></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><font face="tahoma,sans-serif">Regards,<br>Mahmood</font><br><br><br></div></div></div>
<br><div class="gmail_quote">On Sun, Jul 22, 2018 at 8:44 PM, Bill Barth <span dir="ltr"><<a href="mailto:bbarth@tacc.utexas.edu" target="_blank">bbarth@tacc.utexas.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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. <br>
<br>
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.<br>
<br>
Best,<br>
Bill.<br>
<span class="HOEnZb"><font color="#888888"><br>
-- <br>
Bill Barth, Ph.D., Director, HPC<br>
<a href="mailto:bbarth@tacc.utexas.edu">bbarth@tacc.utexas.edu</a> | Phone: (512) 232-7069<br>
Office: ROC 1.435 | Fax: (512) 475-9445<br>
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