Re: [AMBER] How to make pass extra argument "--bind-to none" to mpirun for ORCA when running QMMM from sander?

From: Goetz, Andreas <>
Date: Fri, 31 Jul 2020 10:12:22 +0000

Hi Francesca,

You will have to edit the sander source code where system call to orca is assembled, then recompile.

In file $AMBERHOME/AmberTools/src/sander/qm2_extern_orc_module.F90 replace following line

        trim(call_buffer), trim(orca_path)//'/'//program//' '//trim(inpfile)//' > '//datfile


        trim(call_buffer), trim(orca_path)//'/'//program//' '//trim(inpfile)//' --bind-to none > '//datfile

Then recompile sander. I am afraid there is no easier option at this moment. I hope this works for you.

All the best,

Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771

> On Jul 31, 2020, at 2:42 AM, Francesca Lønstad Bleken <> wrote:
> Hi,
> I wish to run ORCA in parallel with by doing QMMM from sander.
> In order to run ORCA successfully on our cluster with several tasks on the node I need to add "-bind-to none" when calling orca
> as ths: $orcadir/orca jobname.inp "--bind-to none" >> jobname.out
> Now, when I run the QMMM with one task there is no problem (except speed),
> but when I try using 20 tasks I get:
> "SANDER BOMB in subroutine read_results...." for obvious reasons, since
> orca fails with:
> ORCA fisnihed by error termination in GTOInt
> Calling Command: mpirun -np 20 /full/path/to/orca:gtoint_mpi orc_job
> I have a hope that this can be solved by adding " --bind-to none" when sander calls orca, but I do not understand how this may be done.
> I hope there is someone who can help with this!
> Best regards,
> Francesca
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Received on Fri Jul 31 2020 - 03:30:03 PDT
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