You might want to try the ORCA forum since the problem seems to reside in
ORCA.
https://orcaforum.kofo.mpg.de/index.php?sid=89c1171e8020013cf5b3d7a1ea1a513a
On Tue, May 26, 2026 at 5:13 AM Anders Frederiksen via AMBER <
amber.ambermd.org> wrote:
> Hi Clorice,
>
>
> thank you very much for this input. I have tried to implement your path
> definitions in my slurm script, however still to no avail. I have below
> pasted the relevant part of my slurm script to start the simulation
>
>
>
> ml PDC/24.11
> ml amber/24-cpeGNU-24.11-ambertools-24-amdgpu
> ml openmpi/5.0.8
> ml orca/6.1.1
>
> ORCA_PATH=/pdc/software/24.11/other/orca/6.1.1/
> ORCARUN=/pdc/software/24.11/other/orca/6.1.1/orca
> export PATH="/pdc/software/24.11/other/orca/6.1.1/orca:$PATH"
>
> srun $AMBERHOME/bin/sander.MPI -O -i colvar.mdin \
> -o orc_test.mdout \
> -p neutral.prmtop \
> -c rewrapped.rst7 \
> -r cont.rst7 \
> -x orc_test.nc \
>
>
> similarly, my orca template contains
> %pal nprocs 10 end
>
>
> which ORCA correctly catches
>
> ************************************************************
> * Program running with 10 parallel MPI-processes *
> * working on a common directory *
> ************************************************************
> Unfortunately, the simulation still crashes
>
> Calling Command: mpirun -np 10
> /pdc/software/24.11/other/orca/6.1.0/orca_startup_mpi orc_job.int.tmp
> orc_job
> [file orca_tools/qcmsg.cpp, line 394]:
> .... aborting the run
>
> The mpirun call is not something I have inserted anywhere, it seems to me
> to happen on ambers part, though I am not sure if it is an issue that stems
> from the way the program was compiled on the cluster or if there is another
> underlying issue.
>
>
> I will try and mail this thread to Andreas in the hopes that he has a
> solution.
>
>
> Best,
>
> Anders
>
>
>
> ________________________________
> From: Clorice Reinhardt <Clorice.Reinhardt.uvm.edu>
> Sent: Monday, May 25, 2026 11:54:21 PM
> To: amber.ambermd.org; Anders Frederiksen
> Subject: Re: [AMBER] bug when running QM/MM with orca as external program
>
> Hi Anders,
>
> I have not any problems with Amber/ORCA interface. I'm not sure why you
> are calling ORCA in this way... Amber calls ORCA when it needs the forces
> on the atoms at each time step, or to perform the minimization.
>
> Therefore, you only write the command to call AMBER not ORCA in your job
> submission file. The original QM/MM interface paper has a nice flow chart
> if your confused on the flow of information. Amber writes the input files
> for orca at each minimization or time step, you do not need to do this for
> it.
>
> For example, my slurm file looks like the following for QM/M I do (with
> some information redacted 🙂 )
>
>
> module load amber/24
> echo $AMBERHOME
>
> module load gcc/13.3.0
> module load openmpi/5.0.5
> module load orca/6.0.1
>
> ## amber can't find orca unless you explicitly tell it where the paths
> are. Probably could remedy this by passing the path while compiling, but I
> didn't compile the version on the cluster and it works fine
>
> ORCA_PATH=YOURPATH
> ORCARUN=YOURPATHTOEXECUTEABLE
> export PATH="/gpfs1/sw/x86_64/rh7/pkgs/orca/6.0.0/orca:$PATH"
>
> top=my_parmtop
>
> $sander -O -i qmmm_md.in -o qmmm_md.out -p ${top}.prmtop -c
> YOUR_RESTART.rst -r qmmm_md.rst -x qmmm_md.netcdf
>
> I read in an orca template file with into amber (contain these among
> others):
> %pal nprocs 24 end
> %maxcore 3600
>
> Confirming it worked (looking at orc_job.dat which gets produced each time
> orca is called and is the default name of the output file):
> " ************************************************************
> * Program running with 24 parallel MPI-processes *
> * working on a common directory *
> ************************************************************
>
> ------------------------------------------------------------------------------
> ORCA STARTUP CALCULATIONS
> -- RI-GTO INTEGRALS CHOSEN --
>
> ------------------------------------------------------------------------------
> "
>
> Your happy to reach out to me if you have questions. I run a ton of QM/MM
> and have dug into the source code and used the interface with Qchem,
> Gaussian and ORCA without a hitch, but Andreas Goetz is who'd I reach out
> if you have questions. He wrote the original paper on the interface, and
> he's super nice.
>
> https://scholar.google.com/citations?user=PJusscIAAAAJ&hl=en
>
> Clorice
> ________________________________
> From: Anders Frederiksen via AMBER <amber.ambermd.org>
> Sent: Monday, May 25, 2026 9:52 AM
> To: amber.ambermd.org <amber.ambermd.org>
> Subject: [AMBER] bug when running QM/MM with orca as external program
>
> Dear amber forum,
>
> I have in the last week been working with the QM/MM interface of the
> amber programme and especially focussing with performing a QM/MM
> simulation with orca as the external program.
>
> I have had great success running with orca as external program on small
> test systems for short simulations with sander running on multiple
> processors through MPI and orca running on single core through num
> threads = 1.
>
> However, if I want to run any kind of multi processing the QM part of
> the simulation crashes with the error
>
> ORCA finished by error termination in orca_util
> Calling Command: mpirun -np 2
> /pdc/software/24.11/other/orca/6.1.0/orca_util_mpi orc_job orca_hostfile
> orc_job
> [file orca_tools/qcmsg.cpp, line 394]:
> .... aborting the run
>
> This in principle is not surprising if we take a quick look at the orca
> documentation where it states:
>
> Do not start the ORCA driver with mpirun!
>
> I have tested and if I use ORCA the intended way, that is calling ORCA
> with its full path followed by the input file it runs just fine on
> multiple processors and therefore the fix for the amber call should be
> quite simple: Remove the "mpirun -np #MPIprocessors" call when orca is
> initiated.
>
> I should not that this should not be a version dependent thing for orca
> as I have found documentation all the way back in ORCA 3 (i.e.
> documentation from 2015), stating that starting ORCA with mpirun will
> make it crash.
>
> I have tried to work around the issue by using a template file
> (use_template =1) however sadly AMBER seems to read the nprocs flag and
> will make ORCA run through mpirun, leading to the same error as if
> initiated with AMBER input.
>
>
> If anyone have found another workaround I am all ears, though I hope
> this mail reaches a developer as the fix on paper should be rather
> simple, though given my inexperience in development it could not be as
> simple as I want it to be.
>
> Best,
>
> Anders Frederiksen
> Postdoctoral researcher
> KTH, department of Chemistry, Stockholm, Sweden.
>
>
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Received on Tue May 26 2026 - 11:00:03 PDT
