Thank you very much, everything works now.
best
----- Mail original -----
De: "David A Case" <case.biomaps.rutgers.edu>
À: "AMBER Mailing List" <amber.ambermd.org>
Envoyé: Mardi 9 Septembre 2014 17:02:12
Objet: Re: [AMBER] Amber/ Orca problem
On Tue, Sep 09, 2014, Aixiao Li wrote:
> Thank you for your answer, the Orca is running in parallel way and also
> the openmpi-1.6.5 is in the path. I am wondering if I made some mistakes
> in the commande lines since I am very new to the QM/MM in Amber.
>
> My input file (amber_orca.in)
>
> &cntrl
> imin=1, maxcyc=10,
> ntb=0,
> cut=20.,
> ifqnt=1,
> /
> &qmmm
> qmmask='.11-21',
> qmcharge=0,
> spin=1,
> qm_theory='EXTERN',
> /
> &orc
> method='blyp',
> basis='svp',
> num_threads=2,
> /
>
> mpirun -np 3 sander.MPI -O -i amber_orca.in -o amber_orca.out -c his.crd
> -p his.top -r amber_orca.rst& (the np=3 is the maximum cpu that I can
> use, since my test system has only 3 residues)
I think this is wrong: you want to run sander in serial mode (i.e. run sander,
not sander.MPI). The "num_threads" argument (or a template file if you use
that) will fire off orca in parallel. (There is no point in running sander
itself in parallel, since the slow part of each step will be the orca part
anyway.)
>
>
> and it returns error messages like:
>
> HYDU_create_process (./utils/launch/launch.c:36): dup2 error (Bad file descriptor)
> launch_procs (./pm/pmiserv/pmip_cb.c:751): create process returned error
> ......
> .......
I don't recognize these as Amber errors. See if the change suggested above
helps.
...dac
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Received on Wed Sep 10 2014 - 02:30:03 PDT
