Hey David,
I tried to install sander.MPI with mpich following the manual :
i. cd /home/myname
tar xvfj AmberTools18.tar.bz2
ii. export AMBERHOME=/home/myname/amber18
iv. ./configure gnu
v. source /home/myname/amber18/amber.sh
v. make install
vi. cd $AMBERHOME/AmberTools/src
./configure_mpich <compiler-choice> ( I chose gnu).
make install
Nb. I skipped the sudo part cause I alraedy had all related libraries
installed.
However, the program sander.MPI isn't compiled- it is not installed. Is
there any thing that I am missing.
Thanks in advance for helping.
Il giorno mar 14 ago 2018 alle ore 15:37 David A Case <
david.case.rutgers.edu> ha scritto:
> On Tue, Aug 14, 2018, emanuele wrote:
>
> > I am trying to get the free energy for a reduction A + e- → A- using the
> > Thermodynamic Integration (TI) in SANDER.
> >
> > When running a classical TI in SANDER everything goes well, but I am
> > unable to do the same when the system is treated at QM/MM level ( ORCA
> > is used for the QM part).
> >
> > I am running sander in serial on two jobs :
> >
> > mpirun -n 2 /$AMBERHOME$/sander.MPI -ng 2 -groupfile model_step1.group "
> >
> > but the error, which I get, makes me think that there's a problem with
> > recalling MPI .
> >
> > "Open MPI does not support recursive calls of mpirun" (ORCA error).
> >
> > In fact, I know that multisander works calling MPI, so when using more
> > than 1 CPU-core in ORCA (Quantum package), there is a conflict in
> > calling recursively MPI.
>
> Exactly: both sander and ORCA are trying to run in parallel, using the
> same MPI package.
> >
> > Do you have any idea about fixing the problem, ?
>
> A workaround: since sander TI has to be run under MPI, use the serial
> version of ORCA.
>
> A possible(?) fix: install sander.MPI with mpich. ORCA is hard-wired to
> use openmpi, so it's possible that this combination will work.
> (Completely untested!!)
>
> ....dac
>
>
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>
--
*Emanuele Falbo*
PhD student
Penfold group
School of Natural and Environmental Sciences
Bedson Building, Newcastle University
Newcastle upon Tyne, NE1 7RU
w: http://tompenfoldresearch.weebly.com/
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Received on Thu Sep 20 2018 - 04:30:03 PDT
