Emanuele,
You installed serial AmberTools, then mpich, now you have to configure and compile MPI enabled AmberTools, which will build sander.MPI:
cd $AMBERHOME
./configure -mpi gnu
make install
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
> On Sep 20, 2018, at 4:29 AM, emanuele falbo <falbo.emanuele.gmail.com> wrote:
>
> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
>
> *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 - 10:00:01 PDT
