Re: [AMBER] Amber20 with PLUMED not working with multiple CPUs

From: Amanda Buyan <Amanda.Buyan.anu.edu.au>
Date: Tue, 11 Aug 2020 23:23:24 +0000

Hi Viktor,

Ah yes, I ended up trying that, as well as doing a "make distclean," and that seemed to sort out the problem. Thanks for your help!


Amanda

________________________________
From: viktor drobot <linux776.gmail.com>
Sent: 11 August 2020 17:19
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Amber20 with PLUMED not working with multiple CPUs

well, you should also provide MPICC and MPICXX variables so they will point
to the working MPI compiler. Be sure that you're using the same MPI
compiler for Amber and PLUMED. configure log output can give you a hint
whether MPI compiler was found successfully

73, Viktor

, 11 . 2020 ., 7:23 Amanda Buyan <Amanda.Buyan.anu.edu.au>:

> Hi Viktor,
>
> Thanks for the advice! I've tried compiling PLUMED2.5 with MPI support on
> one of our GPU clusters. The install recipe I have done is
>
> ./configure --prefix=/usr --enable-mpi --program-suffix=MPI
> make -j 4
> make install
>
> I've done what you've suggested, in that I add the following line to my
> .bashrc file:
>
> export PLUMED_KERNEL=/usr/lib/libplumedMPIKernel.so
>
> However, I still get the same error where it says that plumed has been
> compiled without MPI support. Do you have any ideas or other flags I can
> try to rectify this?
>
> Best wishes
>
> Amanda
>
>
>
> ________________________________
> From: viktor drobot <linux776.gmail.com>
> Sent: 10 August 2020 17:25
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Amber20 with PLUMED not working with multiple CPUs
>
> Hello. Be sure that you have compiler PLUMED with MPI support. Usually all
> that you need is to specify --enable-mpi flag during configure. To have
> both serial and MPI versions of PLUMED installed on your system you can use
> --program-suffix option.
> So when you need to run *.MPI versions of sander/pmemd you should export
> path of MPI-versioned PLUMED kernel like this:
> export PLUMED_KERNEL=/usr/lib/libplumed-mpiKernel.so (your will be
> different)
> and for serial versions please export path of no-MPI PLUMED kernel:
> export PLUMED_KERNEL=/usr/lib/libplumedKernel.so
>
> 73, Viktor
>
> , 10 . 2020 ., 2:25 Amanda Buyan <Amanda.Buyan.anu.edu.au>:
>
> > Hi everyone,
> >
> >
> > I'm unsure if the last email I got went through, and I'm still having
> > trouble with the same problem.
> >
> >
> > I've managed to compile Amber20 on our GPU cluster, and am running
> > equilibration simulations. When I minimize using sander, running with
> > PLUMED works just fine. However, when I try to run an equilibrium
> > simulation using pmemd.MPI, the program asks me to specify the PLUMED
> > kernel. When I do, it then says that PLUMED isn't available for MPI.
> Has
> > anyone had this particular error before? How would I go about fixing it?
> > I've tried both enabling and disabling the PLUMED library when I compile
> > pmemd.MPI, but that doesn't seem to do anything either....
> >
> >
> > Any advice would be very helpful!
> >
> >
> > Best wishes
> >
> >
> > Amanda
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Aug 11 2020 - 16:30:02 PDT
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