Hello,
Thanks for your valuable suggestion. After updating we are able to
run AMBER12 (sander, pmemd, sander.MPI & pmemd.MPI, pmemd.cuda). But
unfortunately when we are not able to install pmemd.cuda.MPI successfully.
Those are few following errors which we are getting at the end of
installation process.
./cuda/cuda.a(gpu.o): In function `MPI::Intracomm::Clone() const':
gpu.cpp:(.text._ZNK3MPI9Intracomm5CloneEv[MPI::Intracomm::Clone()
const]+0x27): undefined reference to `MPI::Comm::Comm()'
./cuda/cuda.a(gpu.o):gpu.cpp:(.text._ZNK3MPI9Intracomm5SplitEii[MPI::Intracomm::Split(int,
int) const]+0x24): more undefined references to `MPI::Comm::Comm()' follow
./cuda/cuda.a(gpu.o):(.rodata._ZTVN3MPI3WinE[vtable for MPI::Win]+0x48):
undefined reference to `MPI::Win::Free()'
./cuda/cuda.a(gpu.o):(.rodata._ZTVN3MPI8DatatypeE[vtable for
MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
collect2: ld returned 1 exit status
make[3]: *** [pmemd.cuda.MPI] Error 1
make[3]: Leaving directory `/home/test/amber12/src/pmemd/src'
make[2]: *** [cuda_parallel] Error 2
make[2]: Leaving directory `/home/test/amber12/src/pmemd'
make[1]: *** [cuda_parallel] Error 2
make[1]: Leaving directory `/home/test/amber12/src'
make: *** [install] Error 2
We are using cuda version 5.5 with openmpi 1.7.2 built with installed cuda.
We did not understand what the problem is. Please give some suggestion.
Sanjib Paul
On Tue, Sep 3, 2013 at 9:38 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Sep 3, 2013 at 11:01 AM, Sanjib Paul <sanjib88paul.gmail.com>
> wrote:
>
> > Dear Amber users and Developers,
> > We are trying to install
> > AMBER12 in a GPU cluster which contains centOS 6.3 operating system.
> There
> > is no error message coming during compilation. When we run some job
> through
> > SANDER, it is running fine, but at the beginning of output file it is
> > showing like that.
> > -------------------------------------------------------
> > Amber 11 SANDER 2010
> > -------------------------------------------------------
> >
> > But when we are trying to run a job through pmemd.cuda, program is going
> > on. But in the output file nothing is coming except.
> >
> > -------------------------------------------------------
> > Amber 11 SANDER 2010
> > -------------------------------------------------------
> >
> > Program uses 99% memory of the GPU card. We did not understand what to
> do.
> > Can anyone help us?
> >
> >
>
> Update your installation and recompile everything. Just running configure
> (and saying "yes" when asked to apply updates) should do it. Make sure you
> recompile everything (you should see the header change to "Amber 12 SANDER"
> if you were successful.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
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Received on Wed Sep 04 2013 - 07:30:04 PDT
