Hi Anuradha
Look here: https://www.teragrid.org/web/user-support/amber_compile_abe
For build instructions on Abe. There are also job submission scripts and
benchmarks provided on that webpage.
The installation instructions are VERY similar for AMBER 11. You need the
same .soft keys etc and you just do:
cd $AMBERHOME/AmberTools/src/
./configure intel
make install
cd ../../src/
make
Then test it.
Then
cd $AMBERHOME/AmberTools/src/
make clean
./configure -mpi intel
cd ../../src/
make clean
make parallel
This will build you both sander.MPI and pmemd.MPI
All the best
Ross
> -----Original Message-----
> From: Anuradha Mittal [mailto:anuradha.mittal.gmail.com]
> Sent: Saturday, September 18, 2010 8:16 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Amber11 compile issue
>
> This is ncsa abe. They have only amber10. I will try to put in a request.
> Thanks!
>
> On Sat, Sep 18, 2010 at 10:14 PM, Jason Swails
> <jason.swails.gmail.com>wrote:
>
> > Which machine? Do they not already have amber11 installed? Can you put
> in
> > a request for it?
> >
> > On Sat, Sep 18, 2010 at 10:10 PM, Anuradha Mittal <
> > anuradha.mittal.gmail.com
> > > wrote:
> >
> > > I don't have any of these. I am trying to compile on teragrid and
don't
> > > have
> > > permissions to add those libraries there (if that's the solution). Is
> > there
> > > any other way out?
> > >
> > > On Sat, Sep 18, 2010 at 9:05 PM, Jason Swails <jason.swails.gmail.com
> > > >wrote:
> > >
> > > > Hello,
> > > >
> > > > On Sat, Sep 18, 2010 at 10:00 PM, Anuradha Mittal <
> > > > anuradha.mittal.gmail.com
> > > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I am trying to install Amber11 in parallel using intel processor.
> > > > >
> > > > > I am getting the following error:
> > > > > ld: cannot find -lrdmacm
> > > > > make[2]: *** [pmemd.MPI] Error 1
> > > > > make[2]: Leaving directory `/u/ac/amitta2/amber11/src/pmemd/src'
> > > > > make[1]: *** [parallel] Error 2
> > > > > make[1]: Leaving directory `/u/ac/amitta2/amber11/src/pmemd'
> > > > > make: *** [parallel] Error 2
> > > > >
> > > > > which mpif90
> > > > > /usr/local/mvapich2-1.2-intel-ofed-1.2.5.5/bin/mpif90
> > > > >
> > > > > which mpirun
> > > > > /usr/local/mvapich2-1.2-intel-ofed-1.2.5.5/bin/mpirun
> > > > >
> > > > > mpif90 -show
> > > > > ifort -L/usr/local/ofed-1.2.5.5/lib64
> > > > > -I/usr/local/mvapich2-1.2-intel-ofed-1.2.5.5/include
> > > > > -I/usr/local/mvapich2-1.2-intel-ofed-1.2.5.5/include
> > > > > -L/usr/local/mvapich2-1.2-intel-ofed-1.2.5.5/lib -lmpichf90
> > -Wl,-rpath
> > > > > -Wl,/usr/local/mvapich2-1.2-intel-ofed-1.2.5.5/lib -lmpichf90
-lmpich
> > > > > -lpthread -lrdmacm -libverbs -libumad -lrt
> > > > >
> > > >
> > > > Do you see a "librdmacm.so" or "librdmacm.a" in
> > > > usr/local/mvapich2-1.2-intel-ofed-1.2.5.5/lib ? For some reason,
your
> > > > install is having a hard time finding one of these files.
> > > >
> > > >
> > > > >
> > > > > Any help will be much appreciated.
> > > > >
> > > > > Thanks
> > > > > Anu
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Jason M. Swails
> > > > Quantum Theory Project,
> > > > University of Florida
> > > > Ph.D. Graduate Student
> > > > 352-392-4032
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sat Sep 18 2010 - 22:30:03 PDT
