I followed the instructions from that link only. Still I get the mentioned
error. I contacted Amber mailing list and they suggested me to add the
missing libraries.
On Sun, Sep 19, 2010 at 12:03 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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
> > >
> > _______________________________________________
> > 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 - 22:30:04 PDT
