Hi Ross,
Thanks for your suggestion. I did look into the README of MPICH2 (
http://www.mcs.anl.gov/research/projects/mpich2/documentation/files/mpich2-doc-README.txt)
and tried to set up the daemon for MPD:
$ export PATH="/nas/lpeng/src/mpich2-1.0.6p1/bin"
$ which mpd
/nas/lpeng/src/mpich2-1.0.6p1/bin/mpd
$ which mpiexec
/nas/lpeng/src/mpich2-1.0.6p1/bin/mpiexec
$ which mpirun
/nas/lpeng/src/mpich2-1.0.6p1/bin/mpirun
Everything looks fine until I try to ring up the MPD:
$ mpd &
[1] 13151
/usr/bin/env: python2.4: No such file or directory
[1]+ Exit 127 mpd
What happened? why is it trying to access the env subdirectory, which
doesn't even exist bin?
Any leads on your behalf would be appreciated.
Thank you,
Lili
On 09/02/2008, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> Hi Lili,
>
> You should check the manual for mpich2 - this version of mpi requires a
> demon to be running (in this case called MPD) on all of the nodes on which
> you want the code to run. This typically means setting up a machine file or
> equivalent that is read by mpd.
>
> If you just want to run this on the local machine to which you are logged
> in then you can try.
>
> mpd &
> export DO_PARALLEL='mpirun =np 4'
> make test.parallel
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> ------------------------------
> *From:* owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *Lili Peng
> *Sent:* Friday, February 08, 2008 17:52
> *To:* amber.scripps.edu
> *Subject:* Re: AMBER: Error while compiling Amber
>
> Hi Dr. Case,
>
> Thank you for your help. I added the parser.c file, and the serial
> compilation of AMBER worked.
>
> ... Though I have another problem now. It's about compiling Sander in
> parallel. Although I've searched the mailing list archives extensively,
> none of what's been discussed addresses the issue. It has to do with the
> make install function, and I'm trying to do a test run of sander. I have
> already compiled my MPI library (the MPICH2 version). Here's my input code
> (in bold) and the errors:
>
> *$ export AMBERHOME="/nas/lpeng/src/amber9"*
> *$ export MPI_HOME="/nas/lpeng/opt"*
> *$ export CC=icc*
> *$ export FC=ifort*
> *$ ./configure --prefix=/nas/lpeng/opt CC=$CC FC=$FC*
> *$ make*
> *$ make install*
> *$ ./configure -mpich2 -p4 -static ifort_ia32*
> *$ make parallel*
>
> ... and Amber 9 was compiled successfully. Following the compiling
> instructions, I continued on..
>
> *$ export DO_PARALLEL="/nas/lpeng/src/mpich2-1.0.6p1/bin/mpirun -np 4"*
> *$ make test.sander*
>
> Then I get the error:
>
> make: *** No rule ot make target 'test.sander'. Stop.
>
> I also tried:
>
> *$ make test.parallel*
>
> ..and receive in response:
>
> export TESTsander=/nas/lpeng/src/amber9/exe/sander.MPI/exe/sander.MPI;
> make test.sander.BASIC
> make[1]: Entering directory `/nas/lpeng/src/amber9/test'
> cd dmp; ./Run.dmp
> This test not set up for parallel
> cannot run in parallel with #residues < #pes
> cd adenine; ./Run.adenine
> This test not set up for parallel
> cannot run in parallel with #residues < #pes
> ==============================================================
> cd cytosine; ./Run.cytosine
> mpiexec_granite.ucsd.edu: cannot connect to local mpd
> (/tmp/mpd2.console_lpeng); possible causes:
> 1. no mpd is running on this host
> 2. an mpd is running but was started without a "console" (-n option)
> In case 1, you can start an mpd on this host with:
> mpd &
> and you will be able to run jobs just on this host.
> For more details on starting mpds on a set of hosts, see
> the MPICH2 Installation Guide.
> ./Run.cytosine: Program error
> make[1]: *** [test.sander.BASIC] Error 1
> make[1]: Leaving directory `/nas/lpeng/src/amber9/test'
> make: *** [test.sander.BASIC.MPI] Error 2
>
> Do you have any leads on what is causing this to occur? Any input from
> your end would be greatly appreciated.
>
> Sincerely,
> Lili
>
>
> On 07/02/2008, David A. Case <case.scripps.edu> wrote:
>
> > On Thu, Feb 07, 2008, Lili Peng wrote:
> > >
> > >
> > > *$ ./configure -p4 ifort_x86_64*
> >
> > What kind of machine are you compiling on? On the one hand, you say
> > "-p4"
> > (which is for Pentium IV), yet you also say x86_64, which is a very
> > different
> > type of architecture.
> >
> > Typing "uname -m" should give you the information you need. Then choose
> > the
> > correct options.
> >
> > >
> > > *$ ./configure -p4 ifort_ia32 *
> > > yacc parser.y
> > > make[2]: execvp: yacc: Permission denied
> >
> > It looks like you got a lot further this time, so my guess is that you
> > are on
> > an ia32 (aka i386 aka i686) system. You should see that sander and lots
> > of
> > other programs have been compiled. For the above problem:
> >
> > First, try "which yacc" and try to find out if it exists, and if so, why
> > you are getting permission denied.
> >
> > Second, try "which bison": if it looks like you have permissions to run
> > bison,
> > add the line
> >
> > YACC = bison -y
> >
> > to your config.h file (in $AMBERHOME/src).
> >
> > Or, if neither work, put the attached parser.c file in
> > $AMBERHOME/src/leap/src/leap, and try again.
> >
> > ....dac
> >
> >
> >
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Received on Sun Feb 10 2008 - 06:07:41 PST
