Looks like you don't have the right python package,. Check if you have
python, and what version, and where, if you have python version higher
then 2.4, then just make a link "ln -s /[the python installed]
/usr/bin/python2.4". For version lower than 2.4, try that too, although
I am not sure if it's going to work. You didn't mention (or maybe I
missed) your OS and version. That could help us to help you better.
Chen
> 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
> <mailto: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
> <mailto:ross.rosswalker.co.uk> |
> | http://www.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>
> [mailto: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 <mailto: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
> <mailto: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 - 06:07:44 PST
