AMBER Archive (2008)

Subject: Re: AMBER: Error while compiling Amber

From: Lili Peng (lpeng_at_ucsd.edu)
Date: Thu Feb 14 2008 - 03:09:22 CST

Hi Ross, Chen:

I'm running Linux v2.6.9 on a 210-node ROCKS cluster.

That aside, I was able to successfully compile a parallel version of AMBER 9
(finally!). I didn't have to invoke the use of mpd, though, at least not for
running the "test parallel". In fact, the real problem had to do with the
version of the Intel compiler I was using. Initially I was using
v9.0.033and that was resulting in segmentation faults during the "make
parallel" for
TIP5P. Then I downloaded v9.1.039, and the parallel compile went smoothly.

Interesting how 9.1.039 results in a segmentation fault for Divcon in serial
compiles (
http://structbio.vanderbilt.edu/archives/amber-archive/2006/3259.php), but
works fine for parallel compiles. On the other hand, 9.0.033 results in a
segmentation fault for TIP5P for parallel compilations but works fine for
serial compiles. So picky..

Lili

On 09/02/2008, chen <chen_at_hhmi.umbc.edu> wrote:
>
> 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_at_rosswalker.co.uk
>
> > <mailto:ross_at_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_at_rosswalker.co.uk
>
> > <mailto:ross_at_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_at_scripps.edu
> > <mailto:owner-amber_at_scripps.edu>
> > [mailto:owner-amber_at_scripps.edu
> > <mailto:owner-amber_at_scripps.edu>] *On Behalf Of *Lili Peng
> > *Sent:* Friday, February 08, 2008 17:52
>
> > *To:* amber_at_scripps.edu <mailto:amber_at_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_at_scripps.edu
>
> > <mailto:case_at_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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<lpeng_at_ucsd.edu>

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