AMBER Archive (2008)

Subject: Re: AMBER: Error while compiling Amber

From: Jack Lei (leiming72_at_gmail.com)
Date: Thu Feb 14 2008 - 06:50:57 CST

Lili:

Did you try Intel10 compiler?

Best,
Jack.

On Thu, Feb 14, 2008 at 5:09 PM, Lili Peng <lpeng_at_ucsd.edu> wrote:

> 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
> v9.0.033 and 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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