# Re: AMBER: Error while compiling Amber

From: Lili Peng <lpeng.ucsd.edu>
Date: Thu, 14 Feb 2008 14:24:02 -0800

Hi Junmei,

Thanks for your input. I think I'm having the same problem with submitting
parallel jobs. Could you go into more detail about using and specifying
which machine files for each job? I tried to look for this in the MPICH2
manual, but didn't find anything. Any advice from your end would be greatly
appreciated.

Bests,
Lili

On 14/02/2008, Junmei Wang <junmwang.gmail.com> wrote:
>
> I am also running AMBER9 on a rocks cluster. I used intel 10 compilers,
> but intelmpi didn't work for me, neither openmpi. Finally, I used mpich2 to
> run parallel jobs. As it was pointed out, for mpich2, one needs to run mpd
> daemon first. I found the mpich2 installation manual is really helpful (
> http://www.mcs.anl.gov/research/projects/mpich2/documentation/files/mpich2-doc-install.pdf).
>
>
> I only had one problem when I submit multiple parallel jobs: all jobs were
> running on the first several nodes, although many nodes in mpd.hosts have
> no load at all. I solved this problem by using many machine files. It is a
> little bit silly to specify a machine file for each job, but it works. I
> also wrote a simple program to prepare the machine files.
>
> Best
>
> Junmei
>
>
>
> On Thu, Feb 14, 2008 at 11:41 AM, Lili Peng <lpeng.ucsd.edu> wrote:
>
> > Hi Jack,
> >
> > For the serial or parallel? I tried it with te serial, and ran into a
> > segmentation fault during the AMBER compile. (You'd think newer versions of
> > software would work better.) I did not try it with the parallel compile.
> >
> > Lili
> >
> >
> > On 14/02/2008, Jack Lei <leiming72.gmail.com> wrote:
> > >
> > > Lili:
> > >
> > > Did you try Intel10 compiler?
> > >
> > > Best,
> > > Jack.
> > >
> > > On Thu, Feb 14, 2008 at 5:09 PM, Lili Peng <lpeng.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://archive.ambermd.org/200610/0273.html),
> > > > but works fine for parallel compiles. On the other hand, 9.0.033results in a segmentation fault for TIP5P for parallel compilations but
> > > > works fine for serial compiles. So picky..
> > > >
> > > > Lili
> > > >
> > > >
> > > > On 09/02/2008, chen <chen.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.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
> > > > > > 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
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > -----------------------------------------------------------------------
> > > > > The AMBER Mail Reflector
> > > > > To post, send mail to amber.scripps.edu
> > > > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> > > > >
> > > >
> > > >
> > > > <lpeng.ucsd.edu>
> > > >
> > >
> > >
> >
> >
> >
> >
>

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Received on Sun Feb 17 2008 - 06:07:27 PST
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