[mvapich-discuss] charm++ / namd

[Les Faby]

Dear Roland Fehrenbacher & Matthew Koop,

Instructions for building NAMD with Pathscale compilers:

http://www.pathscale.com/building_code/namd.html

Instructions for building other famous packages:

http://www.pathscale.com/building_code/

-- 
Regards ....
Les Faby
Tech Support Engineer
QLogic Corp. 
System Interconnect Group
2071 Stierlin Ct, STE 200
Mountain View, CA 94043
les at pathscale.com
Please CC: your support mail to support at pathscale.com

----- Forwarded message from Roland Fehrenbacher
<Roland.Fehrenbacher at transtec.de> -----

From: Roland Fehrenbacher <Roland.Fehrenbacher at transtec.de>
Date: Fri, 2 Jun 2006 13:32:31 +0200
To: Matthew Koop <koop at cse.ohio-state.edu>
Subject: Re: [mvapich-discuss] charm++ / namd
X-Mailer: VM 7.17 under 21.4 (patch 17) "Jumbo Shrimp" XEmacs Lucid
Cc: mvapich-discuss at cse.ohio-state.edu
Reply-To: rfehrenb at transtec.de

>>>>> "Matthew" == Matthew Koop <koop at cse.ohio-state.edu> writes:

Matthew,

many thanks for your quick reply.

    Matthew> Roland, Are you able to run the OSU benchmarks, such as
    Matthew> osu_bw and osu_latency, or do you see the problem there
    Matthew> as well? If the problem exists there a setup issue needs
    Matthew> to be worked out first.

Yes, everything works fine for other prograns.

    Matthew> If you are able to run basic MPI programs then we'll need
    Matthew> to make sure everything was configured properly for
    Matthew> charm.

    Matthew> Here's what I've done in the past to prepare charm++ for
    Matthew> NAMD:

    Matthew> cd charm-5.9 cd ./src/arch

    Matthew> cp -r mpi-linux-amd64 mpi-linux-amd64-mvapich cd
    Matthew> mpi-linux-amd64-mvapich

    Matthew> * edit conv-mach.h and change:

    Matthew> #define CMK_MALLOC_USE_GNU_MALLOC 1
    Matthew> #define CMK_MALLOC_USE_OS_BUILTIN 0

    Matthew> to

    Matthew> #define CMK_MALLOC_USE_GNU_MALLOC 0
    Matthew> #define CMK_MALLOC_USE_OS_BUILTIN 1

This indeed solved the problem. My hello (simplearrayhello) test works
now. However, I still have a segmentation fault when trying to run the
pgm test:

$ mpiexec  -comm mpich-ib ./pgm 12 10
Megatest is running on 8 processors.
test 0: initiated [bitvector (jbooth)]
mpiexec: Warning: task 0 died with signal 11 (Segmentation fault).
mpiexec: Warning: tasks 1-7 died with signal 15 (Terminated).

I compiled everything with Pathscale 2.3 (including mvapich). Do you
have any experience with Pathscale compilers and charm++? The mvapich
I built works fine with other stuff.

Thanks again,

Roland

    Matthew> * make sure the MVAPICH mpicc and mpiCC are first in your
    Matthew> path. Otherwise, add the full path to the mpicc and mpiCC
    Matthew> commands in conv_mach.sh

    Matthew> cd ../../..

    Matthew> ./build charm++ mpi-linux-amd64-mvapich --no-build-shared

    Matthew> cd tests/charm++/simplearrayhello make

    Matthew> [koop at bm1 simplearrayhello]$ mpirun_rsh -np 2 bm1 bm2
    Matthew> ./hello Running Hello on 2 processors for 5 elements ...

    Matthew> Please let us know if this works for you or if you have
    Matthew> any other problems.

    Matthew> Thanks,

    Matthew> Matthew Koop - Network-Based Computing Lab Ohio State
    Matthew> University


    Matthew> On Thu, 1 Jun 2006, Roland Fehrenbacher wrote:

    >> Hi,
    >> 
    >> I'm trying to get charm++ (http://charm.cs.uiuc.edu/ needed for
    >> namd) to work with mvapich 0.9.7. While I can compile
    >> everything fine, when executing a test job like hello (from
    >> charm++) I get:
    >> 
    >> $ mpiexec -verbose -n 2 -comm mpich-ib ./hello mpiexec:
    >> resolve_exe: using absolute exe "./hello".  mpiexec:
    >> concurrent_init: old master died, reusing his fifo as master.
    >> mpiexec: wait_task_start: start evt 2 task 0 on beo-15.
    >> mpiexec: wait_task_start: start evt 3 task 1 on beo-15.
    >> mpiexec: All 2 tasks started.  read_ib_startup_ports: waiting
    >> for checkins read_ib_startup_ports: version 3 startup
    >> read_ib_startup_ports: rank 0 checked in, 1 left
    >> read_ib_startup_ports: rank 1 checked in, 0 left
    >> read_ib_startup_ports: barrier start mpiexec: Error: read_full:
    >> EOF, only 0 of 4 bytes.
    >> 
    >> , i.e. the job never starts.
    >> 
    >> $ mpirun_rsh -np 2 -hostfile /var/spool/pbs/aux/84.beosrv-c
    >> ./hello
    >> 
    >> doesn't give any output.
    >> 
    >> A run with a single CPU works fine:
    >> 
    >> $ mpiexec -n 1 -comm mpich-ib ./hello Running Hello on 1
    >> processors for 5 elements Hello 0 created Hello 1 created Hello
    >> 2 created Hello 3 created Hello 4 created Hi[17] from element 0
    >> Hi[18] from element 1 Hi[19] from element 2 Hi[20] from element
    >> 3 Hi[21] from element 4 All done End of program
    >> 
    >> Any ideas?
    >> 
    >> Thanks,
    >> 
    >> Roland
    >> 
    >> _______________________________________________ mvapich-discuss
    >> mailing list mvapich-discuss at cse.ohio-state.edu
    >> http://mail.cse.ohio-state.edu/mailman/listinfo/mvapich-discuss
    >> 






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discuss

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