Re: about compile namd2.7

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun Jul 19 2009 - 11:18:33 CDT

On Sun, 2009-07-19 at 18:58 +0800, liupeng012 wrote:

dear peng liu,

> hi!
> everyone!
> now i want to compile the namd2.8beta.
> using opempi/icc,icpc,ifort. complie the
> charmm: mpi-linux-x86_64-smp-mpicxx
> about the namd2.7 using the option as follow.
> CXX = mpicxx
> CXXOPTS = -O3 -m64 -fexpensive-optimizations -ffast-math
> CC = mpicc
> COPTS = -O3 -m64 -fexpensive-optimizations -ffast-math
> the namd2 just appear.
>
> But when i test this namd . it pop up the error message as follow;
>
> bash: /opt/openmpi/bin/orted: No such file or directory
> bash: /opt/openmpi/bin/orted: No such file or directory
> bash: /opt/openmpi/bin/orted: No such file or directory
> bash: /opt/openmpi/bin/orted: No such file or directory
> [console:31022] ERROR: A daemon on node c0102 failed to start as
> expected.
> [console:31022] ERROR: There may be more information available from
> [console:31022] ERROR: the remote shell (see above).
> [console:31022] ERROR: The daemon exited unexpectedly with status 127.
> [console:31022] ERROR: A daemon on node c0104 failed to start as

this is not at all a NAMD problem, but an OpenMPI problem,
or a problem how your machine is set up.

you have to have a working OpenMPI first. so test that installation
with some simple "hello world" type MPI test program. once you
have that working, you can test charm++ in the same way and
once you have that working, you can compile and test NAMD.

cheers,
    axel.

> expected.
> [console:31022] ERROR: There may be more information available from
> [console:31022] ERROR: the remote shell (see above).
> [console:31022] ERROR: The daemon exited unexpectedly with status 127.
> [console:31022] ERROR: A daemon on node c0103 failed to start as
> expected.
> [console:31022] ERROR: There may be more information available from
> [console:31022] ERROR: the remote shell (see above).
> [console:31022] ERROR: The daemon exited unexpectedly with status 127.
> [console:31022] [0,0,0] ORTE_ERROR_LOG: Timeout in
> file ./../../../orte/mca/pls/base/pls_base_orted_cmds.c at line 275
> [console:31022] [0,0,0] ORTE_ERROR_LOG: Timeout in
> file ./../../../../orte/mca/pls/rsh/pls_rsh_module.c at line 1158
> [console:31022] [0,0,0] ORTE_ERROR_LOG: Timeout in
> file ./../../../../orte/mca/errmgr/hnp/errmgr_hnp.c at line 90
> [console:31022] ERROR: A daemon on node c0101 failed to start as
> expected.
> [console:31022] ERROR: There may be more information available from
> [console:31022] ERROR: the remote shell (see above).
> [console:31022] ERROR: The daemon exited unexpectedly with status 127.
>
>
>
> what is wrong??
> thanks!
> peng liu
>
> 2009-07-19
>
> ______________________________________________________________________
> liupeng012

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.

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