From: Istomin, Andrei (ayistomi_at_uncc.edu)
Date: Mon Jul 09 2007 - 22:16:54 CDT
Hi All,
I am new to NAMD and having a problem with running it in parallel on a Mac PPC cluster under OS X. I am trying to run it under LAM-MPI (our PBS is broken).
First of all, I did not compile the NAMD, just downloaded the binary NAMD_2.6_MacOSX-PPC.tar.gz. Was I supposed to compile it with some specific MPI options in order to use MPI?
I start the namd2 by ssh-ing to one of the compute nodes (here node11) and running this script "lammpi.job" (where file "hosts" contains my node list):
lamboot -v hosts
/home/opt/lam/bin/mpiexec -n 4 /home/ayistomi/NAMD_2.6_MacOSX-PPC/namd2 nptsim.namd > nptsim.log
It boots 4 nodes ok, but after about 30 sec crashes when trying to save the coordinates to the DCD file:
node11:~/AR/NAMD/1XQ3_noL/10_npt_sim ayistomi$ ./lammpi.job
LAM 7.1.2/MPI 2 C++/ROMIO - Indiana University
n-1<23624> ssi:boot:base:linear: booting n0 (192.168.1.11)
n-1<23624> ssi:boot:base:linear: booting n1 (192.168.1.12)
n-1<23624> ssi:boot:base:linear: booting n2 (192.168.1.13)
n-1<23624> ssi:boot:base:linear: booting n3 (192.168.1.14)
n-1<23624> ssi:boot:base:linear: finished
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Couldn't open DCD file nptsim_out.dcd: File exists
Charm++ fatal error:
FATAL ERROR: Couldn't open DCD file nptsim_out.dcd: File exists
-----------------------------------------------------------------------------
It seems that [at least] one of the processes that was started with
mpirun did not invoke MPI_INIT before quitting (it is possible that
more than one process did not invoke MPI_INIT -- mpirun was only
notified of the first one, which was on node n8684).
mpirun can *only* be used with MPI programs (i.e., programs that
invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program
to run non-MPI programs over the lambooted nodes.
-----------------------------------------------------------------------------
mpirun failed with exit status 252
It says that when namd2 tries to write coordinates to the DCD file, the file already exists. It did not exist before the run for sure, it was created fresh by the NAMD. But what is the problem if the file even existed, coordinate snapshots are supposed to be added to it during the run.
Could somebody please give me a hint what am I doing wrong? Is this because I did not compile the NAMD from source with MPI options?
Thanks so much for your help.
Andrei
UNC
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