From: Jesper Sørensen (jesorensen_at_ucsd.edu)
Date: Tue Jan 24 2012 - 11:46:11 CST
Yes it was a good start. But I want to make use of the "runbatch_2.8" script tailored for Ranger, and when I use my own compiled version it does not work. It looks like there are several switches/flags set that are intended for a performance speedup on ranger, that I would normally otherwise not set myself, so I want to make use of these.
The updated versions of NAMD, charm++, tcl and fftw also does not make it possible to follow the script on the site completely, although I have made a functioning version.
Here is the error I get when I try to use my own compiled version of NAMD 2.8 with a modified runbatch_2.8.
-- Running on 32 processors: ++mpiexec ++remote-shell /share/home/00288/tg455591/NAMD_scripts/mpiexec ++runscript tacc_affinity /share/home/01859/jsx/Apps/NAMD_2.8_M D6/namd2 heat.conf charmrun> /usr/bin/setarch x86_64 -R mpirun -np 32 ++mpiexec ++remote-shell /share/home/00288/tg455591/NAMD_scripts/mpiexec ++runscript tacc_affinity /share/hom e/01859/jsx/Apps/NAMD_2.8_MD6/namd2 heat.conf Warning: Command line arguments for program should be given after the program name. Assuming that ++remote-shell is a command line argument for the program. Unrecognized argument ++mpiexec ignored. Need to provide machinefile or a list of machines Without hostfile option, hostnames must be specified on command line. usage: mpirun_rsh [-v] [-rsh|-ssh] [-paramfile=pfile] [-debug] -[tv] [-xterm] [-show] [-legacy] [-use_xlauncher][xlauncher-width W] -np N (-hostfile hfile | h1 h2 .. hN) a.out args Where: v => Show version and exit rsh => to use rsh for connecting ssh => to use ssh for connecting paramfile => file containing run-time MVICH parameters debug => run each process under the control of gdb tv => run each process under the control of totalview xterm => run remote processes under xterm show => show command for remote execution but dont run it legacy => use old startup method (1 ssh/process) np => specify the number of processes h1 h2... => names of hosts where processes should run or hostfile => name of file contining hosts, one per line a.out => name of MPI binary args => arguments for MPI binary -- Best, Jesper On Jan 23, 2012, at 9:26 AM, George M Giambasu wrote: > This link might be a good start: > > https://www.xsede.org/wwwteragrid/archive/web/user-support/namd_compile_ranger.html > > 2012/1/23 Jesper Sørensen <jesorensen_at_ucsd.edu>: >> Dear NAMD list, >> >> I was wondering who compiled NAMD on Ranger (TACC) >> >> The version in: >> /share/home/00288/tg455591/NAMD_scripts/runbatch_2.8 >> >> There is not a problem with it, but I was wondering if I could get a copy of the install instructions. I need to compile a version with modified source code and I would like one that performs equally fast. >> >> Best regards, >> Jesper >>
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