Re: about replica exchange example in lib of 2.10 NAMD

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Tue Oct 20 2015 - 20:10:00 CDT

You can also run with mpirun on a single workstation. Have a look at
the error. It has something to do with a Tcl variable called
"$temperature".

Jeff

–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Fri, Oct 16, 2015 at 12:11 AM, jc guo <guojc123_at_gmail.com> wrote:
> Hi,
>
> I saw some were asking about this,
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-2012/3508.html
>
> but I did not get clear answer from above, is the replica exchange not work
> for single node? only works on the cluster? since I do not know how to find
> my nodelist in our workstation, so could you help me.
>
> I download source code of NAMD 2.10, and follow the compile step in
> note.txt, such as,
>
> tar xzf NAMD_2.10_Source.tar.gz
> cd NAMD_2.10_Source
> tar xf charm-6.6.1.tar
>
>
> Build and test the Charm++/Converse library (MPI version):
> cd charm-6.6.1
> env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --with-production
> cd mpi-linux-x86_64/tests/charm++/megatest
> make pgm
> mpirun -n 4 ./pgm (run as any other MPI program on your cluster)
> cd ../../../../..
>
> Download and install TCL and FFTW libraries:
> (cd to NAMD_2.10_Source if you're not already there)
> wget
> http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
> tar xzf fftw-linux-x86_64.tar.gz
> mv linux-x86_64 fftw
> wget
> http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz
> wget
> http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz
> tar xzf tcl8.5.9-linux-x86_64.tar.gz
> tar xzf tcl8.5.9-linux-x86_64-threaded.tar.gz
> mv tcl8.5.9-linux-x86_64 tcl
> mv tcl8.5.9-linux-x86_64-threaded tcl-threaded
>
> Optionally edit various configuration files:
> (not needed if charm-6.6.1, fftw, and tcl are in NAMD_2.10_Source) already
> in same directory.
>
> Set up build directory and compile:
> MPI version: ./config Linux-x86_64-g++ --charm-arch mpi-linux-x86_64
> cd Linux-x86_64-g++
> make (or gmake -j4, which should run faster)
>
> Quick tests using one and two processes (network version):
> (this is a 66-atom simulation so don't expect any speedup)
> ./namd2
> ./namd2 src/alanin
> ./charmrun +p2 ./namd2
> ./charmrun +p2 ./namd2 src/alanin
>
> Longer test using four processes:
> wget http://www.ks.uiuc.edu/Research/namd/utilities/apoa1.tar.gz
> tar xzf apoa1.tar.gz
> ./charmrun +p4 ./namd2 apoa1/apoa1.namd
>
> above two test case works, but when I ran replica module in NAMD, follows
> such steps,
>
> cd example (in replica directory)
> mkdir output
> (cd output; mkdir 0 1 2 3 4 5 6 7)
> mpirun namd2 +replicas 8 job0.conf +stdout output/%d/job0.%d.log
> error happens, likes,
>
>
> Converse/Charm++ Commit ID:
> v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-Dec-08-28969
> Warning> Randomization of stack pointer is turned on in kernel, thread
> migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space'
> as root to disable it, or try run with '+isomalloc_sync'.
> CharmLB> Load balancer assumes all CPUs are same.
> Charm++> Running on 1 unique compute nodes (8-way SMP).
> Charm++> cpu topology info is gathered in 0.001 seconds.
> Info: NAMD 2.10 for Linux-x86_64-MPI
> Info:
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: for updates, documentation, and support information.
> Info:
> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 60601 for mpi-linux-x86_64
> Info: Built Mon Sep 28 02:01:43 SGT 2015 by tanmingchen on tanmingchen
> Info: 1 NAMD 2.10 Linux-x86_64-MPI 1 tanmingchen tanmingchen
> Info: Running on 1 processors, 1 nodes, 1 physical nodes.
> Info: CPU topology information available.
> Info: Charm++/Converse parallel runtime startup completed at 0.0263531 s
> Info: 83.3789 MB of memory in use based on /proc/self/stat
> Info: Configuration file is ../lib/replica/example/job0.conf
> Info: Changed directory to ../lib/replica/example
> replica_neighbors proc passes internal consistency check
> TCL: Reduction callback proc set to save_callback
> TCL: can't read "temperature": no such variable
> FATAL ERROR: can't read "temperature": no such variable
> while executing
> "temperature $temperature"
> invoked from within
> "if {$i_run} { #restart
> bincoordinates $restart_root.$replica_id.coor
> binvelocities $restart_root.$replica_id.vel
> extendedSystem $restart_root.$r..."
> (file "~/gg/namd/NAMD_2.10_Source/lib/replica/umbrella.namd" line 90)
> invoked from within
> "source ~/gg/namd/NAMD_2.10_Source/lib/replica/umbrella.namd"
> invoked from within
> "if { ! [catch numPes] } { source
> ~/gg/namd/NAMD_2.10_Source/lib/replica/umbrella.namd}"
> (file "job0.conf" line 5)
> [0] Stack Traceback:
> [0:0] CmiAbortHelper+0x63 [0xc56ca3]
> [0:1] _Z8NAMD_diePKc+0x84 [0x5e5a94]
> [0:2] _Z18after_backend_initiPPc+0x212 [0x5ea7d2]
> [0:3] main+0x1a [0x57f34a]
> [0:4] __libc_start_main+0xf5 [0x7f7e901dfec5]
> [0:5] [0x58217c]
>
>
>
> could you help me? Is replica only can work on cluster, not support my
> workstation's information looks like?
>
> grep 'core id' /proc/cpuinfo | sort -u | wc -l
> 4
> grep 'processor' /proc/cpuinfo | sort -u | wc -l
> 8
>
> Sorry to disturb you, hope I could get some help from any of you.
>
> Best regards,
> JC Guo

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