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[ESPResSo] Parallel Simulations and System Initialization


From: Lorenzo Isella
Subject: [ESPResSo] Parallel Simulations and System Initialization
Date: Thu, 31 Jan 2008 16:11:01 +0100

Dear All,
I am asking really two different things.
(1) I am completely new to running codes in parallel. My machine runs
Debian Testing and is a  64-bit machine with two CPU's.
I installed the OpenMpi library and configured espresso with the
command (without any special options, I thought the script may pick up
the MPI installation by itself):
$ /home/iselllo/internet_downloads/espresso-2.0.5e/configure
CPPFLAGS=-I/usr/include/tcl8.4
Judging from the output of the command, it is not clear (to me)
whether the MPI library works out of the box. I cut and paste the
whole output below:

$ /home/iselllo/internet_downloads/espresso-2.0.5e/configure
CPPFLAGS=-I/usr/include/tcl8.4
Testing whether we are in the source directory...no
Running configure-ac...
checking build system type... Xeon_64-pc-linux
checking host system type... Xeon_64-pc-linux
checking target system type... Xeon_64-pc-linux
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
****************************************************************
*                   Check the compiler and MPI                 *
****************************************************************
checking for style of include used by make... GNU
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking whether gcc and cc understand -c and -o together... yes
checking for mpcc... no
checking for mpxlc... no
checking for mpicc... mpicc
checking whether the mpicc command works out of the box for MPI... yes
configure-ac: trying to find a LAM environment
checking for mpirun... /usr/bin/mpirun
configure-ac: mpirun binary for LAM not found, if you want to use LAM,
please add it to your PATH
configure-ac: trying to find a MPICH environment
checking whether the mpicc command works without flags... no
configure-ac: did not find mpi.h, please specify its location via CPPFLAGS
configure-ac: did not find mpich library, please specify its location
and name via LDFLAGS
checking for mpirun... /usr/bin/mpirun
configure-ac: mpirun not found or not from MPICH, please make it first
in your PATH
checking for mpcc... (cached) mpicc
checking whether the mpicc command works out of the box for MPI... yes
configure-ac: trying to find a generic MPI
checking for mpirun... /usr/bin/mpirun
configure-ac: found a generic MPI environment
checking how to inline functions... static inline
checking the compiler type... gcc
checking whether the compiler accepts -fast... no
checking whether the compiler accepts -m64... yes
checking whether the compiler accepts -march=noconamo... no
checking whether the compiler accepts -msse2 -mfpmath=sse... yes
checking whether the compiler accepts -malign-double... no
checking whether the compiler accepts -O3... yes
checking whether the compiler accepts -Wno-unused-function... yes
checking whether the compiler accepts -Wall... yes
checking whether the compiler accepts -ffast-math... yes
checking whether the compiler accepts -floop-optimize... yes
checking whether the compiler accepts -funroll-loops... yes
checking whether the compiler accepts -fomit-frame-pointer... yes
checking whether the compiler accepts -finline-limit=1000000... yes
****************************************************************
*                          Check for programs                  *
****************************************************************
checking for gawk... (cached) mawk
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking whether ln -s works... yes
checking for doxygen... no
checking for pdflatex... /usr/bin/pdflatex
checking for makeindex... /usr/bin/makeindex
checking for bibtex... /usr/bin/bibtex
****************************************************************
*                   Check for headers and libraries            *
****************************************************************
checking for libtcl8.5... no
checking for libtcl8.4... yes
checking for tcl.h... yes
checking for X... no
checking for libfftw3... yes
checking for fftw3.h... yes
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking for sys/socket.h... (cached) yes
checking types of arguments for select... int,fd_set *,struct timeval *
checking return type of signal handlers... void
checking for size_t... yes
checking for working strtod... yes
checking for atexit... yes
checking for floor... yes
checking for getcwd... yes
checking for gethostbyname... yes
checking for memset... yes
checking for pow... yes
checking for rint... yes
checking for select... yes
checking for socket... yes
checking for sqrt... yes
****************************************************************
*                   Other settings                             *
****************************************************************
checking whether to enable the chooser... no
checking the name of the configuration header... myconfig.h
****************************************************************
*                   Creating output files                      *
****************************************************************
configure-ac: creating ./config.status
config.status: creating Makefile-am
config.status: creating scripts/Makefile
config.status: creating testsuite/Makefile
config.status: creating doc/Makefile
config.status: creating doc/ug/Makefile
config.status: creating doc/ug/figures/Makefile
config.status: creating doc/dg/Makefile
config.status: creating config/myconfig.h
config.status: creating chooser/Espresso
config.status: creating mpiwrap/Espresso
config.status: creating testsuite/test.sh
config.status: creating Espresso
config.status: creating acconfig.h
config.status: linking
/home/iselllo/internet_downloads/espresso-2.0.5e/Makefile to Makefile
config.status: executing depfiles commands
****************************************************************
*                   Configuration summary                      *
****************************************************************
platform detected       = Xeon_64-pc-linux

Compiler settings:
------------------
MPI                     = generic
compiler                = mpicc
linker                  = mpicc
c compiler flags        = -finline-limit=1000000 -fomit-frame-pointer
-funroll-loops -floop-optimize -ffast-math -Wall -Wno-unused-function
-O3 -msse2 -mfpmath=sse -m64
c preprocessor flags    = -I/usr/include/tcl8.4
linker flags            =
libraries               = -lfftw3  -ltcl8.4  -lm
using debug flags       = no
using profiling flags   = no
inline                  =
WARNING: a generic MPI version may or may not work, look at the
Espresso script in

Libraries:
----------
Tcl version             = tcl8.4
Tk version              = none
FFTW version            = 3
efence                  = no

Other settings:
---------------
using Espresso chooser  = no
local config header     = myconfig.h
installation prefix     = /home/iselllo/Espresso
pdflatex                = /usr/bin/pdflatex
makeindex               = /usr/bin/makeindex
bibtex                  = /usr/bin/bibtex
doxygen                 = no


Should I use some additional flags? Furthermore, now, when I try
running one of my codes, I get this message:

$ ./Espresso test_interaction.tcl
libibverbs: Fatal: couldn't read uverbs ABI version.
--------------------------------------------------------------------------
[0,1,0]: OpenIB on host erlive153.jrc.it was unable to find any HCAs.
Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
libibverbs: Fatal: couldn't read uverbs ABI version.
--------------------------------------------------------------------------
[0,1,1]: OpenIB on host erlive153.jrc.it was unable to find any HCAs.
Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
0: Script directory: /home/iselllo/Espresso/share/espresso/scripts

*******************************************************
*                                                     *
*                    - Espresso -                     *
*                    ============                     *
*      A MPI Parallel Molecular Dynamics Program      *
*                                                     *
*                                                     *
* (c) 2002-2006                                       *
* Max-Planck-Institute for Polymer Research           *
* Mainz, Germany                                      *
*                                                     *
*******************************************************

the density is, 0.01
the box side is, 79.3700525984
Ok after allocating a few particles
every is, 2400
the total number of time steps is, 2400000
delta_t is, 0.00125
the number of iterations while ramping the potential is, 800
delta_cap is, 4980.0
t=0.0 E=145739.079185


which sounds like something is going wrong here...
I do not have a clue at what is going on, but I have a feeling that
setting up the right flags or libraries at the configuration time may
iron out these glitches.


(2) My plan now is to run several simulations varying the initial
conditions of my initially randomly displaced particles in a box. By
varying the initial conditions, I mean changing the initial random
positions of the particles i.e. re-setting the seed of the random
number generator to a different value each time.
I read about the command:
t_random seed <seed(0)> ... <seed(n_nodes-1)>
on page 80 of the userguide, but I wonder if I can simply reset a
single number of if I have to go through this whole list of things of
seeds. I am looking for something "practical".
Say I want to run 5 simulation, I would like e.g. to use 10 as the
seed for simulation 1, 20 for 2 and so on, just a number per
simulation.

Many thanks

Lorenzo



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