AMBER Archive (2003)

Subject: parallel sander jobs die with error: "MPI_COMM_RANK : Null communicator"

From: chris switzer (switzer_at_mail.ucr.edu)
Date: Sat Jun 14 2003 - 21:00:51 CDT

Hi:

I am taking another shot at getting parallel sander (amber7) to run on a
Beowulf cluster (Linux 2.4.9-31smp i686). As near as I can tell the Machine
file conforms to all suggestions I got 6 months back. What I observe is
that seconds after a parallel sander submission the job dies and gives the
output error:

1 - MPI_COMM_RANK : Null communicator
[1] Aborting program !
0 - MPI_COMM_RANK : Null communicator
Killed by signal 15.
Killed by signal 15.

The machine file I am using is provided below.

Thanks in advance for help.

Chris Switzer

setenv MPICH_HOME /usr/local/mpich-1.2.5..9_gnu

setenv MPICH_INCLUDE $MPICH_HOME/include
setenv MPICH_LIBDIR $MPICH_HOME/lib
setenv MPICH_LIB mpich
setenv GM_LIBDIR /usr/local/gm-1.6.4-Linux/lib
setenv GM_LIB gm
#
setenv MACHINE "linux/FreeBSD PC"
setenv MACH Linux
setenv MACHINEFLAGS " -DMPI"

# CPP is the cpp for this machine
setenv CPP "/lib/cpp -traditional -I$MPICH_INCLUDE"

# SYSDIR is the name of the system-specific source directory relative to src/*/
setenv SYSDIR Machines/standard

# COMPILER ALIASES:

# LOADER/LINKER:
setenv LOAD "g77 -O3"
setenv LOADCC "gcc -O3"
setenv LOADLIB "-lm -L$MPICH_LIBDIR -l$MPICH_LIB -L$GM_LIBDIR -l$GM_LIB"

setenv G77_COMPAT "-fno-globals -ff90 -funix-intrinsics-hide"

# little or no optimization:
setenv L0 "g77 -c -g"

# modest optimization (local scalar):
setenv L1 "g77 -c -O -m486 -malign-double -ffast-math -fomit-frame-pointer
$G77_COMPAT"

# high scalar optimization (but not vectorization):
setenv L2 "g77 -c -O3 -m486 -malign-double -ffast-math -fomit-frame-pointer
$G77_COMPAT"

# high optimization (may be vectorization, not parallelization):
setenv L3 "g77 -c -O3 -m486 -malign-double -ffast-math -fomit-frame-pointer
$G77_COMPAT"

# ranlib, if it exists
setenv RANLIB ranlib

# spasms configuration
#SPASMS MACHINE.f2c_spasms_config
#SPASMS unix
#SPASMS n390
#SPASMS large