AMBER Archive (2005)

Subject: AMBER: Sander Replica Exchange exits with unit 6 error

From: Jordi Rodrigo (rodrigo_at_aspirine.u-strasbg.fr)
Date: Mon Jan 17 2005 - 07:25:14 CST

Hi Carlos,

Here is the result of an interactive submission of the work:

 RUNNING MULTISANDER VERSION OF SANDER AMBER8
     Total processors = 4
     Number of groups = 2

     Looping over processors:
        WorldRank is the global PE rank
        NodeID is the local PE rank in current group

        Group = 0
        WorldRank = 0
        NodeID = 0

        WorldRank = 1
        NodeID = 1

        Group = 1
        WorldRank = 2
        NodeID = 0

        WorldRank = 3
        NodeID = 1

  Unit 6 Error on OPEN: mdout.rem.001

  Unit 6 Error on OPEN: mdout.rem.000
ERROR: 0031-619 Partition manager received unexpected signal 9: Killed
ERROR: 0031-250 task 1: Killed
ERROR: 0031-250 task 3: Killed

Again the mdout.rem.000 and mdout.rem.001 contains the first 100 first
steps
of dynamic. So maybe it is a problem of compilation.

For compilation, here is our config.h

#==============================================================================
# AMBER Makefile configuration for compiler/architecture: AIX
# Generated via command: ./configure -mpi
#
# Configuration script written mainly by Joe Krahn, Scott Brozell, and
# Dave Case, with contributions from lots of people.
#==============================================================================

#------------------------------------------------------------------------------
# Main AMBER source root directory
#------------------------------------------------------------------------------
AMBER_SRC=/amber8sources/

#------------------------------------------------------------------------------
# AMBERBUILDFLAGS provides a hook into the build process for installers;
# for example, to build debug versions of the amber programs
# make -e AMBERBUILDFLAGS="-DDEBUG -g"
#------------------------------------------------------------------------------
AMBERBUILDFLAGS=

#------------------------------------------------------------------------------
# LOCALFLAGS is intended for program specific modifications to the
# Fortran build process and may be modified by the program's local
makefile
#------------------------------------------------------------------------------
LOCALFLAGS=

#------------------------------------------------------------------------------
# Availability and method of delivery of math and optional libraries
#------------------------------------------------------------------------------
USE_BLASLIB=$(VENDOR_SUPPLIED)
USE_LAPACKLIB=$(SOURCE_COMPILED)
USE_LMODLIB=$(LMOD_UNAVAILABLE)

#------------------------------------------------------------------------------
# C compiler
#------------------------------------------------------------------------------
CC= xlc
CPLUSPLUS=xlC
ALTCC=xlc
CFLAGS=-O2 $(AMBERBUILDFLAGS)
ALTCFLAGS= $(AMBERBUILDFLAGS)
CPPFLAGS=-DCLINK_PLAIN $(AMBERBUILDFLAGS)

#------------------------------------------------------------------------------
# Fortran preprocessing and compiler.
# FPPFLAGS holds the main Fortran options, such as whether MPI is used.
#------------------------------------------------------------------------------
FPPFLAGS= -P -I$(AMBER_SRC)/include -DREM -DMPI -DESSL -DNMLEQ
-DCLINK_PLAIN
-Drs6000 -DPOE $(AMBERBUILDFLAGS)
FPP= /lib/cpp -I/usr/lpp/ppe.poe/include/thread64 $(FPPFLAGS)
FC= mpxlf90_r
FFLAGS= -qfixed -c $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FOPTFLAGS= -qfixed -O3 -qmaxmem=-1 -qarch=auto -qtune=auto -c
$(LOCALFLAGS)
$(AMBERBUILDFLAGS)
FPP_PREFIX= _
FREEFORMAT_FLAG= -qfree

#------------------------------------------------------------------------------
# Loader:
#------------------------------------------------------------------------------
LOAD= mpxlf90_r $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADCC= xlc $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADLIB= -lmpi -L/usr/lib -lblas -L/usr/lib -lessl -L/usr/local/lib
-llapack
LOADPTRAJ= mpxlf90_r $(LOCALFLAGS) $(AMBERBUILDFLAGS)
XHOME= /usr/X11R6

#------------------------------------------------------------------------------
# Other stuff:
#------------------------------------------------------------------------------
.SUFFIXES: .f90
SYSDIR=lib
AR=ar rvs
M4=m4 -B50000
RANLIB=/bin/true
SFX=
MAKEDEPEND=$(AMBER_SRC)/../bin/amber_makedepend

# default rules for Fortran and C compilation:

.f.o: $<
        $(FPP) $< > $(FPP_PREFIX)$<
        $(FC) -c $(FFLAGS) -o $@ $(FPP_PREFIX)$<

.f90.o: $<
        $(FPP) $< > $(FPP_PREFIX)$<
        $(FC) -c $(FFLAGS) -o $@ $(FPP_PREFIX)$<

.c.o:
        $(CC) -c $(CFLAGS) $(CPPFLAGS) -o $@ $<

Remark that we did not use for MPI, the -I/tatata/mpi/include but
-I/usr/lpp/ppe.poe/include/thread64 as recommanded by our local
administrator.

Thanks again.

Gilles and Jordi
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