AMBER Archive (2006)

Subject: AMBER: amber 9 installation problem

From: Ed Pate (pate_at_math.wsu.edu)
Date: Wed Dec 13 2006 - 18:34:19 CST

Dear Amber community:

I am trying to install Amber 9 on an opteron 275-based cluster with
infiniband interconnects and Portland Group compilers. I hope someone can
help me see my problem.

The serial installation appears to go OK, although some of the test file
differences in the TEST_FAILURES.DAT file for the qmmm tests are higher
than I would expect from round off.

For the parallel installation, the config.h file generated from the
./configure command was modified to change the architecture/compiler flag
from p7 to k8-64 and the C compiler flag was changed from m32 to m64.
XLIBS was changed to /usr/X11R6/lib64. The entire config.h file is at the
end of this email. The compile appears to go OK.

Using the "make test.parallel" command in $AMBERHOME/test on 1 compute
node (4 processors), everything appears to go OK until the /Run.noesy
test. This results in a segmentation fault. I removed the /Run.noesy
test from the Makefile, redo the test sequence. The test process now
finally hangs with the following output:

export TESTsander=/home/pate/amber9a.d/amber9/exe/sander.MPI; cd
jar_multi; ./Run.jar
         WorldRank = 1
         NodeID = Group = 1
         WorldRank = 2
         NodeID = 0

   Running multisander version of sander amber9
      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 = 3
         NodeID = 1

            1

         WorldRank = 0
         NodeID = 0

(end of "make test.parallel" output)

I retry the test program using 2 compute nodes (8 processors). The
process now quickly fails with a segmentation fault in the /Run.nonper
test.

I would appreciate any suggestions as to what I am doing wrong trying to
install Amber 9.

Thanks for the help.

Ed Pate

config.h file follows:

#==============================================================================
# AMBER Makefile configuration for compiler/architecture: pgf90
# Generated via command: ./configure -mpich -opteron pgf90
#
# 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=/home/pate/amber9a.d/amber9/src

#------------------------------------------------------------------------------
# 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=$(SOURCE_COMPILED)
USE_LAPACKLIB=$(SOURCE_COMPILED)
USE_LMODLIB=$(LMOD_UNAVAILABLE)

#------------------------------------------------------------------------------
# C compiler
#------------------------------------------------------------------------------
CC= gcc
CPLUSPLUS=g++
CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m64
CPPFLAGS= $(AMBERBUILDFLAGS)

#------------------------------------------------------------------------------
# Fortran preprocessing and compiler.
# FPPFLAGS holds the main Fortran options, such as whether MPI is used.
#------------------------------------------------------------------------------
FPPFLAGS= -I/usr/local/mvapich/include -P -DMPI $(AMBERBUILDFLAGS)
FPP= cpp -traditional $(FPPFLAGS)
FC= pgf90
FFLAGS= -tp k8-64 -O1 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FOPTFLAGS= -tp k8-64 -Mscalarsse -Mvect=sse -Mflushz -fast -O3
$(LOCALFLAGS) $(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= -Mfree

#------------------------------------------------------------------------------
# Loader:
#------------------------------------------------------------------------------
LOAD= pgf90 -tp k8-64 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADCC= gcc -m64 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADLIB= -L/usr/ofed/lib64 -L/usr/local/mvapich-pgi/lib -lmpichf90 -lmpich
-L/usr/ofed/lib64 -libverbs -lpthread -lpthread -lrt
LM= -lm
LOADPTRAJ= pgf90 -tp k8-64 -Mnomain $(LOCALFLAGS) $(AMBERBUILDFLAGS)
XHOME= /usr/X11R6
XLIBS= -L /usr/X11R6/lib64

#------------------------------------------------------------------------------
# Other stuff:
#------------------------------------------------------------------------------
.SUFFIXES: .f90
EMPTY=
AR=ar rv $(EMPTY)
M4=m4
RANLIB=ranlib
SFX=
NETCDF=
NETCDFLIB=
MODULEDIR=-module $(EMPTY)
MAKEDEPEND=$(AMBER_SRC)/../bin/amber_makedepend
SLKO=skipDFTB

# default rules for Fortran and C compilation:

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

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

(end of config.h)

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