AMBER Archive (2009)

Subject: Re: [AMBER] parallel installation of amber on sun

From: Per Jr. Greisen (pgreisen_at_gmail.com)
Date: Fri Apr 03 2009 - 05:22:45 CDT


Hi

I start the compilation with

./configure_amber -mpi -nosanderidc sparc

/lib/cpp -P -DBINTRAJ -DMPI nose_hoover.f > _nose_hoover.f
 "nose_hoover.f", line 455: Can't find include file mpif.h
 *** Error code 2
 make: Fatal error: Command failed for target `nose_hoover.o'
 Current working directory
 /xbar/nas1/gappl/gappl/ggamess/amber10/amber10/src/sander
 *** Error code 1
 make: Fatal error: Command failed for target `parallel'

this I change by adding the following to the configure_amber

fppflags="$fppflags -I/opt/SUNWhpc/HPC8.0/include "

and than this line as well
from
if [ -f /opt/SUNWspro/lib/libsunperf.so ]; then
to
if [ -f /opt/SS12/SUNWspro/lib/libsunperf.so ]; then

after the changes I make clean and than
./configure_amber -mpi -nosanderidc sparc
which gives the error I sent earlier.

The config_amber.h

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

#------------------------------------------------------------------------------
# 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=$(VENDOR_SUPPLIED)
USE_LAPACKLIB=$(VENDOR_SUPPLIED)

#------------------------------------------------------------------------------
# C compiler
#------------------------------------------------------------------------------
CC= cc
CPLUSPLUS=CC
CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-I/opt/SUNWhpc/HPC5.0/include/ -DSYSV $(AMBERBUILDFLAGS)
CPPFLAGS= -DBINTRAJ -I../netcdf/include $(AMBERBUILDFLAGS)

#------------------------------------------------------------------------------
# Fortran preprocessing and compiler.
# FPPFLAGS holds the main Fortran options, such as whether MPI is used.
#------------------------------------------------------------------------------
FPPFLAGS= -P -DNO_SANDER_DIVCON -I/opt/SUNWhpc/HPC8.0/include
-DBINTRAJ -DMPI $(AMBERBUILDFLAGS)
FPP= /lib/cpp $(FPPFLAGS)
FC= f90
FFLAGS= -O1 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FOPTFLAGS= -O2 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= -free

#------------------------------------------------------------------------------
# Loader:
#------------------------------------------------------------------------------
LOAD= f90 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADCC= cc $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADLIB= -lmpi -xlic_lib=sunperf -lm
XHOME= /usr/openwin
XLIBS= -L/usr/X11R6/lib

#------------------------------------------------------------------------------
# Other stuff:
#------------------------------------------------------------------------------
.SUFFIXES: .f90
EMPTY=
AR=ar rv
M4=m4 -B50000
RANLIB=ranlib
SFX=
NETCDF=netcdf.mod
NETCDFLIB=../netcdf/lib/libnetcdf.a
MODULEDIR=-M
testsanderDIVCON=skipsanderDIVCON
INCDIVCON=
LIBDIVCON=

# Location for executables, etc:

BINDIR=/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/bin
LIBDIR=/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/lib
INCDIR=/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/include
DATDIR=/xbar/nas1/gappl/gappl/ggamess/amber10/amber10/dat

# default rules for Fortran and C compilation:

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

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

LM= -lm

I am not quite sure if these are the information you asked for.

Thanks in advance

On Fri, Apr 3, 2009 at 11:39 AM, Atro Tossavainen
<atro.tossavainen+amber_at_helsinki.fi> wrote:
>> module load mpi/8.0
>>
>> without changing anything I get an error
>
> In which part of what?
>
>> that it cannot find the file
>> mpih.f hence I include the following flag for the compiler
>
> What are the parameters you are giving to ./configure_amber?
>
> What's the config_amber.h file like after you have run this?
>
> --
> Atro Tossavainen (Mr.)               / The Institute of Biotechnology at
> Systems Analyst, Techno-Amish &     / the University of Helsinki, Finland,
> +358-9-19158939  UNIX Dinosaur     / employs me, but my opinions are my own.
> < URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS
>
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