> Hi Nicee,
>
>> I compiled AMBER successfully in serial but while compiling in parallel
>> the
>> error was coming. I have set all the paths and ld_library path as given
>> in the
>> manual. As such I request you to kindly have a look into the problem.
>>
>> The error is as below:
>>
>> /usr/local/lib/libmpi.so: file not recognized: File format not
>> recognized
>> make[1]: *** [sander.MPI] Error 1
>> make[1]: Leaving directory `/home/nicee/amber9/src/sander'
>> make: *** [parallel] Error 2
>
> Are you sure /usr/local/lib/libmpi.so is the correct library to be using?
>
> What does your $AMBERHOME/src/config.h file look like?
>
> Additionally what do you get with:
>
> which mpif90
> mpif90 -show
>
>>From the above it looks to me like you are linking to a library which was not
>> built for the architecture you are running on. Are you sure the compiler you
>> are using matches the one MPI was built with?
>
> Or for some reason it is trying to execute libmpi.so. We would need to see what
> your config.h file looks like and what the above commands give to help much
> more.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not be
> read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
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>
Respected Sir,
Thank you for your reply and help.
The $AMBERHOME/src/config.h file is as below:
#==============================================================================
# AMBER Makefile configuration for compiler/architecture: ifort_ia64
# Generated via command: ./configure -mpi ifort_ia64
#
# Configuration script written mainly by Joe Krahn, Scott Brozell, and
# Dave Case, with contributions from lots of people.
#==============================================================================
#------------------------------------------------------------------------------
# Main AMBER source root directory
#------------------------------------------------------------------------------
AMBER_SRC=/home/nicee/amber9/src
#------------------------------------------------------------------------------
# AMBERBUILDFLAGS provides a hook into the build process for installers;
# for example, to build debug versions of the amber programs
# make -e AMBERBUILDFLAGS="-DDEBUG -g"
#------------------------------------------------------------------------------
AMBERBUILDFLAGS=
#------------------------------------------------------------------------------
# LOCALFLAGS is intended for program specific modifications to the
# Fortran build process and may be modified by the program's local makefile
#------------------------------------------------------------------------------
LOCALFLAGS=
#------------------------------------------------------------------------------
# Availability and method of delivery of math and optional libraries
#------------------------------------------------------------------------------
USE_BLASLIB=$(SOURCE_COMPILED)
USE_LAPACKLIB=$(SOURCE_COMPILED)
USE_LMODLIB=$(LMOD_UNAVAILABLE)
#------------------------------------------------------------------------------
# C compiler
#------------------------------------------------------------------------------
CC= icc
CPLUSPLUS=icpc
CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2
CPPFLAGS= $(AMBERBUILDFLAGS)
#------------------------------------------------------------------------------
# Fortran preprocessing and compiler.
# FPPFLAGS holds the main Fortran options, such as whether MPI is used.
#------------------------------------------------------------------------------
FPPFLAGS= -P -DMPI $(AMBERBUILDFLAGS)
FPP= cpp -traditional $(FPPFLAGS)
FC= ifort
FFLAGS= -w95 -ftz -O2 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FOPTFLAGS= -w95 -ftz -O3 -IPF_fma -IPF_fp_relaxed -ip $(LOCALFLAGS)
$(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= -FR
#------------------------------------------------------------------------------
# Loader:
#------------------------------------------------------------------------------
LOAD= ifort $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADCC= icc $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADLIB= -lmpi
LM= -lm
LOADPTRAJ= ifort -nofor_main $(LOCALFLAGS) $(AMBERBUILDFLAGS)
XHOME= /usr/X11R6
XLIBS= -L /usr/X11R6/lib
#------------------------------------------------------------------------------
# Other stuff:
#------------------------------------------------------------------------------
.SUFFIXES: .f90
EMPTY=
AR=ar rv $(EMPTY)
M4=m4
RANLIB=ranlib
SFX=
NETCDF=
NETCDFLIB=
MODULEDIR=-I
MAKEDEPEND=$(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 $. $<
--------------------------------------------------------------------------------------------
By giving the commands....which mpif90 and mpif90 -show, i got following result:
/usr/bin/which: no mpif in
(/opt/intel/cc/10.1.015/bin:/opt/intel/fc/10.1.015/bin:/usr/lib/qt-3.3/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/nicee/bin:/home/nicee/amber9/exe:/home/nicee:/bin:/include:home/nicee/dejavu_linux/exe:)
/usr/bin/which: no 90 in
(/opt/intel/cc/10.1.015/bin:/opt/intel/fc/10.1.015/bin:/usr/lib/qt-3.3/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/nicee/bin:/home/nicee/amber9/exe:/home/nicee:/bin:/include:home/nicee/dejavu_linux/exe:)
As such I believe there is some problem with the mpi library....will I have to
install mpi library first? Kindly help.
Thanking you.
With due regards,
Nicee.
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Received on Tue Jan 19 2010 - 21:00:02 PST
