Hi,
I am having some issues trying to compile the development version of amber12 parallel on the cluster at my university. I am able to compile the serial version, however I get an MPI related error when I then try to compile the parallel version. The configuration of amber12 parallel seems to proceed without a problem.
I am using intel compilers and intel MPI. Here is the exit output error when I try to compile:
FILE_SOURCE -DBINTRAJ -I/home/cd709/include -DMPI -I/apps/intel/2013/mkl/include -shared-intel \
-o mdgx.MPI CompFrc.o BSpline.o Grid.o Random.o mdgxVector.o Matrix.o ChargeMap.o pmeRecip.o mleRecip.o pmeDirect.o CrdManip.o CellManip.o Topology.o Trajectory.o SpecialMath.o Nonbonded.o Bonded.o Parse.o Command.o Constraints.o Thermostats.o Barostats.o Integrator.o Timings.o Manual.o VirtualSites.o Buckingham.o ThermoDyn.o ChargeFit.o ParamFit.o Debug.o BroadcastCommand.o MPIMap.o MPITypeCast.o ptrajmask.o ../sff/AmberNetcdf.o mdgx.o -lfftw3 -L/home/cd709/amber12/lib -L/home/cd709/amber12/lib -lnetcdf -lm
/apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to `MPIR_Err_return_comm'
/apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to `MPIR_Grequest_set_lang_f77'
/apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to `b_use_gettimeofday'
/apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to `MPID_Wtick'
/apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to `MPIR_Err_create_code'
/apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to `i_malloc'
/apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to `MPIR_Keyval_set_fortran90'
/apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to `i_free'
/apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to `MPIR_Keyval_set_fortran'
/apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to `MPID_Wtime_todouble'
make[2]: *** [mdgx.MPI] Error 1
make[2]: Leaving directory `/export71/home/cd709/amber12/AmberTools/src/mdgx'
make[1]: *** [parallel] Error 2
make[1]: Leaving directory `/export71/home/cd709/amber12/AmberTools/src'
make: *** [install] Error 2
The following are set:
$MPI_HOME to /apps/intel/ict/mpi/3.1.038
$LD_LIBRARY_PATH to /apps/intel/2013/mkl/lib/64:/apps/intel/2013/lib/64:/apps/intel/ict/mpi/3.1.038/lib:/home/cd709/amber12/lib
$PATH to /usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/pbs/default/bin:/home/cd709/bin:/apps/intel/2013/bin:/apps/intel/ict/mpi/3.1.038/bin
(both mpicc and mpif90 are in /apps/intel/ict/mpi/3.1.038/bin)
Here is the output from the configuration step:
-bash-4.1$ ./configure -mpi intel
Checking for updates...
AmberTools13 is up to date
Amber13 is up to date
Searching for python2... Found python2.6: /usr/bin/python2.6
Detected icc version 13
Detected ifort version 13
Using Intel MKL libraries in /apps/intel/2013/mkl/lib/intel64
MKL Version 10 or 11 assumed.
Testing the icc compiler:
icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
OK
Testing the ifort compiler:
ifort -O0 -o testp testp.f
OK
Testing mixed C/Fortran compilation:
icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c
ifort -O0 -c -o testp.f.o testp.f
icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -L/apps/intel/2013/lib/ -lifport -lifcore -lsvml
OK
Testing pointer size:
icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size test_pointer_size.c
Detected 64 bit operating system.
Testing flex: OK
Configuring NetCDF (may be time-consuming)...
NetCDF configure succeeded.
Checking for zlib: OK
Checking for libbz2: OK
Configuring fftw-3.3 for mdgx (may be time-consuming)...
fftw-3.3 configure succeeded.
The configuration file, config.h, was successfully created.
The next step is to type 'make install'
Cleaning the src directories. This may take a few moments.
Configure complete.
Here is my config.h file:
# Amber configuration file, created with: ./configure -mpi intel
###############################################################################
# (1) Location of the installation
BASEDIR=/home/cd709/amber12
BINDIR=/home/cd709/amber12/bin
LIBDIR=/home/cd709/amber12/lib
INCDIR=/home/cd709/amber12/include
DATDIR=/home/cd709/amber12/dat
LOGDIR=/home/cd709/amber12/logs
###############################################################################
# (2) If you want to search additional libraries by default, add them
# to the FLIBS variable here. (External libraries can also be linked into
# NAB programs simply by including them on the command line; libraries
# included in FLIBS are always searched.)
FLIBS= -lsff_mpi -lpbsa -lfftw3 -larpack -L/home/cd709/lib -L$(BASEDIR)/lib -
lnetcdf -Wl,--start-group /apps/intel/2013/mkl/lib/intel64/libmkl_intel_lp64.a /
apps/intel/2013/mkl/lib/intel64/libmkl_sequential.a /apps/intel/2013/mkl/lib/int
el64/libmkl_core.a -Wl,--end-group -lpthread -L/apps/intel/2013/lib/ -lifport -l
ifcore -lsvml
FLIBS_PTRAJ= -larpack -L/home/cd709/lib -Wl,--start-group /apps/intel/2013/mkl/
lib/intel64/libmkl_intel_lp64.a /apps/intel/2013/mkl/lib/intel64/libmkl_sequenti
al.a /apps/intel/2013/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -L
/apps/intel/2013/lib/ -lifport -lifcore -lsvml
FLIBSF= -larpack -L/home/cd709/lib -Wl,--start-group /apps/intel/2013/mkl/lib/i
ntel64/libmkl_intel_lp64.a /apps/intel/2013/mkl/lib/intel64/libmkl_sequential.a
/apps/intel/2013/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lsvml
FLIBS_FFTW3= -lfftw3
###############################################################################
# (3) Modify any of the following if you need to change, e.g. to use gcc
# rather than cc, etc.
SHELL=/bin/sh
INSTALLTYPE=parallel
BUILDAMBER=amber
# Set the C compiler, etc.
# The configure script should be fine, but if you need to hand-edit,
# here is some info:
# Example: CC-->gcc; LEX-->flex; YACC-->yacc (built in byacc)
# Note: If your lexer is "really" flex, you need to set
# LEX=flex below. For example, on some distributions,
# /usr/bin/lex is really just a pointer to /usr/bin/flex,
# so LEX=flex is necessary. In general, gcc seems to need flex.
# The compiler flags CFLAGS and CXXFLAGS should always be used.
# By contrast, *OPTFLAGS and *NOOPTFLAGS will only be used with
# certain files, and usually at compile-time but not link-time.
# Where *OPTFLAGS and *NOOPTFLAGS are requested (in Makefiles,
# makedepend and depend), they should come before CFLAGS or
# CXXFLAGS; this allows the user to override *OPTFLAGS and
# *NOOPTFLAGS using the BUILDFLAGS variable.
#
CC=mpicc
CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -I/home/cd709/inclu
de -DMPI $(CUSTOMBUILDFLAGS) -I/apps/intel/2013/mkl/include
CNOOPTFLAGS=
COPTFLAGS=-ip -O3 -xHost -DBINTRAJ -DHASGZ -DHASBZ2
AMBERCFLAGS= $(AMBERBUILDFLAGS)
CXX=icpc
CPLUSPLUS=icpc
CXXFLAGS= -DMPI $(CUSTOMBUILDFLAGS)
CXXNOOPTFLAGS=
CXXOPTFLAGS=-O3
AMBERCXXFLAGS= $(AMBERBUILDFLAGS)
NABFLAGS=
PBSAFLAG=
LDFLAGS=-shared-intel $(CUSTOMBUILDFLAGS)
AMBERLDFLAGS=$(AMBERBUILDFLAGS)
LEX= flex
YACC= $(BINDIR)/yacc
AR= ar rv
M4= m4
RANLIB=ranlib
# Set the C-preprocessor. Code for a small preprocessor is in
# ucpp-1.3; it gets installed as $(BINDIR)/ucpp;
# this can generally be used (maybe not on 64-bit machines like altix).
CPP= ucpp -l
# These variables control whether we will use compiled versions of BLAS
# and LAPACK (which are generally slower), or whether those libraries are
# already available (presumably in an optimized form).
LAPACK=skip
BLAS=skip
F2C=skip
# These variables determine whether builtin versions of certain components
# can be used, or whether we need to compile our own versions.
UCPP=install
C9XCOMPLEX=skip
# For Windows/cygwin, set SFX to ".exe"; for Unix/Linux leave it empty:
# Set OBJSFX to ".obj" instead of ".o" on Windows:
SFX=
OSFX=.o
MV=mv
RM=rm
CP=cp
# Information about Fortran compilation:
FC=mpif90
FFLAGS= $(LOCALFLAGS) $(CUSTOMBUILDFLAGS) -I$(INCDIR) $(NETCDFINC) -I/apps/inte
l/2013/mkl/include
FNOOPTFLAGS= -O0
FOPTFLAGS= -ip -O3 -xHost
AMBERFFLAGS=$(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= -FR
LM=-lm
FPP=cpp -traditional -P
FPPFLAGS= -DMKL -DBINTRAJ -DMPI $(CUSTOMBUILDFLAGS)
AMBERFPPFLAGS=$(AMBERBUILDFLAGS)
FCREAL8=
XHOME= /usr
XLIBS= -L/usr/lib64 -L/usr/lib
MAKE_XLEAP=install_xleap
NETCDF=$(BASEDIR)/include/netcdf.mod
NETCDFLIB=-L$(BASEDIR)/lib -lnetcdf
NETCDFINC=-I$(BASEDIR)/include
PNETCDF=
PNETCDFLIB=
FFTWLIB=-lfftw3
ZLIB=-lz
BZLIB=-lbz2
HASFC=yes
MTKPP=
XBLAS=
FFTW3=$(LIBDIR)/libfftw3.a
MDGX=yes
COMPILER=intel
MKL=/apps/intel/2013/mkl
MKL_PROCESSOR=intel64
#CUDA Specific build flags
NVCC=
PMEMD_CU_INCLUDES=
PMEMD_CU_LIBS=
PMEMD_CU_DEFINES=
#PMEMD Specific build flags
PMEMD_F90=mpif90 -DMPI -DMKL -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC
_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT
PMEMD_FOPTFLAGS=-ipo -O3 -no-prec-div -xHost
PMEMD_CC=mpicc
PMEMD_COPTFLAGS=-ipo -O3 -no-prec-div -xHost -D_FILE_OFFSET_BITS=64 -D_LARGEFILE
_SOURCE -DBINTRAJ -DMPI
PMEMD_FLIBSF=-Wl,--start-group /apps/intel/2013/mkl/lib/intel64/libmkl_intel_lp6
4.a /apps/intel/2013/mkl/lib/intel64/libmkl_sequential.a /apps/intel/2013/mkl/li
b/intel64/libmkl_core.a -Wl,--end-group -lpthread
PMEMD_LD= mpif90
LDOUT= -o
#for NAB:
MPI=mpi
#1D-RISM
RISM=no
#3D-RISM NAB
RISMSFF=
SFF_RISM_INTERFACE=
TESTRISMSFF=
#3D-RISM SANDER
RISMSANDER=
SANDER_RISM_INTERFACE=
FLIBS_RISMSANDER=
TESTRISMSANDER=
#PUPIL
PUPILLIBS=-lrt -lm -lc -L${PUPIL_PATH}/lib -lPUPIL -lPUPILBlind
#Python interpreter we are using
PYTHON=/usr/bin/python2.6
Any suggestions would be greatly appreciated.
Many thanks,
Callum
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Received on Fri Oct 26 2012 - 08:30:02 PDT
