----- Forwarded message from Robert Konecny <rok.ucsd.edu> -----
Date: Tue, 30 Apr 2019 09:28:40 -0700
From: Robert Konecny <rok.ucsd.edu>
To: david.case.rutgers.edu
Subject: AT19 cpptraj MPI build issue (Linux, x86_64, gnu)
Hi Dave,
I'm not sure where should I report it so I'm sending this to you, hope this is
OK.
This is all on CentOS Linux release 7.4.1708, 3.10.0-693.2.2.el7.x86_64
kernel.
I'm updating AmberTools to version 19 by using '$AMBERHOME/update_amber
--upgrade'. Both serial and CUDA configured and compiled fine but when trying
to configure OpenMPI build ('./configure -mpi gnu') this fails with this
message:
CPPTRAJ configure failed. Check '/software/repo/moleculardynamics/amber/18/AmberTools/src/cpptraj_config.log' for details.
Configure failed due to the errors above!
And the log file shows:
Error: gnu compilers specified but need cray based on CXX = mpiCC
I have set CXX env. variable to mpiCC and I guess the checks in
$AMBERHOME/AmberTools/src/cpptraj/configure misinterpret it. Clearing CXX
('unset CXX') fixes this issue, './configure -mpi gnu' proceeds without errors
and the compilation is fine too.
I'm attaching config.h, if that helps.
Thanks,
Robert
# Amber configuration file.
# Created at Mon Apr 29 13:27:02 PDT 2019 via ./configure -mpi gnu
###############################################################################
# (1) Location of the installation
BASEDIR=/software/repo/moleculardynamics/amber/18
AMBER_PREFIX=/software/repo/moleculardynamics/amber/18
BINDIR=/software/repo/moleculardynamics/amber/18/bin
LIBDIR=/software/repo/moleculardynamics/amber/18/lib
INCDIR=/software/repo/moleculardynamics/amber/18/include
DATDIR=/software/repo/moleculardynamics/amber/18/dat
LOGDIR=/software/repo/moleculardynamics/amber/18/logs
AMBER_SOURCE=/software/repo/moleculardynamics/amber/18
###############################################################################
# (2) If you want NAB 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_mpi -lfftw3 -larpack -llapack -lblas -lnetcdf -lgfortran -w
FLIBS_PTRAJ= -larpack -llapack -lblas -lgfortran -w
FLIBSF= -larpack -llapack -lblas
FLIBS_FFTW3= -lfftw3_mpi -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-->bison -y
# 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.
# AMBERBUILDFLAGS provides a hook into all stages of the build process.
# It can be used to build debug versions, invoke special features, etc.
# Example: make AMBERBUILDFLAGS='-O0 -g' sander
#
CC=mpicc
CFLAGS=-fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN
-DMPI $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
CNOOPTFLAGS=
COPTFLAGS=-O3 -mtune=native
AMBERCFLAGS= $(AMBERBUILDFLAGS)
WARNFLAGS=-Wall -Wno-unused-function
CXX=mpicxx
CPLUSPLUS=mpicxx
CXXFLAGS=-fPIC -DMPI $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
CXXNOOPTFLAGS=
CXXOPTFLAGS=-fPIC -O3
AMBERCXXFLAGS= $(AMBERBUILDFLAGS)
NABFLAGS= $(AMBERBUILDFLAGS)
PBSAFLAG=$(AMBERBUILDFLAGS)
FP_FLAGS=
LDFLAGS= $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
AMBERLDFLAGS=$(AMBERBUILDFLAGS)
LEX= flex
YACC= bison -y
AR= ar rv
M4= m4
RANLIB=ranlib
VB=.
# Set the C-preprocessor. Code for a small preprocessor is in
# ucpp-1.3; it gets installed as $(BINDIR)/ucpp;
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=install
BLAS=install
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
WINE=
# Information about Fortran compilation:
FC=mpif90
FFLAGS= -fPIC $(LOCALFLAGS) $(CUSTOMBUILDFLAGS) -I$(INCDIR) $(NETCDFINC) $(AMBERBUILDFLAGS)
FNOOPTFLAGS= -O0
FOPTFLAGS= -O3 -mtune=native
AMBERFFLAGS=$(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= -ffree-form
LM=-lm
FPP=cpp -traditional -P
FPPFLAGS= -DBINTRAJ -DEMIL -DMPI $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
AMBERFPPFLAGS=$(AMBERBUILDFLAGS)
FCREAL8=-fdefault-real-8
NOFORTRANMAIN=-lgfortran -w
FWARNFLAGS=-Wall -Wno-unused-function
XHOME= /usr
XLIBS=
MAKE_XLEAP=install_xleap
NETCDF=$(INCDIR)/netcdf.mod
NETCDFLIB=$(LIBDIR)/libnetcdf.a
NETCDFLIBF=$(LIBDIR)/libnetcdff.a $(LIBDIR)/libnetcdf.a
NETCDFINC=-I$(INCDIR)
PNETCDFLIB=
PNETCDFINC=
PNETCDFDEF=
FFTWLIB=-lfftw3_mpi -lfftw3
SANDERAPI_LIB=
SANDERAPI_DEF=
SANDERAPI_DEP=
BUILD_SANDERAPI=skip_sanderapi
EMIL=EMIL
EMILLIB=$(LIBDIR)/libemil.a -lstdc++
FEP_MODE=gti
ZLIB=-lz
BZLIB=-lbz2
HASFC=yes
XBLAS=
FFTW3=$(LIBDIR)/libfftw3_mpi.a $(LIBDIR)/libfftw3.a
MDGX=parallel
COMPILER=gnu
MKL=
MKL_PROCESSOR=
READLINE=readline/libreadline.a
#CUDA Specific build flags
NVCC=
PMEMD_CU_INCLUDES=
PMEMD_CU_LIBS=
PMEMD_CU_DEFINES=
PMEMD_CU_EXTRA=
PBSA_CU_LIBS=
#PMEMD Specific build flags
PMEMD_F90=mpif90 -DMPI -DBINTRAJ -DEMIL -DPUBFFT -DGNU_HACKS
PMEMD_FOPTFLAGS=-O3 -mtune=native $(AMBERBUILDFLAGS)
PMEMD_CC=mpicc
PMEMD_COPTFLAGS=-O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI $(AMBERBUIL
DFLAGS)
PMEMD_FLIBSF=-larpack -llapack -lblas $(LIBDIR)/libemil.a -lstdc++
PMEMD_LD=mpif90 $(AMBERBUILDFLAGS)
LDOUT= -o
PMEMD_GNU_BUG303=-fno-tree-vectorize
PMEMD_INTEL_BUG360=
# build pmemd.gem?
PMEMD_GEM=no
#for SFF:
SFF_INTEL_BUG361=
#for NAB:
MPI=mpi
#1D-RISM
RISM=no
#3D-RISM NAB
RISMSFF=
SFF_RISM_INTERFACE=
TESTRISMSFF=
#3D-RISM SANDER
RISMSANDER=
SANDER_RISM_INTERFACE=
FLIBS_RISMSANDER=
#for EMIL:
EMIL_MPIFLAGS=-DUSE_MPI
#PUPIL
PUPILLIBS=-lrt -lm -lc -L${PUPIL_PATH}/lib -lPUPIL -lPUPILBlind
#Python interpreter we are using and install options
PYTHON=/software/repo/moleculardynamics/amber/18/bin/amber.python
PYTHON_INSTALL=--prefix=$(AMBER_PREFIX)
SKIP_PYTHON=no
PYTHONPATH=$(AMBER_PREFIX)/lib/python2.7/site-packages
PYTHONLOG=> build.log
PYSANDER=skip
PYTRAJ=pytraj
LIBCPPTRAJ=libcpptraj
MAKE_SAXS=install
#For LIO QM GPU Library
LIOLIBS=
#For Fireball QM Library
FBLIBS=
# OS-specific rules for making shared objects
SHARED_SUFFIX=.so
MAKE_SHARED=-shared
# PLUMED related variables:
PLUMED_INCLUDE_FILE=
PLUMED_LOAD=Plumed.o -ldl -Wl,-export-dynamic
PLUMED_DEPENDENCIES=Plumed.o
# MEMEMBED for packmol_memgen
MEMEMBED=yes
----- End forwarded message -----
--
====================================================================
David A. Case | david.case.rutgers.edu
Dept. of Chemistry & Chemical Biology |
Rutgers University | office: +1-848-445-5885
174 Frelinghuysen Road, Rm. 208b | cell: +1-609-751-8668
Piscataway, NJ 08854 USA | web: casegroup.rutgers.edu
====================================================================
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 30 2019 - 13:00:03 PDT
