Hi all,
I am trying to compile AMBER 9 on a Mac Pro 4.1 (2 x 2.26 GHz Quad-Core
Intel Xeon) with Mac OS X vers 10.6.1 (Snow Leopard). I have successfully
installed the serial version.
When trying to install the parallel version, I have found the following
problem:
MacPro:src root# make clean
OUTPUT at the bottom of the message: CLEAN.LOG
MacPro:src root# ./configure -openmpi ifort_macosx
OUTPUT at the bottom of the message: CONFIG.LOG
MacPro:src root# make parallel
OUTPUT at the bottom of the message: MAKE.LOG
I have also attempted to modify the config.h file, and I get a successful
compilation (see config.h at the bottom of the message). When I run the
test.parallel, I get the following error message:
MacPro:test root# make test.parallel
export TESTsander=/usr/local/amber9/exe/sander.MPI; make test.sander.BASIC
cd dmp; ./Run.dmp
This test not set up for parallel
cannot run in parallel with #residues < #pes
cd adenine; ./Run.adenine
This test not set up for parallel
cannot run in parallel with #residues < #pes
=============================================
cd cytosine; ./Run.cytosine
--------------------------------------------------------------------------
It looks like opal_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can fail
during opal_init; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
opal_paffinity_base_select failed
--> Returned value -13 instead of OPAL_SUCCESS
--------------------------------------------------------------------------
[MacPro.local:47329] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file
../../orte/runtime/orte_init.c at line 77
[MacPro.local:47329] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file
../../../../orte/tools/orterun/orterun.c at line 541
./Run.cytosine: Program error
make[1]: *** [test.sander.BASIC] Error 1
make: *** [test.sander.BASIC.MPI] Error 2
Can you please help me?
Thanks
File contents:
********************************************************************
********************CONFIG.h (successful compil*********************
#==============================================================================
# AMBER Makefile configuration for compiler/architecture: ifort_macosx
# Generated via command: ./configure -openmpi ifort_macosx
#
# 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=/usr/local/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=-I/usr/local/openmpi/include
#------------------------------------------------------------------------------
# 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)
USE_LMODLIB=$(LMOD_UNAVAILABLE)
#------------------------------------------------------------------------------
# C compiler
#------------------------------------------------------------------------------
CC= gcc -m64
CPLUSPLUS=g++
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= -I/usr/local/openmpi/include -P -DMPI -DMKL $(AMBERBUILDFLAGS)
FPP= cpp -traditional $(FPPFLAGS)
FC= ifort
FFLAGS= -w95 -mp1 -O0 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FOPTFLAGS= -w95 -mp1 -ip -O3 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= -FR
#------------------------------------------------------------------------------
# Loader:
#------------------------------------------------------------------------------
LOAD= ifort $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADCC= gcc -m64 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADLIB= -L/usr/local/openmpi/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte
-lopen-pal -lutil -L/opt/intel/Compiler/11.1/080/Frameworks/mkl/lib/em64t
-lmkl_lapack -lmkl_intel_ilp64 -lguide -lpthread
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 $. $<
********************************************************************
**********************************CLEAN.LOG********************************
cd lib; make clean
/bin/rm malloc_test new2oldparm *.o _*.f *.a
cd blas; make clean
/bin/rm -f *.o blas.a _*.f
cd lapack; make clean
/bin/rm -f *.o lapack.a _*.f
cd lmod; make clean
/bin/rm -f *.a
cd xmin; make clean
/bin/rm -f ieee.o xmin.o _*.f
cd lmod; make clean
/bin/rm -f ieee.o lmod.o _*.f
cd arpack; make clean
/bin/rm -f *.o _*.f arpack.a
cd addles; make clean
/bin/rm *.o _*.f addles
cd sander; make clean
/bin/rm sander sander.LES psander sander.PIMD
/bin/rm ambmask
/bin/rm *.o
/bin/rm _*.f
/bin/rm *.mod
/bin/rm *.d
/bin/rm *nbflag
cd ../dcqtp; make clean
cd mod; make clean
rm -f ../dcqtp *.mod
rm -f ../src/qmmm/libdivcon.a
cd ../obj; rm -f *.o *.f
cd dcqtp; make clean
cd mod; make clean
rm -f ../dcqtp *.mod
rm -f ../src/qmmm/libdivcon.a
cd ../obj; rm -f *.o *.f
cd ptraj; make clean
cd pdb; make clean
rm -f pdbrun.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o ms.o libpdb.a
/bin/rm -f main.o rdparm.o dispatch.o help.o utility.o second.o io.o
trajectory.o evec.o torsion.o mask.o rms.o display.o interface.o energy.o
experimental.o ptraj.o actions.o analyze.o thermo.o pubfft.o rdparm ptraj
/bin/rm _*.f
cd nmr_aux; make clean
cd prepare_input; make clean
/bin/rm *.o _*.f makeDIST_RST makeANG_RST makeSHF.cp makeCHIR_RST.cp \
makeDIP_RST.protein.cp makeDIP_RST.dna.cp
cd fantasian; make clean
/bin/rm *.o _*.f fantasian
cd nmode; make clean
/bin/rm *.o _*.f nmode nmanal
cd resp; make clean
/bin/rm *.o _*.f resp reformat replace_charges
cd protonate; make clean
/bin/rm *.o _*.f pol_h protonate gwh
cd etc; make clean
/bin/rm *.o _*.f ambpdb nucgen elsize
cd antechamber; make clean
rm -f *.o am1bcc antechamber atomtype bondtype charmmgen crdgrow database
espgen parmcal parmchk prepgen respgen top2mol2 translate
cd mm_pbsa; make clean
/bin/rm *.o _*.f make_crd_hg molsurf
cd pbsa; make clean
/bin/rm pbsa
/bin/rm *.o
/bin/rm _*.f
/bin/rm *.mod
/bin/rm *.d
cd anal; make clean
/bin/rm *.o _*.f anal
cd leap; make clean
cd src/Wc; make clean
/bin/rm *.o *.a
cd src/Xmu; make clean
/bin/rm *.o *.a
cd src/Xpm; make clean
/bin/rm *.o *.a
cd src/Xraw; make clean
/bin/rm *.o *.a
cd src/leap; make clean
/bin/rm *.o xaLeap teLeap utilMakeHelp utilDescribeTopology utilCrd2Off
mol2_to_off utilConvertWaterBox utilLib2Pdb *\~
/bin/rm XaLeap_wcl
/bin/rm *.gprof
/bin/rm parser.c
/bin/rm helptext.c
cd pmemd; make clean
cd src && rm -f *.f90 *.o *.mod pmemd *.d work.pc*
cd build_amoeba; make clean
/bin/rm amoeba_parm new_crd_to_dyn new_to_old_crd
/bin/rm amoeba_parm.f new_crd_to_dyn.f new_to_old_crd.f fix_new_inpcrd_vel.f
/bin/rm *.o
/bin/rm *.mod
cd netcdf/src; make clean
cd netcdf/lib && rm -f libnetcdf.a
cd netcdf/include && rm -f *.mod
********************************************************************
****************************CONFIG.LOG********************************
AMBERHOME is set to /usr/local/amber9
Setting up Amber configuration file for architecture: ifort_macosx
Using parallel communications library: openmpi
MPI_HOME is set to /usr/local/openmpi
MKL_HOME is set to /opt/intel/Compiler/11.1/080/Frameworks/mkl
Using MKL libraries from /opt/intel/Compiler/11.1/080/Frameworks/mkl/lib/32
The configuration file, config.h, was successfully created.
********************************************************************
*****************************MAKE.LOG********************************
Starting installation of Amber9 (parallel) at Tue Feb 2 18:50:01 CET 2010.
cd sander; make parallel
./checkparconf
cpp -traditional -I/usr/local/openmpi/include -P -DMPI -DMKL evb_vars.f >
_evb_vars.f
ifort -c -w95 -mp1 -O0 -FR -o evb_vars.o _evb_vars.f
cpp -traditional -I/usr/local/openmpi/include -P -DMPI -DMKL evb_input.f
> _evb_input.f
ifort -c -w95 -mp1 -O0 -FR -o evb_input.o _evb_input.f
cpp -traditional -I/usr/local/openmpi/include -P -DMPI -DMKL evb_init.f >
_evb_init.f
ifort -c -w95 -mp1 -O0 -FR -o evb_init.o _evb_init.f
_evb_init.f(171): error #5102: Cannot open include file 'mpif-common.h'
include 'mpif-common.h'
--------------^
_evb_init.f(327): error #6404: This name does not have a type, and must
have an explicit type. [MPI_INTEGER]
call mpi_bcast ( ndim, 1, MPI_INTEGER, 0, commworld, ierr )
-----------------------------^
_evb_init.f(367): error #6404: This name does not have a type, and must
have an explicit type. [MPI_DOUBLE_PRECISION]
call mpi_bcast ( xdat_dia(n)% q, ndim, MPI_DOUBLE_PRECISION, 0,
commworld, ierr )
------------------------------------------------^
_evb_init.f(372): error #6404: This name does not have a type, and must
have an explicit type. [MPI_CHARACTER]
call mpi_bcast ( xdat_dia(n)% filename, 512, MPI_CHARACTER, 0,
commworld, ierr )
------------------------------------------------------^
compilation aborted for _evb_init.f (code 1)
make[1]: *** [evb_init.o] Error 1
make: *** [parallel] Error 2
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Received on Wed Feb 03 2010 - 04:30:03 PST
