Dan,
I removed -static term and compiling for parallel sander.MPI passed.
But the test failed:
login4$ cd $AMBERHOME/test
login4$ export DO_PARALLEL
login4$ export DO_PARALLEL='mpirun -np 4'
login4$ make test.parallel
export TESTsander=/share/home/01879/amber9/exe/sander.MPI; make
test.sander.BASIC
make[1]: Entering directory `/share/home/01879/amber9/test'
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
/share/home/01879/amber9/exe/sander.MPI: error while loading shared
libraries: libmkl_lapack.so: cannot open shared object file: No such
file or directory
/share/home/01879/amber9/exe/sander.MPI: error while loading shared
libraries: libmkl_lapack.so: cannot open shared object file: No such
file or directory
/share/home/01879/amber9/exe/sander.MPI: error while loading shared
libraries: libmkl_lapack.so: cannot open shared object file: No such
file or directory
/share/home/01879/amber9/exe/sander.MPI: error while loading shared
libraries: libmkl_lapack.so: cannot open shared object file: No such
file or directory
./Run.cytosine: Program error
make[1]: *** [test.sander.BASIC] Error 1
make[1]: Leaving directory `/share/home/01879/qxshao/amber9/test'
make: *** [test.sander.BASIC.MPI] Error 2
==================================================================================================================
Thanks,
Yubo
On Fri, Feb 3, 2012 at 12:11 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I think this might be related to use of the '-static' flag during
> configuration. Your openmpi distribution may have been built without
> static libraries (which is not uncommon). Try configuring without
> '-static' and see if that works for you.
>
> -Dan
>
> On Fri, Feb 3, 2012 at 11:03 AM, Yubo Fan <pengpengtadie.gmail.com> wrote:
>> Hello,
>>
>> I tried to compile Amber 9 on a cluster. Intel 10.1 and openmpi 1.2.1
>> were used. The config.h is:
>> #==============================================================================
>> # AMBER Makefile configuration for compiler/architecture: ifort_x86_64
>> # Generated via command: ./configure -openmpi -bintraj -static ifort_x86_64
>> #
>> # 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=/share/home/01879/qxshao/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=$(VENDOR_SUPPLIED)
>> USE_LAPACKLIB=$(VENDOR_SUPPLIED)
>> USE_LMODLIB=$(LMOD_UNAVAILABLE)
>>
>> #------------------------------------------------------------------------------
>> # C compiler
>> #------------------------------------------------------------------------------
>> CC= gcc
>> CPLUSPLUS=g++
>> CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2
>> CPPFLAGS= -DBINTRAJ -I../netcdf/include $(AMBERBUILDFLAGS)
>>
>> #------------------------------------------------------------------------------
>> # Fortran preprocessing and compiler.
>> # FPPFLAGS holds the main Fortran options, such as whether MPI is used.
>> #------------------------------------------------------------------------------
>> FPPFLAGS= -I/opt/apps/intel10_1/openmpi/1.2.4/include -P -DMPI -DMKL
>> -DBINTRAJ $(AMBERBUILDFLAGS)
>> FPP= cpp -traditional $(FPPFLAGS)
>> FC= mpif90
>> FFLAGS= -w95 -mp1 -O0 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
>> FOPTFLAGS= -w95 -mp1 -ip -O3 -tpp7 -axWP $(LOCALFLAGS) $(AMBERBUILDFLAGS)
>> FREEFORMAT_FLAG= -FR
>>
>> #------------------------------------------------------------------------------
>> # Loader:
>> #------------------------------------------------------------------------------
>> LOAD= mpif90 -static $(LOCALFLAGS) $(AMBERBUILDFLAGS)
>> LOADCC= gcc -static $(LOCALFLAGS) $(AMBERBUILDFLAGS)
>> LOADLIB= -L/opt/apps/intel10_1/openmpi/1.2.4/lib -lmpi_f90 -lmpi_f77
>> -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil
>> /opt/apps/intel/mkl/10.0.1.014/lib/em64t/libmkl_lapack.a
>> /opt/apps/intel/mkl/10.0.1.014/lib/em64t/lib
>> mkl_em64t.a -L/opt/apps/intel/mkl/10.0.1.014/lib/em64t -lguide -lpthread
>> LM= -lm
>> LOADPTRAJ= mpif90 -static -nofor_main $(LOCALFLAGS) $(AMBERBUILDFLAGS)
>> XHOME= /usr/X11R6
>> XLIBS= -L/usr/X11R6/lib64 -L/usr/X11R6/lib
>>
>> #------------------------------------------------------------------------------
>> # Other stuff:
>> #------------------------------------------------------------------------------
>> .SUFFIXES: .f90
>> EMPTY=
>> AR=ar rv $(EMPTY)
>> M4=m4
>> RANLIB=ranlib
>> SFX=
>> NETCDF=netcdf.mod
>> NETCDFLIB=../netcdf/lib/libnetcdf.a
>> MODULEDIR=-I
>> MAKEDEPEND=$(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 $. $<
>>
>> ==================================================================================
>>
>> The compiling (make parallel) failed with error message:
>>
>>
>> cd ../lmod; cp lmodprmtop ../../exe; chmod 0755 ../../exe/lmodprmtop
>> mpif90 -static -FR -o sander.MPI evb_vars.o evb_input.o evb_init.o
>> evb_alloc.o evb_dealloc.o check_input.o evb_io.o evb_keywrd.o
>> exchange_CM.o evb_mcp.o evb_force.o diabatic.o evb_2stdebug.o
>> egap_umb_2stdebug.o exchange_gauss.o exchange_warshel.o morsify.o
>> morse_anal2num.o evb_matrix.o evb_ntrfc.o out_evb.o constants.o
>> stack.o qmmm_module.o trace.o lmod.o decomp.o icosasurf.o egb.o
>> findmask.o pb_force.o pb_exmol.o pb_mpfrc.o pb_direct.o pb_list.o
>> np_force.o sa_driver.o relax_mat.o nmr.o multisander.o sander.o
>> trajene.o cshf.o nmrcal.o pearsn.o printe.o runmin.o rdparm.o mdread.o
>> locmem.o runmd.o getcor.o degcnt.o decnvh.o fastwt.o parallel.o
>> shake.o ene.o mdwrit.o minrit.o set.o dynlib.o mdfil.o nmlsrc.o
>> ew_force.o ew_setup.o ew_box.o ew_bspline.o ew_fft.o nonbond_list.o
>> short_ene.o ew_recip.o pcshift.o align.o rfree.o rgroup.o random.o
>> amopen.o debug.o ew_recip_reg.o ew_handle_dips.o ew_dipole_recip.o
>> mexit.o new_time.o extra_pts.o thermo_int.o matinv.o assert.o mmtsb.o
>> mmtsb_client.o erfcfun.o veclib.o is_init.o constantph.o prn_dipoles.o
>> ips.o sglds.o amoeba_valence.o amoeba_multipoles.o amoeba_recip.o
>> amoeba_interface.o amoeba_direct.o amoeba_mdin.o amoeba_adjust.o
>> amoeba_self.o amoeba_vdw.o amoeba_induced.o amoeba_runmd.o bintraj.o
>> spatial_recip.o spatial_fft.o parms.o qm_mm.o qm_link_atoms.o
>> qm_nb_list.o qm_extract_coords.o qm_ewald.o qm_gb.o qm_zero_charges.o
>> qm_print_info.o qm_assign_atom_types.o qm2_allocate_e_repul.o
>> qm2_calc_charges.o qm2_calc_rij_and_eqns.o qm2_dihed.o qm2_energy.o
>> qm2_fock.o qm2_get_qm_forces.o qm2_get_qmmm_forces.o qm2_h1elec.o
>> qm2_hcore_qmqm.o qm2_hcore_qmmm.o qm2_identify_peptide_links.o
>> qm2_load_params_and_allocate.o qm2_repp.o qm2_rotate_qmqm.o qm2_scf.o
>> qm2_setup_orb_exp.o qm2_smallest_number.o qm2_dftb_module.o
>> qm2_dftb_broyden.o qm2_dftb_dispersion_egr.o
>> qm2_dftb_dispersion_params.o qm2_dftb_dispersionread.o
>> qm2_dftb_eglcao.o qm2_dftb_energy.o qm2_dftb_ewevge.o
>> qm2_dftb_externalchgrad.o qm2_dftb_externalshift.o qm2_dftb_fermi.o
>> qm2_dftb_forces.o qm2_dftb_gamma.o qm2_dftb_gammamat.o
>> qm2_dftb_get_qmmm_forces.o qm2_dftb_gettab.o qm2_dftb_load_params.o
>> qm2_dftb_long_range.o qm2_dftb_main.o qm2_dftb_my_gradient.o
>> qm2_dftb_my_mulliken.o qm2_dftb_repulsiv.o qm2_dftb_self.o
>> qm2_dftb_shift.o qm2_dftb_short_range.o qm2_dftb_skpar.o
>> qm2_dftb_slkode.o qm2_dftb_slktrafo.o \
>> qm_div.o force.o \
>> ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
>> ../lib/nxtsec.o ../lib/sys.a ../netcdf/lib/libnetcdf.a
>> -L/opt/apps/intel10_1/openmpi/1.2.4/lib -lmpi_f90 -lmpi_f77 -lmpi
>> -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil
>> /opt/apps/intel/mkl/10.0.1.014/lib/em64t/libmkl_lapack.a
>> /opt/apps/intel/mkl/10.0.1.014/lib/em64t/libmkl_em64t.a
>> -L/opt/apps/intel/mkl/10.0.1.014/lib/em64t -lguide -lpthread
>> ld: cannot find -lmpi_f90
>> make[1]: *** [sander.MPI] Error 1
>> make[1]: Leaving directory `/share/home/01879/qxshao/amber9/src/sander'
>> make: *** [parallel] Error 2
>>
>> ===============================================================
>>
>> Help needed.
>>
>> Thanks,
>> Yubo
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Postdoctoral Associate
> BioMaPS Institute, Rutgers University
> 610 Taylor Road
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Feb 03 2012 - 13:30:04 PST
