It sounds like you need to source Intel's MKL script (something like
mklvars.sh or something). It should be in a similar location to
ifortvars.sh or iccvars.sh which you needed to source to set up your
environment correctly.
If you still can't get it to work, just unset MKL_HOME and recompile
without the Intel MKL.
HTH,
Jason
On Fri, Feb 3, 2012 at 4:13 PM, Yubo Fan <pengpengtadie.gmail.com> wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 03 2012 - 16:30:02 PST
