Hi Jorgen,
The issue you have here is that in order to link statically you need a
static version of the MPI library, so libmpi.a whereas chances are you only
have libmpi.so and so can only link dynamically to the MPI library. This is
why it is complaining that it can't find the MPI library.
If you want to build a static MPI executable then you need to build yourself
a static version of MPI first. This varies by MPI distribution but often
there is docs about building statically in the installation instructions.
Often you do something like:
cd $MPI_HOME
./configure --prefix=/foo/bar -CC=gcc -CFLAGS=-static -FC=gfortran
-FFLAGS=-static -CXX=g++ -CXXFLAGS=-static etc...
All the best
Ross
> -----Original Message-----
> From: Jorgen Simonsen [mailto:jorgen589.gmail.com]
> Sent: Wednesday, January 25, 2012 12:39 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] installation of sander.MPI
>
> That is also how I understood it (mpicc -static/ mpif90 -static) but
> it gives me this error
>
> cd ../lmod; cp lmodprmtop ../../exe; chmod 0755 ../../exe/lmodprmtop
> /opt/SUNWhpc/HPC8.2.1c/gnu/bin/mpif90 -static -ffree-form -o
> sander.MPI constants.o nose_hoover.o nose_hoover_vars.o
> nose_hoover_init.o stack.o qmmm_module.o qm2_dftb_module.o trace.o
> lmod.o decomp.o icosasurf.o egb.o remd.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 csa.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 softcore.o molecule.o xref.o
> dssp.o qm_mm.o qm_link_atoms.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_broyden.o
> qm2_dftb_dispersion_egr.o qm2_dftb_dispersion_params.o
> qm2_dftb_dispersionread.o qm2_dftb_scf.o qm2_dftb_energy.o
> qm2_dftb_ewevge.o qm2_dftb_externalshift.o qm2_dftb_fermi.o
> qm2_dftb_get_qm_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_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 qm2_dftb_read_cm3.o
> qm2_dftb_cm3.o qm2_dftb_ewald.o qm2_dftb_gb.o \
> pimd_vars.o pimd_force.o pimd_init.o cmd_vars.o
> cmd_matrix.o lscivr_vars.o lsc_init.o lsc_xp.o evb_vars.o evb_mathf.o
> evb_init.o evb_bcast.o evb_dealloc.o check_input.o evb_io.o
> evb_keywrd.o exchange_gauss.o exchange_warshel.o react_flux_init.o
> react_path.o react_flux.o kappa_keck.o schlegel_dg.o schlegel_full.o
> schlegel_diis.o schlegel_gmres.o schlegel_gbasis.o schlegel_pgbasis.o
> bnd_strtch.o ang_bend.o dihed_tors.o torinternal.o evb_gfchk.o
> bmat_inv.o bmat_grad.o unitv.o crossv.o cart2internal.o wdc_bmat.o
> select_coord.o schlegel_uff.o schlegel_poh_uff.o schlegel_poh_irc.o
> schlegel_hcn_cart.o schlegel_hcn_int_irc.o schlegel_hcn_cart_irc.o
> evb_outoptions.o evb_2stdebug.o egap_umb_2stdebug.o dg_debug.o
> evb_io_debug.o bmat_debug.o bmat_inv_debug.o evb_io_debug2.o
> morse_anal2num.o xwarshel_anal2num.o xgauss_anal2num.o vdw_anal2num.o
> rcdbonds_anal2num.o rcbond_anal2num.o dg_grad_anal2num.o evb_input.o
> evb_alloc.o evb_matrix.o morsify.o mod_vdw.o evb_ntrfc.o evb_force.o
> out_evb.o dbonds_anal2num.o bond_anal2num.o evb_umb.o
> evb_umb_primitive.o qm_div.o force.o \
> ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
> ../lib/nxtsec.o ../lib/sys.a mt19937.o ncsu-abmd-hooks.o
> ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o ncsu-cftree.o ncsu-colvar-math.o
> ncsu-colvar-type.o ncsu-colvar-utils.o ncsu-colvar.o ncsu-constants.o
> ncsu-cv-ANGLE.o ncsu-cv-DISTANCE.o ncsu-cv-HANDEDNESS.o
> ncsu-cv-MULTI_RMSD.o ncsu-cv-N_OF_BONDS.o ncsu-cv-N_OF_STRUCTURES.o
> ncsu-cv-R_OF_GYRATION.o ncsu-cv-TORSION.o ncsu-lexer.o ncsu-parser.o
> ncsu-pmd-hooks.o ncsu-rmsd.o ncsu-sander-hooks.o ncsu-sander-proxy.o
> ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o
> ../netcdf/lib/libnetcdf.a -L/opt/SUNWhpc/HPC8.2.1c/gnu/include/lib64
> /usr/bin/ld: cannot find -lmpi
> collect2: ld returned 1 exit status
> make[1]: *** [sander.MPI] Error 1
> make[1]: Leaving directory `/xbar/nas1/hpc1/amber10/src/sander'
> make: *** [parallel] Error 2
> ~/amber10/src
>
>
> On Wed, Jan 25, 2012 at 9:16 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > On Wed, Jan 25, 2012 at 2:48 PM, Jorgen Simonsen
> <jorgen589.gmail.com>wrote:
> >
> >> ok I am not quite sure where to add it
> >> so if I compile with -static I get the following error
> >>
> >> Configuring netcdf; (may be time-consuming)
> >> configure: WARNING: No F90 compiler found. F90 API will not be
> built.
> >> configure: error: Could not link conftestf.o and conftest.o
> >> netcdf configure returned 1
> >> NETCDF configure failed! Check the netcdf_config.log file
> >>
> >
> > What do you mean "compile with -static"? What I had meant was to
> replace
> > all instances of "mpif90" and "mpicc" with "mpif90 -static" and
> "mpicc
> > -static", respectively. Sorry for not making that clear. What
> happens if
> > you do that?
> >
> >
> >>
> >>
> >>
> >> On Wed, Jan 25, 2012 at 8:23 PM, Jason Swails
> <jason.swails.gmail.com>
> >> wrote:
> >> > Hmm... can you try adding the "-static" flag to the end of the
> "mpif90"
> >> > lines in the config.h file (which will hopefully force static
> linking).
> >> > The shared library libgfortran.so.1 is not available (at least not
> in the
> >> > standard library paths or anywhere specified by LD_LIBRARY_PATH)
> wherever
> >> > you are trying to run, but it was linked into the executable
> (which is
> >> why
> >> > you are getting this error message). You'll have to recompile if
> you
> >> > choose this route.
> >> >
> >> > Alternatively, if you can find this library file
> (libgfortran.so.1), you
> >> > can add that directory to your LD_LIBRARY_PATH like so:
> >> >
> >> > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH\:/folder/containing/lib/
> >> >
> >> > This shouldn't happen in general if "gfortran" is the same on the
> node
> >> that
> >> > you compiled it on as it is on the node that you're trying to run
> on.
> >> >
> >> > HTH,
> >> > Jason
> >> >
> >> > On Wed, Jan 25, 2012 at 2:09 PM, Jorgen Simonsen
> <jorgen589.gmail.com
> >> >wrote:
> >> >
> >> >> it returns the following
> >> >>
> >> >> opt/SUNWhpc/HPC8.2.1c/gnu/bin/mpif90 -show
> >> >> gfortran -I/opt/SUNWhpc/HPC8.2.1c/gnu/include/64
> >> >> -I/opt/SUNWhpc/HPC8.2.1c/gnu/lib/lib64 -Wl,--enable-new-dtags
> >> >> -Wl,-rpath,/opt/mx/lib/lib64
> >> >> -Wl,-rpath,/opt/SUNWhpc/HPC8.2.1c/gnu/lib/lib64
> >> >> -I/opt/SUNWhpc/HPC8.2.1c/gnu/lib/lib64
> >> >> -J/opt/SUNWhpc/HPC8.2.1c/gnu/lib/lib64
> >> >> -L/opt/SUNWhpc/HPC8.2.1c/gnu/lib/lib64 -lmpi -lopen-rte -lopen-
> pal
> >> >> -lnsl -lrt -lm -ldl -lutil -lpthread -lmpi_f77 -lmpi_f90
> >> >>
> >> >> On Wed, Jan 25, 2012 at 6:56 PM, Jason Swails
> <jason.swails.gmail.com>
> >> >> wrote:
> >> >> > What does
> >> >> >
> >> >> > /opt/SUNWhpc/HPC8.2.1c/gnu/bin/mpif90 -show
> >> >> >
> >> >> > return?
> >> >> >
> >> >> > All the best,
> >> >> > Jason
> >> >> >
> >> >> > On Wed, Jan 25, 2012 at 12:18 PM, Jorgen Simonsen <
> >> jorgen589.gmail.com
> >> >> >wrote:
> >> >> >
> >> >> >> hi all
> >> >> >>
> >> >> >> I have compiled amber10 with the following settings
> >> >> >>
> >> >> >> ./configure_amber -intelmpi -static gfortran
> >> >> >>
> >> >> >> and it compiles fine but when I try to test it I get the
> following
> >> error
> >> >> >>
> >> >> >> export DO_PARALLEL='mpirun -np 2'
> >> >> >> make test.parallel
> >> >> >>
> >> >> >> sander.MPI: error while loading shared libraries:
> libgfortran.so.1:
> >> >> >> cannot open shared object file: No such file or directory
> >> >> >> ./Run.cytosine: Program error
> >> >> >> make[1]: *** [test.sander.BASIC] Error 1
> >> >> >>
> >> >> >> my config_amber is like this
> >> >> >>
> >> >> >> # C compiler
> >> >> >>
> >> >> >>
> >> >>
> >> #-------------------------------------------------------------------
> -----------
> >> >> >> CC= gcc
> >> >> >> CPLUSPLUS=g++
> >> >> >> CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m64
> >> >> >> $(AMBERBUILDFLAGS)
> >> >> >> 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/SUNWhpc/HPC8.2.1c/gnu/include/ -P -DBINTRAJ -
> DMPI
> >> >> >> $(AMBERBUILDFLAGS)
> >> >> >> FPP= cpp -traditional $(FPPFLAGS)
> >> >> >> FC= /opt/SUNWhpc/HPC8.2.1c/gnu/bin/mpif90
> >> >> >> FFLAGS= -O0 -fno-range-check -fno-second-underscore
> $(LOCALFLAGS)
> >> >> >> $(AMBERBUILDFLAGS)
> >> >> >> FOPTFLAGS= -O3 -fno-range-check -fno-second-underscore
> $(LOCALFLAGS)
> >> >> >> $(AMBERBUILDFLAGS)
> >> >> >> FREEFORMAT_FLAG= -ffree-form
> >> >> >>
> >> >> >>
> >> >> >>
> >> >>
> >> #-------------------------------------------------------------------
> -----------
> >> >> >> # Loader:
> >> >> >>
> >> >> >>
> >> >>
> >> #-------------------------------------------------------------------
> -----------
> >> >> >> LOAD= /opt/SUNWhpc/HPC8.2.1c/gnu/bin/mpif90 $(LOCALFLAGS)
> >> >> >> $(AMBERBUILDFLAGS)
> >> >> >> LOADCC= gcc $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> >> >> >> LOADLIB=
> >> >> >> LM= -lm
> >> >> >> XHOME= /usr/X11R6
> >> >> >> XLIBS= -L/usr/X11R6/lib64 -L/usr/X11R6/lib
> >> >> >>
> >> >> >>
> >> >> >>
> >> >>
> >> #-------------------------------------------------------------------
> -----------
> >> >> >> :
> >> >> >>
> >> >> >> _______________________________________________
> >> >> >> 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
> >> >>
> >> >> _______________________________________________
> >> >> 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
> >>
> >> _______________________________________________
> >> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Jan 25 2012 - 15:30:02 PST
