Thanks finally I was able to compile the program. Next I run the
test.parallel as described in the Makefile but there are certain tests
that fail - the following cases fail
cd rdc && ./Run.dip
cd noesy && ./Run.noesy
and gives the following
./Run.dip: Program error
./Run.noesy: Program error
where would it crash on these two?
Thanks
On Thu, Jan 26, 2012 at 12:10 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Jan 26 2012 - 06:30:03 PST
