Dear Jason,
Thanks a lot for the help,
Best,
Peter
Sendt fra min iPad
Den 25/04/2012 kl. 18.09 skrev "Jason Swails" <jason.swails.gmail.com>:
> Try adding AMBERHOME/lib to your LD_LIBRARY_PATH:
>
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH\:$AMBERHOME/lib # for bash/sh
>
> setenv LD_LIBRARY_PATH "$LD_LIBRARY_PATH:$AMBERHOME/lib" # for csh/tcsh
>
> Then retry. It may be worth perusing
> http://jswails.wikidot.com/installing-amber12-and-ambertools-12<http://jswails.wikidot.com/installing-amber12-and-ambertools-12#toc7>
> which
> has a section about building in parallel (and what to do if you've used
> configure_mpich2 and configure_openmpi).
>
> HTH,
> Jason
>
> On Wed, Apr 25, 2012 at 8:45 AM, Peter Fojan <fp.nano.aau.dk> wrote:
>
>> Hi again,
>> sorry for being not precise.
>> I did install amber12 single processor version and gnu compiler without
>> any problem or error message and tests did pass all of them.
>> Next step I did was installing mpich2 as in the manual and downloaded from
>> this site
>> http://www.mcs.anl.gov/research/projects/mpich2/mpich2-1.4.1p1
>> and unpacked and installed mpich2 in
>> $AMBERHOME/AmberTools/src
>>
>> i ran ./configure_mpich2 gnu
>> make install
>> it installed without error message.
>>
>> in $AMBERHOME
>> I did run
>> ./configure -mpi gnu
>> configure ran wiothout any comment
>>
>> make install proceeded until:
>> mpif90 -DBINTRAJ -DMPI -ffree-form -I../../AmberTools/src/pbsa
>> -I../../AmberTools/src/sqm -I../../AmberTools/src/rism -I../../include
>> -I/usr/local/amber12/include -I/usr/local/amber12/include -o sander.MPI
>> file_io_dat.o constants.o state.o memory_module.o stack.o nose_hoover.o
>> nose_hoover_vars.o nose_hoover_init.o trace.o rmsgrd.o lmod.o rand2.o
>> lmodC.o xminC.o decomp.o icosasurf.o egb.o remd.o findmask.o relax_mat.o
>> nmr.o multitmd.o multisander.o sander.o trajene.o cshf.o nmrcal.o
>> mtmdcall.o pearsn.o printe.o runmin.o rdparm.o sander_lib.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 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
>> constantph.o prn_dipoles.o ips.o sglds.o iwrap2.o emap.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 binrestart.o spatial_recip.o spatial_fft.o
>> parms.o softcore.o mbar.o linear_response.o molecule.o xref.o dssp.o
>> charmm.o crg_reloc.o amd.o qm_mm.o qm_ewald.o qmmm_vsolv.o
>> qm2_extern_module.o qm2_extern_adf_module.o qm2_read_adf_results.o
>> KFReader.o ArrayList.o qm2_extern_gms_module.o qm2_extern_tc_module.o
>> qm2_extern_gau_module.o qm2_extern_orc_module.o qm2_extern_nw_module.o
>> qmmm_adaptive_module.o prn_qmmm_dipole.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_dihed.o schlegel_angle.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
>> force.o \
>> -L/usr/local/amber12/lib -lsqm -lFpbsa \
>> ../lib/nxtsec.o ../lib/sys.a ncsu-abmd-hooks.o
>> ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o ncsu-cftree.o ncsu-colvar.o
>> ncsu-colvar-math.o ncsu-colvar-type.o ncsu-colvar-utils.o ncsu-constants.o
>> ncsu-cv-ANGLE.o ncsu-cv-COM_ANGLE.o ncsu-cv-COM_DISTANCE.o
>> ncsu-cv-COM_TORSION.o ncsu-cv-COS_OF_DIHEDRAL.o ncsu-cv-DISTANCE.o
>> ncsu-cv-HANDEDNESS.o ncsu-cv-LCOD.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-cv-PCA.o ncsu-read-pca.o
>> ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o mt19937.o
>> -L/usr/local/amber12/lib -lnetcdf \
>> -larpack -llapack -lblas \
>>
>> /usr/local/amber12/lib/libmpich.so: undefined reference to `MPL_trfree'
>> /usr/local/amber12/lib/libmpich.so: undefined reference to `MPL_env2str'
>> /usr/local/amber12/lib/libmpich.so: undefined reference to `MPL_trlevel'
>> /usr/local/amber12/lib/libmpich.so: undefined reference to `MPL_trvalid'
>> /usr/local/amber12/lib/libmpich.so: undefined reference to `MPL_trmalloc'
>> /usr/local/amber12/lib/libmpich.so: undefined reference to `MPL_trspace'
>> /usr/local/amber12/lib/libmpich.so: undefined reference to `MPL_env2range'
>> /usr/local/amber12/lib/libmpich.so: undefined reference to `MPL_trcalloc'
>> /usr/local/amber12/lib/libmpich.so: undefined reference to `MPL_env2int'
>> /usr/local/amber12/lib/libmpich.so: undefined reference to `MPL_trdump'
>> /usr/local/amber12/lib/libmpich.so: undefined reference to `MPL_env2bool'
>> /usr/local/amber12/lib/libmpich.so: undefined reference to `MPL_trstrdup'
>> /usr/local/amber12/lib/libmpich.so: undefined reference to `MPL_trrealloc'
>> /usr/local/amber12/lib/libmpich.so: undefined reference to
>> `MPL_TrSetMaxMem'
>> /usr/local/amber12/lib/libmpich.so: undefined reference to `MPL_trinit'
>> /usr/local/amber12/lib/libmpich.so: undefined reference to
>> `MPL_trDebugLevel'
>> /usr/local/amber12/lib/libmpich.so: undefined reference to `MPL_trid'
>> collect2: ld returned 1 exit status
>> make[2]: *** [sander.MPI] Error 1
>> make[2]: Leaving directory `/usr/local/amber12/src/sander'
>> make[1]: *** [parallel] Error 2
>> make[1]: Leaving directory `/usr/local/amber12/src'
>> make: *** [install] Error 2
>>
>> I hope I did not miss out on anything.
>>
>> which mpif90
>> /usr/local/amber12/bin/mpif90
>>
>> gnu compilers gcc 4.4.5
>> gfortran 4.4.5
>>
>> best,
>> Peter
>> ''~''
>> ( o o )
>> +-------------------------oooO--(_)--Oooo----------------------------+
>> Peter Fojan, PhD Tel. 0045/9940 7491
>> Associate Professor email: fp.nano.aau.dk
>> Molecular Engineering Group web: www.nano.aau.dk
>> <SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New';
>> mso-fareast-font-family: 'Times New Roman'; mso-fareast-theme-font: mi
>> ________________________________________
>> Fra: David A Case [case.biomaps.rutgers.edu]
>> Sendt: 25. april 2012 14:16
>> Til: AMBER Mailing List
>> Emne: Re: [AMBER] AMBER12 installation error
>>
>> On Wed, Apr 25, 2012, Peter Fojan wrote:
>>
>>> I just tried to install the mpi version of amber12 and just to be on the
>>> safe side also installed the suggested version of mpich2.
>>> but i do get the following error message and the installation stops.
>>>
>>> -larpack -llapack -lblas \
>>>
>>> /usr/local/amber12/lib/libmpich.so: undefined reference to `MPL_trfree'
>>>
>>> Anybody has any suggestions what to do?
>>
>> Give more details? What compiler? What is the result of "which mpif90"?
>> Can you give the full command that failed, probably starting with
>> "mpif90...."
>> Can you be more explicit when you say that you "installed the suggested
>> version of mpich2"? (That is, tell us what you actually did, not what you
>> intended to do or thought you did.)
>>
>> ...thanks...dac
>>
>>
>> _______________________________________________
>> 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
Received on Wed Apr 25 2012 - 10:00:03 PDT
