Dear ângela
The problems you are seeing come about because you are mixing a 32 bit
compiler with a load of 64 bit libraries hence all the compatabilities / not
found errors.
By the fact that you have a lib64 directory I assume you are running an
x86_64 compatible chip and operating system.
You start by seeing if you have the x86_64 versions of the Intel compilers
installed. These will be in intel_fce_80 and intel_cce_80. If you have them
then you can change your environment files to point to the fce and cce
versions. Note the following is unecessary:
> % export
> PATH=$PATH:$AMBERHOME/exe:/scratch/programs/intel_fc_80/bin/:/
scratch/programs/intel_cc_80/bin/
You don't need to explicitly put the intel compilers in your path - this is
done when you source the ifortvars.sh and iccvars.sh files.
If you don't have the fce and cce versions of the compilers then you should
uninstall the 32 bit ones, go to the Intel website and download the fce and
cce versions and install these.
Your .bashrc file should then look something like this:
#AMBER
export AMBERHOME=/scratch/programs/amber9/
export PATH=$PATH:/scratch/programs/amber9/exe/
#Intel compilers
source /scratch/programs/intel_cce_80/bin/iccvars.sh
source /scratch/programs/intel_fce_80/bin/ifortvars.sh
Then make sure you do
cd $AMBERHOME/src
make clean
make
All the best
Ross
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Ângela dos Reis
> Sent: Friday, April 27, 2007 04:14
> To: amber.scripps.edu
> Subject: AMBER: Problems installing Amber9
>
> Hi,
> I'm trying to install amber9 and i'm having some error that i
> can't figure
> out how to solve. I'd apreciate some help. I write down here
> some steps
> followed during the instalation, some information about the
> instalation path
> and the errors.
> Thanks
>
> % ls /scratch/programs/
> amber intel_cc_80 intel_fc_80 lam mpich
>
> % locate pgi
> /usr/local/pgi/....
>
> % locate fftw
> /usr/lib64/libfftw3....
>
> % export GOTO=/usr/lib64/
>
> % export AMBERHOME=/scratch/programs/amber/amber9
> % export
> PATH=$PATH:$AMBERHOME/exe:/scratch/programs/intel_fc_80/bin/:/
scratch/programs/intel_cc_80/bin/
>
> % /scratch/programs/intel_fc_80/bin/ifortvars.sh
>
> % uname -a
> Linux amd-n1 2.6.8-24.10-smp #1 SMP Wed Dec 22 11:54:27 UTC
> 2004 x86_64
> x86_64 x86_64 GNU/Linux
>
> % ./configure -nopar ifort_x86_64
> AMBERHOME is set to /home/amc/amber9_source/amber9
> Setting up Amber configuration file for architecture: ifort_x86_64
> Using parallel communications library: none
> The MKL_HOME environment variable is not defined.
> The MKL is recommended for optimal performance.
>
> The configuration file, config.h, was successfully created.
>
> % ./make serial
> ....
> ....
> a - ../obj/commandqmmm.o
> a - ../obj/initmem2.o
> a - ../obj/allocateMxAtomVarsqmmm.o
> ranlib libdivcon.a
> mv libdivcon.a ../src/qmmm/
> make[3]: warning: Clock skew detected. Your build may be incomplete.
> make[3]: Leaving directory
> `/scratch/programs/amber/amber9/src/dcqtp/mod'
> make[2]: Leaving directory `/scratch/programs/amber/amber9/src/dcqtp'
> ifort -FR -o sander 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.oew_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.ommtsb_client.o
> erfcfun.o veclib.o is_init.o constantph.o prn_dipoles.o ips.o
> sglds.oamoeba_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 ../dcqtp/src/qmmm/libdivcon.a \
> ../lapack/lapack.a ../blas/blas.a \
> ../lib/nxtsec.o ../lib/sys.a
> ld: warning: i386:x86-64 architecture of input file
> `mmtsb_client.o' is
> incompatible with i386 output
> ld: warning: i386:x86-64 architecture of input file `../lib/sys.a(
> wallclock.o)' is incompatible with i386 output
> relax_mat.o(.text+0x793): In function `relax_mat_mp_amatg_.J':
> : undefined reference to `vmldExp2'
> relax_mat.o(.text+0x8044): In function `relax_mat_mp_remarc_.J':
> : undefined reference to `vmldExp2Mask'
> relax_mat.o(.text+0x81f5): In function `relax_mat_mp_remarc_.J':
> : undefined reference to `vmldExp2Mask'
> relax_mat.o(.text+0x84e9): In function `relax_mat_mp_remarc_.J':
> : undefined reference to `vmldExp2'
> relax_mat.o(.text+0x96ea): In function `relax_mat_mp_remarc_.J':
> : undefined reference to `vmldTanh2'
> ene.o(.text+0xef2): In function `angl_.L':
> : undefined reference to `vmldAcos2'
> ene.o(.text+0x16ce): In function `angl_.J':
> : undefined reference to `vmldAcos2'
> ene.o(.text+0x2fea): In function `ephi_.L':
> : undefined reference to `vmldAcos2'
> ene.o(.text+0x3040): In function `ephi_.L':
> : undefined reference to `vmldSinCos2'
> ene.o(.text+0x5685): In function `ephi_.J':
> : undefined reference to `vmldAcos2'
> ene.o(.text+0x56db): In function `ephi_.J':
> : undefined reference to `vmldSinCos2'
> ew_bspline.o(.text+0x45ac): In function
> `ew_bspline_mp_load_prefacs_.L':
> : undefined reference to `vmldSinCos2'
> ew_bspline.o(.text+0x4bd8): In function
> `ew_bspline_mp_load_prefacs_.L':
> : undefined reference to `vmldSinCos2'
> ew_bspline.o(.text+0x51fe): In function
> `ew_bspline_mp_load_prefacs_.L':
> : undefined reference to `vmldSinCos2'
> ew_bspline.o(.text+0x5beb): In function
> `ew_bspline_mp_load_prefacs_.J':
> : undefined reference to `vmldSinCos2'
> ew_bspline.o(.text+0x61fa): more undefined references to `vmldSinCos2'
> follow
> veclib.o(.text+0x93): In function `vdexp_.J':
> : undefined reference to `vmldExp2'
> veclib.o(.text+0x1cf): In function `vdln_.J':
> : undefined reference to `vmldLn2'
> veclib.o(.text+0x324): In function `vdinvsqrt_.J':
> : undefined reference to `vmldInvSqrt2'
> veclib.o(.text+0x34c): In function `vdinvsqrt_.J':
> : undefined reference to `vmldInvSqrt2'
> veclib.o(.text+0x763): In function `vdcos_.J':
> : undefined reference to `vmldCos2'
> veclib.o(.text+0x8a7): In function `vdtanh_.J':
> : undefined reference to `vmldTanh2'
> amoeba_valence.o(.text+0x14ccd): In function
> `amoeba_torsions_mp_am_torsions_readparm_.J':
> : undefined reference to `vmldSinCos2'
> amoeba_valence.o(.text+0x19810): In function
> `amoeba_stretch_torsions_mp_am_stretch_torsions_readparm_.J':
> : undefined reference to `vmldSinCos2'
> amoeba_valence.o(.text+0x1eb6f): In function
> `amoeba_pitorsions_mp_am_pitorsions_readparm_.J':
> : undefined reference to `vmldSinCos2'
> ../dcqtp/src/qmmm/libdivcon.a(getpar.o)(.text+0x37f): In function
> `getpar_.J':
> : undefined reference to `vmldPow2'
> ../dcqtp/src/qmmm/libdivcon.a(assignbasis.o)(.text+0xc37): In function
> `assignbasis_.L':
> : undefined reference to `vmldPow2'
> ../dcqtp/src/qmmm/libdivcon.a(assignbasis.o)(.text+0x1fdf):
> In function
> `assignbasis_.J':
> : undefined reference to `vmldPow2'
> make[1]: *** [sander] Error 1
> make[1]: Leaving directory `/scratch/programs/amber/amber9/src/sander'
> make: *** [serial] Error 2
>
>
> % cd cd /scratch/programs/amber/amber9
> % make clean
> % export AMBERHOME=/scratch/programs/amber/amber9/
> % export PATH=$PATH:/usr/local/pgi/linux86-64/5.1/bin/:$AMBERHOME/exe
> % export
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH://usr/local/pgi/linux86-64/5.1/lib
> % export LM_LICENSE_FILE=/usr/local/pgi/license.dat
> % ./configure -nopar -opteron pgf90
> AMBERHOME is set to /scratch/programs/amber/amber9/
> Setting up Amber configuration file for architecture: pgf90
> Using parallel communications library: none
>
> The configuration file, config.h, was successfully created.
>
> % make serial
> ....
> ....
> cd sander; make serial
> make[1]: Entering directory
> `/scratch/programs/amber/amber9/src/sander'
> ./checkserconf
> cpp -traditional -P evb_vars.f > _evb_vars.f
> pgf90 -c -tp p7 -O1 -Mfree -o evb_vars.o _evb_vars.f
> PGF90-S-0155-Illegal component initialization in derived type
> evb_mat_type
> (_evb_vars.f: 447)
> 0 inform, 0 warnings, 1 severes, 0 fatal for evb_data
> Lowering Error: DATA ast not constant: 57
> PGF90-F-0000-Internal compiler error. Errors in Lowering 1
> (_evb_vars.f: 494)
> PGF90/any Linux/x86 5.1-6: compilation aborted
> make[1]: *** [evb_vars.o] Error 2
> make[1]: Leaving directory `/scratch/programs/amber/amber9/src/sander'
> make: *** [serial] Error 2
>
> or
> % make clean
> % ./configure -nopar -opteron -lmod -verbose pgf90
> % make serial
> ....
> ....
> /usr/bin/as /tmp/pgf90baaaapeFal.s --32 -o mexit.o
> Unlinking /tmp/pgf90aaaaapeFal.ilm
> Unlinking /tmp/pgf90baaaapeFal.s
> make[2]: Leaving directory `/scratch/programs/amber/amber9/src/lib'
> make[2]: Entering directory `/scratch/programs/amber/amber9/src/lib'
> make[2]: `nxtsec.o' is up to date.
> make[2]: Leaving directory `/scratch/programs/amber/amber9/src/lib'
> pgf90 -tp p7 -o addles lesmain.o addspace.o readprm.o
> writprm.o readcrd.o
> writcrd.o pick.o rline.o nxt.o intgr.o find.o of.o geti.o
> unit.o getc.o alert.o echo.o get4c.o getd.o
> wlesprm.o lesprm.o
> les2prm.o checksz.o ../lib/random.o ../lib/mexit.o ../lib/nxtsec.o
> mv addles ../../exe
> make[1]: Leaving directory `/scratch/programs/amber/amber9/src/addles'
> cd sander; make serial
> make[1]: Entering directory
> `/scratch/programs/amber/amber9/src/sander'
> ./checkserconf
> cpp -traditional -P evb_vars.f > _evb_vars.f
> pgf90 -c -tp p7 -O1 -v -V -Minfo=all -Minform=inform
> -Mneginfo -Mfree -o
> evb_vars.o _evb_vars.f
>
> pgf90 5.1-6
> Copyright 1989-2000, The Portland Group, Inc. All Rights Reserved.
> Copyright 2000-2003, STMicroelectronics, Inc. All Rights Reserved.
>
> /usr/local/pgi/linux86/5.1/bin/pgf901 _evb_vars.f -opt 1
> -version -inform
> inform -nohpf -nostatic -x 119 0x100000 -x 15 2 -x 49
> 0x400004 -x 51 0x20 -x
> 57 0x4c -x 58 0x10000 -x 124 0x1000 -x 57 0x10000 -x 58
> 0x31040 -x 48 3328
> -stdinc
> /usr/local/pgi/linux86/5.1/include:/usr/local/include:/usr/lib
> 64/gcc-lib/x86_64-suse-linux/3.3.4/include:/usr/lib64/gcc-lib/
x86_64-suse-linux/3.3.4/32/include:/usr/include
> -def unix -def __unix -def __unix__ -def linux -def __linux
> -def __linux__
> -def __inline__= -def i386 -def __i386 -def __i386__ -def
> __NO_MATH_INLINES
> -def linux86 -def __THROW= -vect 48 -x 0 319 -freeform -output
> /tmp/pgf90aaaaaFeFal.ilm
> PGF90/any Linux/x86 5.1-6
> Copyright 1989-2000, The Portland Group, Inc. All Rights Reserved.
> Copyright 2000-2003, STMicroelectronics, Inc. All Rights Reserved.
> 0 inform, 0 warnings, 0 severes, 0 fatal for evb_nml
> 0 inform, 0 warnings, 0 severes, 0 fatal for evb_amber
> 0 inform, 0 warnings, 0 severes, 0 fatal for evb_parm
> 0 inform, 0 warnings, 0 severes, 0 fatal for evb_xchff
> 0 inform, 0 warnings, 0 severes, 0 fatal for evb_xdat
> 0 inform, 0 warnings, 0 severes, 0 fatal for evb_mv
> PGF90-S-0155-Illegal component initialization in derived type
> evb_mat_type
> (_evb_vars.f: 447)
> 0 inform, 0 warnings, 1 severes, 0 fatal for evb_data
> Lowering Error: DATA ast not constant: 57
> PGF90-F-0000-Internal compiler error. Errors in Lowering 1
> (_evb_vars.f: 494)
> Timing stats:
> init 17 millisecs 51%
> parser 16 millisecs 48%
> Total time 33 millisecs
> PGF90/any Linux/x86 5.1-6: compilation aborted
> pgf90-Fatal-f901 completed with exit code 1
>
> Unlinking /tmp/pgf90aaaaaFeFal.ilm
> make[1]: *** [evb_vars.o] Error 2
> make[1]: Leaving directory `/scratch/programs/amber/amber9/src/sander'
> make: *** [serial] Error 2
>
>
> --
> Cumprimentos
>
> ângela dos reis
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
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Received on Sun Apr 29 2007 - 06:07:38 PDT
