AMBER: Problems installing Amber9

From: Āngela dos Reis <angela.dos.reis.gmail.com>
Date: Fri, 27 Apr 2007 12:14:05 +0100

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/lib64/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
āngela dos reis
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Received on Sun Apr 29 2007 - 06:07:34 PDT
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