AMBER Archive (2007)

Subject: Re: AMBER: Problems installing Amber9

From: Ângela dos Reis (angela.dos.reis_at_gmail.com)
Date: Fri Apr 27 2007 - 12:34:38 CDT

I guess I don't have the intel x86_64 version installed

% ifort -V
Intel(R) Fortran Compiler for 32-bit applications, Version 8.1 Build
20040803Z Package ID: l_fc_p_8.1.018

I've compiled it with :
LOADLIB= <...whatever is there already> -L<path to libsvml.so> -lsvml
but it failed to the test (it migh be because it's a 32 compiler).

i've decided to try it with
./configure -opteron pgf90

and got the following error:

make[2]: Leaving directory `/scratch/programs/amber/amber9_test/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_test/src/addles'
cd sander; make serial
make[1]: Entering directory `/scratch/programs/amber/amber9_test/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_test/src/sander'
make: *** [serial] Error 2

i'm sorry, but it's the first time i'm doing this. I'd apreciate some help
;D
thanks

On 4/27/07, Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
> 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 $AMBERHOME/src
> make clean
> make
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu
> > [mailto:owner-amber_at_scripps.edu] On Behalf Of Ângela dos Reis
> > Sent: Friday, April 27, 2007 04:14
> > To: amber_at_scripps.edu
> > Subject: AMBER: Problems installing Amber9
> >
> > Hi,
> > I'm trying to install amber9 and i'm having some error that i
> > can't figure
> > out how to solve. I'd apreciate some help. I write down here
> > some steps
> > followed during the instalation, some information about the
> > instalation path
> > and the errors.
> > Thanks
> >
> > % ls /scratch/programs/
> > amber intel_cc_80 intel_fc_80 lam mpich
> >
> > % locate pgi
> > /usr/local/pgi/....
> >
> > % locate fftw
> > /usr/lib64/libfftw3....
> >
> > % export GOTO=/usr/lib64/
> >
> > % export AMBERHOME=/scratch/programs/amber/amber9
> > % export
> > PATH=$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_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
>
>
> -----------------------------------------------------------------------
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> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

-- 
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