AMBER Archive (2009)

Subject: RE: [AMBER] amber9 installation problem in SMP IA64

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Wed Feb 11 2009 - 03:36:31 CST

Thanks for the help. But when I run accordingly I get some errors too.
I have posted the error as below:

************************************************************************
                                             
~ # cd /opt/intel/cc/10.1.008/bin/
/opt/intel/cc/10.1.008/bin # source iccvars.sh
/opt/intel/cc/10.1.008/bin # cd /opt/intel/fc/10.1.008/bin/
/opt/intel/fc/10.1.008/bin # source ifortvars.sh
/opt/intel/fc/10.1.008/bin # export MKL_HOME=/opt/intel/mkl/10.0.010
/usr/local/amber9/src # export AMBERHOME=/usr/local/amber9
/usr/local/amber9/src # ./configure -static ifort_ia64
AMBERHOME is set to /usr/local/amber9
Setting up Amber configuration file for architecture: ifort_ia64
Using parallel communications library: none
MKL_HOME is set to /opt/intel/mkl/10.0.010
Using MKL libraries from /opt/intel/mkl/10.0.010/lib/64

The configuration file, config.h, was successfully created.
/usr/local/amber9/src # grep ifort config.h
# AMBER Makefile configuration for compiler/architecture: ifort_ia64
# Generated via command: ./configure -static ifort_ia64
FC= ifort
LOAD= ifort -i-static $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADPTRAJ= ifort -i-static -nofor_main $(LOCALFLAGS) $(AMBERBUILDFLAGS)
/usr/local/amber9/src # make
:
:
:
xaParmEditor.c(519): warning #1011: missing return statement at end of non-void function "XAPEEditDone"
  }
  ^

xaParmEditor.c(534): warning #1011: missing return statement at end of non-void function "XAPESetAtomLabel"
  }
  ^

xaParmEditor.c(550): warning #1011: missing return statement at end of non-void function "XAPESetBondLabel"
  }
  ^

xaParmEditor.c(566): warning #1011: missing return statement at end of non-void function "XAPESetAngleLabel"
  }
  ^

xaParmEditor.c(582): warning #1011: missing return statement at end of non-void function "XAPESetTorsionLabel"
  }
  ^

xaParmEditor.c(597): warning #1011: missing return statement at end of non-void function "XAPESetImproperLabel"
  }
  ^

xaParmEditor.c(613): warning #1011: missing return statement at end of non-void function "XAPESetHBondLabel"
  }
  ^

icc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -o xaTorsionParmTable.o xaTorsionParmTable.c
icc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -o xaImproperParmTable.o xaImproperParmTable.c
icc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -o xaHBondParmTable.o xaHBondParmTable.c
icc -i-static -o xaLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o collection.o container.o internal.o list.o loop.o molecule.o oDouble.o oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o tripos.o graphUtil.o select.o amber.o build.o elements.o library.o chirality.o minimizer.o model..o parmLib.o pdbFile.o tools.o variables.o parser.o help.o helptext.o octree.o commands.o mathop.o block.o restraint.o hybrid.o xTank.o xAction.o x3d.o xBasics.o xaLeapc.o xaUnitEditor.o xaTable.o xaAtomTable.o XrawRegistr.o xaCommand.o xaTools.o xaAtomParmTable.o xaBondParmTable.o xaAngleParmTable.o xaParmEditor.o xaTorsionParmTable.o xaImproperParmTable.o xaHBondParmTable.o ../Xraw/libXaw.a ../Wc/libWcLeap.a ../Xpm/libXpm.a
 ../Xmu/libXmu.a -L/usr/X11R6/lib -lXt -lXext -lSM -lICE -lX11 -lm -lpthread
.../Xraw/libXaw.a(AsciiSrc.o): In function `InitStringOrFile??unw':
AsciiSrc.c:(.text+0x4e82): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
m4 xaLeap.rm4 > XaLeap_wcl
mv teLeap xaLeap ../../../../exe
mv XaLeap_wcl ../../../../dat
make[2]: Leaving directory `/usr/local/amber9/src/leap/src/leap'
Copying shell scripts
cp tleap xleap ../../exe
Copying pixmaps
mkdir ../../dat/pixmap
( cd pixmap ;\
  cp `find . -follow -name CVS -prune -o -type f -print ` ../../../dat/pixmap \
)
Finished with the install of LEaP
make[1]: Leaving directory `/usr/local/amber9/src/leap'

Installation of Amber9 (serial) is complete at Wed Feb 11 12:13:08 MYT 2009..

/usr/local/amber9/src #
/usr/local/lam-7.0.6 # make distclean
/usr/local/lam-7.0.6 # ./configure --prefix=/usr/local/lam CC=icc FC=ifort CXX=icpc
/usr/local/lam-7.0.6 # make install
/usr/local/amber9/src # export MPI_HOME=/opt/mpich/ch-p4mpd
/usr/local/amber9/src # export AMBERHOME=/usr/local/amber9/
/usr/local/amber9/src # rpm -qa|grep mpich
mpich-devel-1.2.7p1-15.2
mpich-1.2.7p1-15.2
/usr/local/amber9/src # ./configure -mpich ifort_ia64
AMBERHOME is set to /usr/local/amber9/
Setting up Amber configuration file for architecture: ifort_ia64
Using parallel communications library: mpich
MPI_HOME is set to /usr/local/lam/
../configure: line 300: /usr/local/lam//bin/mpif90: No such file or directory
MKL_HOME is set to /opt/intel/mkl/10.0.010
Using MKL libraries from /opt/intel/mkl/10.0.010/lib/64

The configuration file, config.h, was successfully created.
/usr/local/amber9/src # make parallel
:
:
:
make[2]: Entering directory `/usr/local/amber9/src/blas'
Makefile:7: warning: overriding commands for target `.f.o'
.../config.h:82: warning: ignoring old commands for target `.f.o'
cpp -traditional -I/opt/mpich/ch-p4mpd/include -P -DMPI -DMKL dummy.f > _dummy.f
ifort -c -w95 -ftz -O3 -IPF_fma -IPF_fp_relaxed -ip -o dummy.o _dummy.f
ar rv blas.a dummy.o
ar: creating blas.a
a - dummy.o
ranlib blas.a
make[2]: Leaving directory `/usr/local/amber9/src/blas'
cd ../lmod; make
make[2]: Entering directory `/usr/local/amber9/src/lmod'
cd xmin; make
make[3]: Entering directory `/usr/local/amber9/src/lmod/xmin'
Makefile:6: warning: overriding commands for target `.f.o'
.../../config.h:82: warning: ignoring old commands for target `.f.o'
cpp -traditional -I/opt/mpich/ch-p4mpd/include -P -DMPI -DMKL xmin.f > _xmin.f
ifort -c -w95 -ftz -O3 -IPF_fma -IPF_fp_relaxed -ip -o xmin.o _xmin.f
make[3]: Leaving directory `/usr/local/amber9/src/lmod/xmin'
cd lmod; make
make[3]: Entering directory `/usr/local/amber9/src/lmod/lmod'
Makefile:6: warning: overriding commands for target `.f.o'
.../../config.h:82: warning: ignoring old commands for target `.f.o'
cpp -traditional -I/opt/mpich/ch-p4mpd/include -P -DMPI -DMKL lmod.f > _lmod.f
ifort -c -w95 -ftz -O3 -IPF_fma -IPF_fp_relaxed -ip -o lmod.o _lmod.f
make[3]: Leaving directory `/usr/local/amber9/src/lmod/lmod'
ar rv lmod.a xmin/*.o lmod/*.o
ar: creating lmod.a
a - xmin/xmin.o
a - lmod/lmod.o
ranlib lmod.a
make[2]: Leaving directory `/usr/local/amber9/src/lmod'
cd ../lmod; cp lmodprmtop ../../exe; chmod 0755 ../../exe/lmodprmtop
ifort -i-static -FR -o sander.MPI 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.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 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 ../lapack/lapack.a ../blas/blas.a \
        ../lib/nxtsec.o ../lib/sys.a -L/usr/local/fftw/lib -L/opt/mpich/ch-p4mpd/lib -lmpichf90 -lmpich -lpthread -lrt /opt/intel/mkl/10.0.010/lib/64/libmkl_lapack.a /opt/intel/mkl/10.0.010/lib/64/libmkl_ipf.a -L/opt/intel/mkl/10.0.010/lib/64 -lguide -lpthread -ldl
/opt/mpich/ch-p4mpd/lib/libmpich.a(farg.o): In function `mpir_iargc_':
(.text+0x22): undefined reference to `_gfortran_iargc'
/opt/mpich/ch-p4mpd/lib/libmpich.a(farg.o): In function `mpir_getarg_':
(.text+0xd2): undefined reference to `_gfortran_getarg_i4'
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory `/usr/local/amber9/src/sander'
make: *** [parallel] Error 2
/usr/local/amber9/src # ptmlxsmp:/usr/local/amber9/src # echo $PATH
/opt/intel/fc/10.1.008/bin:/opt/intel/cc/10.1.008/bin:/sbin:/usr/sbin:/usr/local/sbin:/opt/gnome/sbin:/root/bin:/usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin:/usr/games:/opt/gnome/bin:/opt/kde3/bin:/usr/lib/jvm/jre/bin:/usr/lib/mit/bin:/usr/lib/mit/sbin:/opt/pbs/10.0.0.82981/bin:/usr/local/gromacs/bin:/usr/local/amber9/exe:/usr/local/fftw/bin:/opt/pbs/10.0.0.82981/bin:/usr/local/fftw/bin:/opt/mpich/ch-p4mpd/bin:/opt/mpich/ch-p4/bin
/usr/local/amber9/src #

************************************************************************

Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
 vjramana_at_gmail.com

--- On Wed, 11/2/09, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> From: Ross Walker <ross_at_rosswalker.co.uk>
> Subject: RE: [AMBER] amber9 installation problem in SMP IA64
> To: vjrajamany_at_yahoo.com, "'AMBER Mailing List'" <amber_at_ambermd.org>
> Date: Wednesday, 11 February, 2009, 1:56 AM
> Hi Vijay,
>
> I would highly recommend installing ifort on an Intel IA64
> machine. I have used this many times for AMBER 9 with much
> success. I suspect that gfortran on IA64 has had very little
> if any tweaking to make it produce highly optimized code
> since very few people have access to Itanium machines.
>
> With ifort installed and MKL you should be able to do the
> following. Adjusting for your paths etc:
>
> source /opt/intel/compiler9.0.032/bin/iccvars.sh
> source /opt/intel/compiler9.0.032/bin/ifortvars.sh
> export MKL_HOME=/opt/intel/mkl-8.0.019/
> export AMBERHOME=/usr/local/amber9_serial/
> cd $AMBERHOME/src/
> ./configure -static ifort_ia64
> make
> cd ../test
> make
>
> Then you can build a parallel version.
>
> export AMBERHOME=/usr/local/amber9_mpi/
> export MPI_HOME= /usr/local/apps/mpich-gm-1.2.6-intel9032/
> cd $AMBERHOME/src/
> ./configure -mpich ifort_ia64
> make
> cd ../test
> export DO_PARALLEL='mpirun -np 2'
> make test.parallel
> cd ../src/pmemd/
> ./configure sgi_altix ifort mpich_gm
> > enter directories for mpi
> make
> make install
> cd $AMBERHOME/test/
> make test.pmemd
>
> You might need to hack the config.h files a little bit but
> this approach should generally work (even though you are
> using sgi_altix for the machine type for PMEMD it should
> work on non-altix IA64 boxes).
>
> Good luck,
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | 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.
>
>
>
>
>
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