AMBER Archive (2008)

Subject: AMBER: amber 9 compilation error with mvapich and intel compilers

From: Amit Bajaj (amit_at_dmsystems.in)
Date: Sat Dec 20 2008 - 08:17:03 CST

Hi

We are trying to compile Amber 9 (sander) with mvapich(we got it as part of mellanox OpenFabrics Enterprise Distribution for Linux on RHEL 4(64 bit) on Intel 5400 series processor

we are using intel compilers 10.x and getting the following error,

make[2]: Leaving directory `/amber9/src/lmod'
cd ../lmod; cp lmodprmtop ../../exe; chmod 0755 ../../exe/lmodprmtop
ifort -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 m!
 mt!
sb_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_externals!
 hi!
ft.o qm2_dftb_fermi.o qm2_dftb_forces.o qm2_dftb_gamma.o qm2_dftb_
b.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 ../netcdf/lib/libnetcdf.a -L/usr/lib64 -L/usr/mpi/intel/mvapich-1.0.1/lib/shared -L/usr/mpi/intel/mvapich-1.0.1/lib -lmpichf90nc -lmpichfarg -lmpich -L/usr/lib64 -libverbs -libumad -libcommon -lpthread -lpthread -lrt
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(viainit.o)(.text+0x197b): In function `MPID_VIA_Init':
: warning: Using 'gethostbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/usr/lib64/libc.a(malloc.o)(.text+0x1880): In function `free':
: multiple definition of `free'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o)(.text+0xb76): first defined here
ld: Warning: size of symbol `free' changed from 302 in /usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o) to 255 in /usr/lib64/libc.a(malloc.o)
/usr/lib64/libc.a(malloc.o)(.text+0x38f0): In function `malloc':
: multiple definition of `malloc'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o)(.text+0xca4): first defined here
ld: Warning: size of symbol `malloc' changed from 374 in /usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o) to 461 in /usr/lib64/libc.a(malloc.o)
/usr/lib64/libc.a(malloc.o)(.text+0x3fd0): In function `realloc':
: multiple definition of `realloc'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o)(.text+0x93e): first defined here
ld: Warning: size of symbol `realloc' changed from 568 in /usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o) to 927 in /usr/lib64/libc.a(malloc.o)
/usr/lib64/libc.a(malloc.o)(.text+0x4c0): In function `_int_new_arena':
: multiple definition of `_int_new_arena'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o)(.text+0x3f0): first defined here
ld: Warning: size of symbol `_int_new_arena' changed from 772 in /usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o) to 224 in /usr/lib64/libc.a(malloc.o)
/usr/lib64/libc.a(malloc.o)(.text+0xff0): In function `_int_free':
: multiple definition of `_int_free'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o)(.text+0x22cc): first defined here
ld: Warning: size of symbol `_int_free' changed from 1012 in /usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o) to 1897 in /usr/lib64/libc.a(malloc.o)
/usr/lib64/libc.a(malloc.o)(.text+0x1980): In function `_int_malloc':
: multiple definition of `_int_malloc'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o)(.text+0xe1a): first defined here
ld: Warning: size of symbol `_int_malloc' changed from 4520 in /usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o) to 3581 in /usr/lib64/libc.a(malloc.o)
/usr/lib64/libc.a(malloc.o)(.text+0x2860): In function `_int_memalign':
: multiple definition of `_int_memalign'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o)(.text+0x6f4): first defined here
ld: Warning: size of symbol `_int_memalign' changed from 494 in /usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o) to 524 in /usr/lib64/libc.a(malloc.o)
/usr/lib64/libc.a(malloc.o)(.text+0x2a70): In function `_int_valloc':
: multiple definition of `_int_valloc'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o)(.text+0x3d5e): first defined here
ld: Warning: size of symbol `_int_valloc' changed from 416 in /usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o) to 71 in /usr/lib64/libc.a(malloc.o)
/usr/lib64/libc.a(malloc.o)(.text+0x2c30): In function `_int_realloc':
: multiple definition of `_int_realloc'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o)(.text+0x1fc2): first defined here
ld: Warning: size of symbol `_int_realloc' changed from 778 in /usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o) to 1273 in /usr/lib64/libc.a(malloc.o)
/usr/lib64/libc.a(malloc.o)(.text+0x4370): In function `__malloc_check_init':
: multiple definition of `__malloc_check_init'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o)(.text+0x60c0): first defined here
ld: Warning: size of symbol `__malloc_check_init' changed from 144 in /usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(malloc.o) to 164 in /usr/lib64/libc.a(malloc.o)
/usr/lib64/libibverbs.a(src_libibverbs_la-init.o)(.text+0xdb): In function `load_driver':
: warning: Using 'dlopen' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(viapriv.o)(.text+0x155): In function `viadev_ext_sendq_send':
: undefined reference to `prepare_coalesced_pkt'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(cancel.o)(.text+0x83): In function `MPI_Cancel':
: undefined reference to `MPID_SendCancel'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(cancel.o)(.text+0x135): In function `MPI_Cancel':
: undefined reference to `MPID_SendCancel'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(waitall.o)(.text+0x8f): In function `MPI_Waitall':
: undefined reference to `MPID_SendComplete'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(waitall.o)(.text+0x160): In function `MPI_Waitall':
: undefined reference to `MPID_SendComplete'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(waitany.o)(.text+0x131): In function `MPI_Waitany':
: undefined reference to `MPID_SendIcomplete'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(waitany.o)(.text+0x3f6): In function `MPI_Waitany':
: undefined reference to `MPID_SendIcomplete'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(viasend.o)(.text+0x10a): In function `MPID_VIA_eager_send':
: undefined reference to `eager_coalesce'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(mpid_hsend.o)(.text+0xa0): In function `MPID_IssendDatatype':
: undefined reference to `MPID_IssendContig'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(mpid_hsend.o)(.text+0x14f): In function `MPID_IssendDatatype':
: undefined reference to `MPID_IssendContig'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(mpid_hsend.o)(.text+0x20a): In function `MPID_IsendDatatype':
: undefined reference to `MPID_IsendContig'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(mpid_hsend.o)(.text+0x2f2): In function `MPID_IsendDatatype':
: undefined reference to `MPID_IsendContig'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(mpid_hsend.o)(.text+0x3d9): In function `MPID_SendDatatype':
: undefined reference to `MPID_SendContig'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(mpid_hsend.o)(.text+0x482): In function `MPID_SendDatatype':
: undefined reference to `MPID_SendContig'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(testall.o)(.text+0x72): In function `MPI_Testall':
: undefined reference to `MPID_SendIcomplete'
/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(testall.o)(.text+0x4ac): In function `MPI_Testall':
: undefined reference to `MPID_SendIcomplete'
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory `/amber9/src/sander'
make: *** [parallel] Error 2

please guide,how to setup correct environment and right config.h,
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