Are you able to compile with the GNU compilers? How recent is your fftw3
installation? Perhaps there is one already on the system that the
configure script is reaching out and finding.
On Fri, Oct 11, 2019 at 4:05 PM Margarita I. Bernal-Uruchurtu <mabel.uaem.mx>
wrote:
> Hello,
>
> I've been trying to compile amber18 in a Linux cluster with no success so
> far.
>
> Using intel/17 compilers as:
>
>
> amber18/bin:/opt/software/common/intel/compilers_and_libraries_2017.0.098/linux/bin/intel64/gdb-igfx:/opt/software/common/intel/compilers_and_libraries_2017.0.098/linux/bin/intel64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin)
>
>
> I configure with no problem, and then during the make install, it ends with
> an error after a warning.
>
>
> ipo: warning #11062: /home/SEBOMD/amber18/lib/libfftw3.a is an archive, but
> has no symbols (this can happen if ar is used where xiar is needed)
>
>
> /home/SEBOMD/amber18/lib/librism.a(rism3d_potential_c.o): In function
> `rism3d_potential_c_mp_uvparticlemeshewaldpotentialfortran_':
>
> rism3d_potential_c.F90:(.text+0x172b): undefined reference to
> `fftw_alloc_real'
>
> rism3d_potential_c.F90:(.text+0x173a): undefined reference to
> `fftw_alloc_complex'
>
> rism3d_potential_c.F90:(.text+0x3667): undefined reference to
> `fftw_plan_dft_r2c_3d'
>
> rism3d_potential_c.F90:(.text+0x49aa): undefined reference to
> `fftw_plan_dft_c2r_3d'
>
> rism3d_potential_c.F90:(.text+0x82fb): undefined reference to
> `fftw_execute_dft_r2c'
>
> rism3d_potential_c.F90:(.text+0x9f26): undefined reference to
> `fftw_execute_dft_c2r'
>
> rism3d_potential_c.F90:(.text+0xae6a): undefined reference to
> `fftw_destroy_plan'
>
> rism3d_potential_c.F90:(.text+0xae76): undefined reference to
> `fftw_destroy_plan'
>
> rism3d_potential_c.F90:(.text+0xbc4e): undefined reference to `fftw_free'
>
> rism3d_potential_c.F90:(.text+0xbc5a): undefined reference to `fftw_free'
>
> /home/SEBOMD/amber18/lib/librism.a(rism3d_fft.o): In function
> `rism3d_fft_c_mp_rism3d_fft_new_':
>
> rism3d_fft.F90:(.text+0x7f5): undefined reference to
> `fftw_plan_many_dft_r2c'
>
> rism3d_fft.F90:(.text+0xfa1): undefined reference to
> `fftw_plan_many_dft_c2r'
>
> /home/SEBOMD/amber18/lib/librism.a(rism3d_fft.o): In function
> `rism3d_fft_c_mp_rism3d_fft_destroy_':
>
> rism3d_fft.F90:(.text+0x136a): undefined reference to `fftw_destroy_plan'
>
> rism3d_fft.F90:(.text+0x1383): undefined reference to `fftw_destroy_plan'
>
> /home/SEBOMD/amber18/lib/librism.a(rism3d_fft.o): In function
> `rism3d_fft_c_mp_rlft3i_':
>
> rism3d_fft.F90:(.text+0x1c80): undefined reference to
> `fftw_execute_dft_r2c'
>
> rism3d_fft.F90:(.text+0x2475): undefined reference to
> `fftw_execute_dft_r2c'
>
> rism3d_fft.F90:(.text+0x3347): undefined reference to
> `fftw_execute_dft_c2r'
>
> rism3d_fft.F90:(.text+0x3b3f): undefined reference to
> `fftw_execute_dft_c2r'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `safemem_mp_safemem_realloc_1d_real_':
>
> safemem.F90:(.text+0x98): undefined reference to `fftw_alloc_real'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `safemem_mp_safemem_dealloc_pointer_1d_real_':
>
> safemem.F90:(.text+0x5be): undefined reference to `fftw_free'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `safemem_mp_safemem_realloc_2d_real_':
>
> safemem.F90:(.text+0x71a): undefined reference to `fftw_alloc_real'
>
> /home/dlaage/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `safemem_mp_safemem_dealloc_pointer_2d_real_':
>
> safemem.F90:(.text+0xd37): undefined reference to `fftw_free'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `safemem_mp_safemem_realloc_3d_real_':
>
> safemem.F90:(.text+0xe9a): undefined reference to `fftw_alloc_real'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `safemem_mp_safemem_dealloc_pointer_3d_real_':
>
> safemem.F90:(.text+0x16f9): undefined reference to `fftw_free'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `safemem_mp_safemem_realloc_4d_real_':
>
> safemem.F90:(.text+0x18b3): undefined reference to `fftw_alloc_real'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `safemem_mp_safemem_dealloc_pointer_4d_real_':
>
> safemem.F90:(.text+0x2405): undefined reference to `fftw_free'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `safemem_mp_safemem_realloc_5d_real_interp_':
>
> safemem.F90:(.text+0x2560): undefined reference to `fftw_alloc_real'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `safemem_mp_safemem_realloc_5d_real_':
>
> safemem.F90:(.text+0x35a2): undefined reference to `fftw_alloc_real'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `safemem_mp_safemem_dealloc_pointer_5d_real_':
>
> safemem.F90:(.text+0x42bd): undefined reference to `fftw_free'
>
> /home/SEBOMD/amber18/lib/librism.a(rism3d_closure_c.o): In function
> `rism3d_closure_c_mp_particlemeshewaldforce_':
>
> rism3d_closure_c.F90:(.text+0x19cc1): undefined reference to
> `fftw_plan_dft_r2c_3d'
>
> rism3d_closure_c.F90:(.text+0x1a155): undefined reference to
> `fftw_plan_dft_c2r_3d'
>
> rism3d_closure_c.F90:(.text+0x1a5fc): undefined reference to
> `fftw_execute_dft_r2c'
>
> rism3d_closure_c.F90:(.text+0x1acd0): undefined reference to
> `fftw_execute_dft_c2r'
>
> make[2]: *** [/home/SEBOMD/amber18/bin/sander] Error 1
>
> make[2]: Leaving directory
> `/panfs/panasas/cnt0024/dcp7156/SEBOMD/amber18/AmberTools/src/sander'
>
> make[1]: *** [serial] Error 2
>
> make[1]: Leaving directory
> `/panfs/panasas/cnt0024/dcp7156/SEBOMD/amber18/AmberTools/src'
>
> make: *** [install] Error 2
>
>
> I've also tried with gnu compilers. I'm using gcc/4.9.4 The configuration
> ends with no errors, and then, during the compilation, there is an error
> that it seems to me it is related to the same library.
>
>
> make[3]: Leaving directory
> `/panfs/panasas/cnt0024/dcp7156/SEBOMD/amber18/AmberTools/src/rism'
>
> gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
> -DHASBZ2 -D__PLUMED_HAS_DLOPEN \
>
> -o Plumed.o Plumed.c
>
> gfortran -DBINTRAJ -DEMIL -fPIC -ffree-form -I../pbsa -I../sqm
> -I../rism -I../../../include -I/home/SEBOMD/amber18/include
> -I/home/SEBOMD/amber18/include -o /home/dlaage/SEBOMD/amber18/bin/sander
> file_io_dat.o constants.o state.o memory_module.o stack.o nose_hoover.o
> nose_hoover_init.o trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o decomp.o
> icosasurf.o egb.o remd.o findmask.o relax_mat.o nmr.o multitmd.o
> multisander.o sander.o trajene.o cshf.o nmrcal.o mtmdcall.o pearsn.o
> printe.o runmin.o rdparm.o sander_lib.o mdread.o locmem.o runmd.o relaxmd.o
> quench.o getcor.o degcnt.o decnvh.o fastwt.o parallel.o shake.o rattle.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
> pol_gauss.o ew_recip.o pcshift.o align.o csa.o rfree.o rgroup.o amopen.o
> debug.o ew_recip_reg.o ew_handle_dips.o ew_bndpol.o ew_dipole_recip.o
> mexit.o new_time.o extra_pts.o thermo_int.o matinv.o assert.o erfcfun.o
> sinr_t.o md_scheme.o constantph.o constante.o prn_dipoles.o ips.o sglds.o
> iwrap2.o emap.o emil.o mdin_emil_dat.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
> ../rism/amber_rism_interface.SANDER.o AmberNetcdf.o bintraj.o binrestart.o
> spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o linear_response.o
> molecule.o xref.o dssp.o charmm.o crg_reloc.o amd.o scaledMD.o barostats.o
> random.o les.o music_module.o abfqmmm_module.o qm_mm.o qm_ewald.o
> qmmm_vsolv.o qm2_extern_util_module.o qm2_extern_module.o
> qm2_extern_adf_module.o qm2_read_adf_results.o KFReader.o ArrayList.o
> qm2_extern_gms_module.o qm2_extern_tc_module.o qm2_extern_gau_module.o
> qm2_extern_orc_module.o qm2_extern_nw_module.o qm2_extern_qc_module.o
> qm2_extern_mrcc_module.o qm2_extern_genmpi_module.o qmmm_adaptive_module.o
> prn_qmmm_dipole.o sebomd_module.o sebomd_arrays.o \
>
> pimd_vars.o pimd_force.o pimd_init.o cmd_vars.o cmd_matrix.o
> lscivr_vars.o lsc_init.o lsc_xp.o force.o -L/home/SEBOMD/amber18/lib -lsqm
> \
>
> nfe-abmd-hooks.o nfe-bbmd-ctxt.o nfe-bbmd-hooks.o nfe-colvar.o
> nfe-colvar-math.o nfe-colvar-type.o nfe-colvar-utils.o nfe-constants.o
> nfe-cv-ANGLE.o nfe-cv-COM_ANGLE.o nfe-cv-COM_DISTANCE.o
> nfe-cv-COM_TORSION.o nfe-cv-COS_OF_DIHEDRAL.o nfe-cv-DISTANCE.o
> nfe-cv-HANDEDNESS.o nfe-cv-LCOD.o nfe-cv-MULTI_RMSD.o nfe-cv-N_OF_BONDS.o
> nfe-cv-N_OF_STRUCTURES.o nfe-cv-R_OF_GYRATION.o nfe-cv-TORSION.o
> nfe-pmd-hooks.o nfe-rmsd.o nfe-sander-hooks.o nfe-sander-proxy.o
> nfe-stsm-hooks.o nfe-cv-PCA.o nfe-read-pca.o nfe-cv-SIN_OF_DIHEDRAL.o
> nfe-cv-PAIR_DIHEDRAL.o nfe-cv-PATTERN_DIHEDRAL.o nfe-cv-DF_COM_DISTANCE.o
> nfe-smd-hooks.o nfe-umbrella.o nfe-utils.o nfe-value.o mt19937.o
> xray_fftpack.o xray_FFT.o xray_fourier.o xray_globals.o xray_interface.o
> xray_real_space.o xray_reciprocal_space.o xray_utils.o \
>
> -lFpbsa ../lib/nxtsec.o /home/SEBOMD/amber18/lib/libemil.a -lstdc++ \
>
> ../sebomd/sebomd.a \
>
> ../lib/sys.a /home/SEBOMD/amber18/lib/libnetcdff.a
> /home/SEBOMD/amber18/lib/libnetcdf.a \
>
> -lrism /home/SEBOMD/amber18/lib/libfftw3.a -larpack -llapack -lblas
> -lxblas-amb \
>
> Plumed.o -ldl -Wl,-export-dynamic
>
> /home/SEBOMD/amber18/lib/librism.a(rism3d_potential_c.o): In function
> `__rism3d_potential_c_MOD_uvparticlemeshewaldpotentialfortran':
>
> rism3d_potential_c.F90:(.text.unlikely+0x33c): undefined reference to
> `fftw_alloc_real'
>
> rism3d_potential_c.F90:(.text.unlikely+0x34c): undefined reference to
> `fftw_alloc_complex'
>
> rism3d_potential_c.F90:(.text.unlikely+0x10a6): undefined reference to
> `fftw_plan_dft_r2c_3d'
>
> rism3d_potential_c.F90:(.text.unlikely+0x1138): undefined reference to
> `fftw_plan_dft_c2r_3d'
>
> rism3d_potential_c.F90:(.text.unlikely+0x15d8): undefined reference to
> `fftw_execute_dft_r2c'
>
> rism3d_potential_c.F90:(.text.unlikely+0x1d97): undefined reference to
> `fftw_execute_dft_c2r'
>
> rism3d_potential_c.F90:(.text.unlikely+0x1e40): undefined reference to
> `fftw_destroy_plan'
>
> rism3d_potential_c.F90:(.text.unlikely+0x1e4c): undefined reference to
> `fftw_destroy_plan'
>
> rism3d_potential_c.F90:(.text.unlikely+0x2490): undefined reference to
> `fftw_free'
>
> rism3d_potential_c.F90:(.text.unlikely+0x249d): undefined reference to
> `fftw_free'
>
> /home/SEBOMD/amber18/lib/librism.a(rism3d_fft.o): In function
> `__rism3d_fft_c_MOD_rlft3i':
>
> rism3d_fft.F90:(.text+0x84c): undefined reference to `fftw_execute_dft_c2r'
>
> rism3d_fft.F90:(.text+0xb73): undefined reference to `fftw_execute_dft_r2c'
>
> rism3d_fft.F90:(.text+0xe20): undefined reference to `fftw_execute_dft_r2c'
>
> rism3d_fft.F90:(.text+0x1019): undefined reference to
> `fftw_execute_dft_c2r'
>
> /home/SEBOMD/amber18/lib/librism.a(rism3d_fft.o): In function
> `__rism3d_fft_c_MOD_rism3d_fft_destroy':
>
> rism3d_fft.F90:(.text+0x10bd): undefined reference to `fftw_destroy_plan'
>
> rism3d_fft.F90:(.text+0x10d2): undefined reference to `fftw_destroy_plan'
>
> /home/SEBOMD/amber18/lib/librism.a(rism3d_fft.o): In function
> `__rism3d_fft_c_MOD_rism3d_fft_new':
>
> rism3d_fft.F90:(.text+0x15f1): undefined reference to
> `fftw_plan_many_dft_r2c'
>
> rism3d_fft.F90:(.text+0x18da): undefined reference to
> `fftw_plan_many_dft_c2r'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `__safemem_MOD_safemem_dealloc_pointer_5d_real':
>
> safemem.F90:(.text+0xd9a): undefined reference to `fftw_free'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `__safemem_MOD_safemem_dealloc_pointer_4d_real':
>
> safemem.F90:(.text+0xe76): undefined reference to `fftw_free'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `__safemem_MOD_safemem_dealloc_pointer_3d_real':
>
> safemem.F90:(.text+0xf52): undefined reference to `fftw_free'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `__safemem_MOD_safemem_dealloc_pointer_2d_real':
>
> safemem.F90:(.text+0x102e): undefined reference to `fftw_free'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `__safemem_MOD_safemem_dealloc_pointer_1d_real':
>
> safemem.F90:(.text+0x10fa): undefined reference to `fftw_free'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `__safemem_MOD_safemem_realloc_5d_real':
>
> safemem.F90:(.text+0x293d): undefined reference to `fftw_alloc_real'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `__safemem_MOD_safemem_realloc_4d_real':
>
> safemem.F90:(.text+0x327c): undefined reference to `fftw_alloc_real'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `__safemem_MOD_safemem_realloc_3d_real':
>
> safemem.F90:(.text+0x3899): undefined reference to `fftw_alloc_real'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `__safemem_MOD_safemem_realloc_2d_real':
>
> safemem.F90:(.text+0x3dad): undefined reference to `fftw_alloc_real'
>
> /home//SEBOMD/amber18/lib/librism.a(safemem.o): In function
> `__safemem_MOD_safemem_realloc_1d_real':
>
> safemem.F90:(.text+0x40dd): undefined reference to `fftw_alloc_real'
>
> /home/SEBOMD/amber18/lib/librism.a(safemem.o):safemem.F90:(.text+0x5051):
> more undefined references to `fftw_alloc_real' follow
>
> /home/SEBOMD/amber18/lib/librism.a(rism3d_closure_c.o): In function
> `__rism3d_closure_c_MOD_particlemeshewaldforce':
>
> rism3d_closure_c.F90:(.text+0x1ed7): undefined reference to
> `fftw_plan_dft_r2c_3d'
>
> rism3d_closure_c.F90:(.text+0x1f6b): undefined reference to
> `fftw_plan_dft_c2r_3d'
>
> rism3d_closure_c.F90:(.text+0x1fde): undefined reference to
> `fftw_execute_dft_r2c'
>
> rism3d_closure_c.F90:(.text+0x2102): undefined reference to
> `fftw_execute_dft_c2r'
>
> collect2: error: ld returned 1 exit status
>
> make[2]: *** [/home/SEBOMD/amber18/bin/sander] Error 1
>
> make[2]: Leaving directory
> `/panfs/panasas/cnt0024/dcp7156/SEBOMD/amber18/AmberTools/src/sander'
>
> make[1]: *** [serial] Error 2
>
> make[1]: Leaving directory
> `/panfs/panasas/cnt0024/dcp7156/SEBOMD/amber18/AmberTools/src'
>
> make: *** [install] Error 2
>
>
> I'd very much appreciate your help in finding a way to solve this problem.
>
>
> Best,
>
>
> Margarita
>
>
>
> Science is built with facts, as a house is with stones, but a collection of
> facts is no more a science than a heap of stones is a house. - Henri
> Poincaré
> °°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
> Margarita I. Bernal-Uruchurtu
> Centro de Investigaciones Química, UAEM
> +52.777.329.7000 ext 6003
> mabel.uaem.mx
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Oct 11 2019 - 13:30:02 PDT
