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
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Received on Fri Oct 11 2019 - 13:30:02 PDT
