AMBER Archive (2008)

Subject: AMBER: PMEND 9 compilation problems

From: Nick Holway (nick.holway_at_gmail.com)
Date: Tue Jul 29 2008 - 11:04:36 CDT

Hi,

I'm trying to compile PMEND 9 on 64 bit Rocks 5.0 (ie Centos 5.1) on the
head node which is a HP BL265c blade with an Opteron 2214 CPU. I'm using the
Intel ifort fortran v10 compiler with MKL 9.1. GCC is 4.1.2.

The error I'm seeing is:

ifort -o pmemd gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o
parallel_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o inpcrd_dat.o
dynamics_dat.o img.o parallel.o pme_direct.o pme_recip.o pme_fft.o fft1d.o
bspline.o pme_force.o pbc.o nb_pairlist.o cit.o dynamics.o bonds.o angles.o
dihedrals.o runmd.o loadbal.o shake.o runmin.o constraints.o axis_optimize.o
gb_ene.o veclib.o gb_force.o timers.o pmemd_lib.o runfiles.o file_io.o
bintraj.o pmemd_clib.o pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o
nmr_lib.o get_cmdline.o master_setup.o alltasks_setup.o pme_setup.o
ene_frc_splines.o nextprmtop_section.o
-L/usr/prog/fortran/intel/mkl/9.1//lib/em64t -lmkl_em64t -lpthread -limf
-lsvml
-Wl,-rpath=/usr/prog/jdk/jdk1.5.0_07/jre/lib/i386/server:/usr/prog/sge/gridengine/lib/lx26-amd64:/opt/gridengine/lib/lx26-amd64:/opt/gridengine/lib/lx26-amd64:/usr/prog/fortran/intel/x86_64/lib:/usr/prog/fortran/intel/mkl/9.1/lib/em64t:/usr/prog/eclipse/rac/lib:/usr/prog/openbabel/2.0.2/lib:/usr/prog/tripos/EAInventor_v4.3_Linux/lib
gb_ene.o: In function `gb_ene_mod_mp_calc_born_radii_':
gb_ene.f90:(.text+0x31f): undefined reference to `vdinvsqrt_'
gb_ene.f90:(.text+0x6bf): undefined reference to `vdinv_'
gb_ene.f90:(.text+0x6dc): undefined reference to `vdinv_'
gb_ene.f90:(.text+0xb21): undefined reference to `vdln_'
gb_ene.f90:(.text+0xb3e): undefined reference to `vdln_'
gb_ene.o: In function `gb_ene_mod_mp_gb_ene_':
gb_ene.f90:(.text+0x2758): undefined reference to `vdinvsqrt_'
gb_ene.f90:(.text+0x2b12): undefined reference to `vdinv_'
gb_ene.f90:(.text+0x2b2f): undefined reference to `vdinv_'
gb_ene.f90:(.text+0x2f8c): undefined reference to `vdln_'
gb_ene.f90:(.text+0x2fa9): undefined reference to `vdln_'
gb_ene.f90:(.text+0x4d5f): undefined reference to `vdinv_'
gb_ene.f90:(.text+0x4fe0): undefined reference to `vdexp_'
gb_ene.f90:(.text+0x539c): undefined reference to `vdinvsqrt_'
gb_ene.f90:(.text+0x53ce): undefined reference to `vdinv_'
gb_ene.f90:(.text+0x5531): undefined reference to `vdexp_'
gb_ene.f90:(.text+0x554b): undefined reference to `vdinvsqrt_'
gb_ene.f90:(.text+0x6229): undefined reference to `vdinvsqrt_'
gb_ene.f90:(.text+0x645d): undefined reference to `vdinv_'
gb_ene.f90:(.text+0x6476): undefined reference to `vdinv_'
gb_ene.f90:(.text+0x66a2): undefined reference to `vdln_'
make[1]: *** [pmemd] Error 1
make[1]: Leaving directory `/tmp/nick/amber9/src/pmemd/src'
make: *** [all] Error 2

This is my config.h:

MATH_DEFINES =
MATH_LIBS =
IFORT_RPATH =
/usr/prog/jdk/jdk1.5.0_07/jre/lib/i386/server:/usr/prog/sge/gridengine/lib/lx26-amd64:/opt/gridengine/lib/lx26-amd64:/opt/gridengine/lib/lx26-amd64:/usr/prog/fortran/intel/x86_64/lib:/usr/prog/fortran/intel/mkl/9.1/lib/em64t:/usr/prog/eclipse/rac/lib:/usr/prog/openbabel/2.0.2/lib:/usr/prog/tripos/EAInventor_v4.3_Linux/lib
MATH_DEFINES = -DMKL
MATH_LIBS = -L/usr/prog/fortran/intel/mkl/9.1//lib/em64t -lmkl_em64t
-lpthread
FFT_DEFINES = -DPUBFFT
FFT_INCLUDE =
FFT_LIBS =
NETCDF_HOME =
NETCDF_DEFINES =
NETCDF_MOD =
NETCDF_LIBS =
MPI_DEFINES =
MPI_INCLUDE =
MPI_LIBDIR =
MPI_LIBS =
DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
CPP = /lib/cpp
CPPFLAGS = -traditional -P
F90_DEFINES = -DFFTLOADBAL_2PROC

F90 = ifort
MODULE_SUFFIX = mod
F90FLAGS = -c -auto
F90_OPT_DBG = -g -traceback
F90_OPT_LO = -tpp7 -O0
F90_OPT_MED = -tpp7 -O2
F90_OPT_HI = -tpp7 -xW -ip -O3
F90_OPT_DFLT = $(F90_OPT_HI)

CC = gcc
CFLAGS =

LOAD = ifort
LOADFLAGS =
LOADLIBS = -limf -lsvml -Wl,-rpath=$(IFORT_RPATH)

Thanks in advance for any help.

Nick

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