AMBER Archive (2009)

Subject: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9

From: Kito (kitobhai_at_rediffmail.com)
Date: Wed Nov 25 2009 - 01:11:00 CST

Hi Again,

I was able to compile pmemd by removing the MATH_LIBS and MATH_DEFINES

What does removing the above does to pmemd?

Thanks

Kito

On Wed, 25 Nov 2009 12:10:57 +0530 wrote

>Hi Amber Experts/Users,

I am having difficulties with pmemd installation

My h/w and s/w configuration is

Linux Enterprise, OpenMPI, AMD x86_64, Intel Compiliers

My config.h file is

MATH_DEFINES =

MATH_LIBS =

IFORT_RPATH = /opt/gridengine/lib/lx26-amd64:/usr/lib/perl5/5.8.8

MATH_DEFINES = -DMKL

MATH_LIBS = -L$(MKL_HOME)/lib/em64t -lguide -lpthread

FFT_DEFINES = -DPUBFFT

FFT_INCLUDE =

FFT_LIBS =

NETCDF_HOME =

NETCDF_DEFINES =

NETCDF_MOD =

NETCDF_LIBS =

MPI_HOME = /opt/mpi/openmpi/1.3.3/intel/

MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI

MPI_INCLUDE = -I$(MPI_HOME)/include

MPI_LIBDIR = $(MPI_HOME)/lib

MPI_LIBS = -L$(MPI_LIBDIR)

DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC

CPP = /lib/cpp

CPPFLAGS = -traditional -P

F90_DEFINES = -DFFTLOADBAL_2PROC

F90 = mpif90

MODULE_SUFFIX = mod

F90FLAGS = -c

F90_OPT_DBG = -g -traceback

F90_OPT_LO = -O0

F90_OPT_MED = -O2

F90_OPT_HI = -axWPT -ip -O3

F90_OPT_DFLT = $(F90_OPT_HI)

CC = mpicc

CFLAGS =

LOAD = mpif90

LOADFLAGS =

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

The error I get is

mpif90 -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/opt/intel/Compiler/11.1/046/mkl//lib/em64t -lguide -lpthread -L/opt/mpi/openmpi/1.3.3/intel//lib -limf -lsvml -Wl,-rpath=/opt/gridengine/lib/lx26-amd64:/usr/lib/perl5/5.8.8

gb_ene.o: In function `gb_ene_mod_mp_gb_ene_':

gb_ene.f90:(.text+0x19de): undefined reference to `vdinvsqrt_'

gb_ene.f90:(.text+0x1c93): undefined reference to `vdinv_'

gb_ene.f90:(.text+0x1cac): undefined reference to `vdinv_'

gb_ene.f90:(.text+0x1fde): undefined reference to `vdln_'

gb_ene.f90:(.text+0x1ff7): undefined reference to `vdln_'

gb_ene.f90:(.text+0x3b98): undefined reference to `vdinv_'

gb_ene.f90:(.text+0x3dd9): undefined reference to `vdexp_'

gb_ene.f90:(.text+0x4254): undefined reference to `vdinvsqrt_'

gb_ene.f90:(.text+0x4289): undefined reference to `vdinv_'

gb_ene.f90:(.text+0x43df): undefined reference to `vdexp_'

gb_ene.f90:(.text+0x43fc): undefined reference to `vdinvsqrt_'

gb_ene.f90:(.text+0x5403): undefined reference to `vdinvsqrt_'

gb_ene.f90:(.text+0x55b1): undefined reference to `vdinv_'

gb_ene.f90:(.text+0x55ca): undefined reference to `vdinv_'

gb_ene.f90:(.text+0x57b2): undefined reference to `vdln_'

gb_ene.o: In function `gb_ene_mod_mp_calc_born_radii_':

gb_ene.f90:(.text+0x678a): undefined reference to `vdinvsqrt_'

gb_ene.f90:(.text+0x6a3f): undefined reference to `vdinv_'

gb_ene.f90:(.text+0x6a58): undefined reference to `vdinv_'

gb_ene.f90:(.text+0x6d8a): undefined reference to `vdln_'

gb_ene.f90:(.text+0x6da3): undefined reference to `vdln_'

make[1]: *** [pmemd] Error 1

make[1]: Leaving directory `/opt/apps/amber/9/intel-mkl/src/pmemd/src'

make: *** [all] Error 2

Please help... I have gone through the archives and got similar problems but their said solution's doesnt seems to help.

Thanks in advance

Kito

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