AMBER Archive (2008)

Subject: AMBER: Installing PMEMD with Amber10

From: Justin A. Lemkul (jalemkul_at_vt.edu)
Date: Thu May 29 2008 - 08:23:05 CDT

Hello all,

I am installing Amber10 on our cluster (Apple Xserve G5 nodes). The OS on the
nodes is Yellowdog Linux. The installation of AmberTools and Amber10 proceeded
with no problems, but I am having some difficulty installing PMEMD. I have
installed lam-7.1.3 that came with Amber10, and am specifying the following:

./configure macosx_ppc gfortran lam pubfft nobintraj

The config.h file is based on one that I found online
(http://amberonmac.blogspot.com/2008_03_01_archive.html), and is as follows:

MATH_DEFINES =
MATH_LIBS =
FFT_DEFINES = -DPUBFFT
FFT_INCLUDE =
FFT_LIBS =
NETCDF_HOME =
NETCDF_DEFINES =
NETCDF_MOD =
NETCDF_LIBS =
MPI_HOME = /home/rdiv1001/amber10
MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI
MPI_INCLUDE = -I$(MPI_HOME)/include
MPI_LIBDIR = $(MPI_HOME)/lib
MPI_LIBS = -L$(MPI_LIBDIR) -llamf77mpi -lmpi -llam -ldl -lpthread
DIRFRC_DEFINES = -DDIRFRC_COMTRANS -DDIRFRC_EFS
CPP = /usr/bin/cpp
CPPFLAGS = -traditional -P
F90_DEFINES = -DFFTLOADBAL_2PROC

F90 = gfortran
MODULE_SUFFIX = mod
F90FLAGS = -c
F90_OPT_DBG = -g -ftrace=full
F90_OPT_LO = -O0
F90_OPT_MED = -O2
F90_OPT_HI = -O3
F90_OPT_DFLT = $(F90_OPT_HI)

CC = gcc
CFLAGS = -DDBL_C_UNDERSCORE

LOAD = gfortran
LOADFLAGS =
LOADLIBS =

When I proceed with 'make install,' I get the following error:

gfortran -c -O3 erfcfun.f90
gfortran -o pmemd gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o
mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o inpcrd_dat.o dynamics_dat.o img.o
parallel_dat.o parallel.o gb_parallel.o pme_direct.o pme_recip_dat.o
pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o pme_blk_fft.o pme_fft_dat.o
fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o nb_exclusions.o cit.o
dynamics.o bonds.o angles.o dihedrals.o extra_pnts_nb14.o runmd.o loadbal.o
shake.o prfs.o mol_list.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 pme_alltasks_setup.o pme_setup.o ene_frc_splines.o
gb_alltasks_setup.o nextprmtop_section.o -L/home/rdiv1001/amber10/lib
-llamf77mpi -lmpi -llam -ldl -lpthread
prmtop_dat.o: In function `__prmtop_dat_mod__bcast_amber_prmtop_dat':
prmtop_dat.f90:(.text+0x10bc): undefined reference to `get_bytesize_'
prmtop_dat.f90:(.text+0x1124): undefined reference to `get_bytesize_'
prmtop_dat.f90:(.text+0x118c): undefined reference to `get_bytesize_'
extra_pnts_nb14.o: In function
`__extra_pnts_nb14_mod__bcast_extra_pnts_nb14_dat':
extra_pnts_nb14.f90:(.text+0x1bf8): undefined reference to `get_bytesize_'
loadbal.o: In function `__loadbal_mod__start_loadbal_timer':
loadbal.f90:(.text+0xa0): undefined reference to `get_wall_time_'
loadbal.o: In function `__loadbal_mod__update_loadbal_timer':
loadbal.f90:(.text+0xe0): undefined reference to `get_wall_time_'
runmin.o: In function `__runmin_mod__printe':
runmin.f90:(.text+0x5fc): undefined reference to `get_wall_time_'
runmin.f90:(.text+0xa94): undefined reference to `get_wall_time_'
runfiles.o: In function `__runfiles_mod__prntmd':
runfiles.f90:(.text+0x2488): undefined reference to `get_wall_time_'
pmemd.o: In function `MAIN__':
pmemd.f90:(.text+0xd8): undefined reference to `unlimit_stack_'
collect2: ld returned 1 exit status
make[1]: *** [pmemd] Error 1
make[1]: Leaving directory `/home/rdiv1001/amber10/src/pmemd/src'
make: *** [install] Error 2

I would be very grateful if anyone could give me any hints on how to fix this,
I've been trying for quite some time!

Thanks for your attention.

-Justin

========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul_at_vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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