AMBER Archive (2008)

Subject: Re: AMBER: Installing PMEMD with Amber10

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu May 29 2008 - 09:44:38 CDT

Okay, I really don't support this stuff (gfortran or the mac for that
matter - I don't have access to any of this mac stuff, and don't see the
point of using pmemd with a slower compiler). However, the error msg you
have here basically says that the fortran code expects the c routine names
to be decorated with a single underscore. You have specified CFLAGS
= -DDBL_C_UNDERSCORE, which causes the c code to export names with double
trailing underscores, so the next thing I would try is edit your config.h,
changing the CFLAGS entry to just
CFLAGS =
Then do a make clean and a make and see what happens. And please run the
test suite when you get done with all this - I can't guarantee that any of
this code actually works as advertised, even if it compiles and links. I
don't really know what the story here is on gfortran on the mac. The web
page references g95/gfortran, but then lists the fortran compiler as g95,
says something about intel; sorry, but I have no idea what the compiler
really is here (I am presuming it is really gfortran, that the script was
really for g95, but different name mangling conventions occur with gfortran,
that the chip is really intel, or you would be using the ibm compiler, etc.
etc.). Perhaps the guys that support "amberonmac" will comment?
Good luck - Bob Duke

----- Original Message -----
From: "Justin A. Lemkul" <jalemkul_at_vt.edu>
To: <amber_at_scripps.edu>
Sent: Thursday, May 29, 2008 9:23 AM
Subject: AMBER: Installing PMEMD with Amber10

>
> 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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