AMBER Archive (2008)

Subject: Re: AMBER: Installing PMEMD with Amber10

From: Justin A. Lemkul (jalemkul_at_vt.edu)
Date: Thu May 29 2008 - 14:12:26 CDT

Thanks for the tip. I got PMEMD to compile and install without any complaints
after making the change you suggested. However, I have been unable to test the
installation as of yet. I can run all the serial tests interactively on the
head node, but anything in parallel requires submission to a queuing system, so
I'm waiting my turn. I will report back if anything is amiss.

Thanks again,
Justin

Quoting Robert Duke <rduke_at_email.unc.edu>:

> 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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> >
>
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========================================

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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