AMBER Archive (2008)

Subject: Re: AMBER: Installing PMEMD with Amber10

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu May 29 2008 - 15:16:39 CDT

Glad it finally worked! Points for persistence :-) Some of this stuff can
be hard to work out if you don't do it all the time; for me it is often hard
because I don't have access to the system.
Best Regards - Bob

----- Original Message -----
From: "Justin A. Lemkul" <jalemkul_at_vt.edu>
To: <amber_at_scripps.edu>
Sent: Thursday, May 29, 2008 3:12 PM
Subject: Re: AMBER: Installing PMEMD with Amber10

>
> 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
>> > tprmtop_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/
>> >
>> > ========================================
>> > -----------------------------------------------------------------------
>> > The AMBER Mail Reflector
>> > To post, send mail to amber_at_scripps.edu
>> > To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> > to majordomo_at_scripps.edu
>> >
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>>
>
>
>
> ========================================
>
> 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/
>
> ========================================
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu