Read the README under amber9/src/pmemd. In particular, look at the section
on "Beware of Nonstandard MPI Library Installations". Problems generally
boil down to 1) a problem with compiler installation and environment setup,
and/or 2) a problem with mpi installation and environment setup, and/or 3) a
problem with some linux other than redhat, or some version we didn't get to
test on, or something nonstandard about the way that linux is set up (in
terms of library layout, 32 vs 64 bit executable grief, etc.). There are
so many issues on so many different systems that a truly automated install
really is not a real possibility - this fact compounded by the fact that
people are often compiling on some supercomputer frontend with the intent to
run on a non-visible backend, so the system really can't autoconfigure. So
basically, you have to know a bit about the various pieces that go together
to make a running executable. Also look at the amber.scripps.edu webpage
for additional info. In this case the first thing I would do is issue a
'mpif77 -link_info' and see if the suggested library list differs from the
mpi libraries being specified in config.h (but this may instead be a change
in the compiler - I am not sure by just glancing).
Regards - Bob Duke
----- Original Message -----
From: "Sampath Koppole" <sampathkoppole.yahoo.com>
To: <amber.scripps.edu>
Sent: Thursday, December 06, 2007 9:42 AM
Subject: AMBER: PMEMD compilation problems !!
> Hello there,
> I am trying to install PMEMD but the installation
> fails with the follwing message:
>
> -------------------------------------------------------------------------------------------------
> camm25> make install
> cd src && make install
> make[1]: Entering directory
> `/netfs/people/camm/kopposa1/amber9/src/pmemd/src'
> cpp -traditional -P
> -I/usr/people/camm/kopposa1/mpich2-1.0.6/include
> -DPUBFFT -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_EFS
> -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> -DFFTLOADBAL_2PROC gbl_constants.fpp gbl_constants.f90
> .....
> .....
> .....
>
> ifort -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/usr/prog/intel/mkl/100011/lib/em64t -lmkl_em64t
> -lpthread -L/usr/people/camm/kopposa1/mpich2-1.0.6/lib
> -lmpich -lrt -luuid -lpthread -limf -lsvml
> -Wl,-rpath=:/usr/people/camm/kopposa1/gcc/lib64:/usr/prog/msi/LicensePack/linux/lib:/usr/prog/msi/FELIX2004/Linux_2_Intel_32/lib:/usr/prog/msi/2000.3L/Linux_2_Intel_32/biosymso:/usr/prog/msi/CAT470/irix6m3/biosymso:/usr/prog/mdl/isis213/lib:/usr/prog/mdl/ih33/bin:/usr/prog/oracle/Linux/9.2.0/lib:/usr/prog/sge/60u3/lib/lx24-amd64:/usr/scnpr/intel/mkl/90/lib/32:/usr/scnpr/intel/mpi/30/lib:/usr/scnpr/intel/fc/91045/lib
> IPO link: can not find -luuid
> ifort: error: problem during multi-file optimization
> compilation (code 1)
> make[1]: *** [pmemd] Error 1
> make[1]: Leaving directory
> `/netfs/people/camm/kopposa1/amber9/src/pmemd/src'
> make: *** [install] Error 2
> -----------------------------------------------------------
>
> For your information, I have also attached the
> config.h file that was created with "./configure
> linux_em64t ifort mpich2"
>
> ---------------------------------------------------------------------
> MATH_DEFINES =
> MATH_LIBS =
> IFORT_RPATH =
> :/usr/people/camm/kopposa1/gcc/lib64:/usr/prog/msi/LicensePack/linux/lib:/usr/prog/msi/FELIX2004/Linux_2_Intel_32/lib:/usr/prog/msi/2000.3L/Linux_2_Intel_32/biosymso:/usr/prog/msi/CAT470/irix6m3/biosymso:/usr/prog/mdl/isis213/lib:/usr/prog/mdl/ih33/bin:/usr/prog/oracle/Linux/9.2.0/lib:/usr/prog/sge/60u3/lib/lx24-amd64:/usr/prog/intel/fce/101008/lib/:/usr/prog/intel/mkl/100011/lib/64:/usr/prog/intel/mkl/100011/lib/em64t
> MATH_DEFINES = -DMKL
> MATH_LIBS = -L/usr/prog/intel/mkl/100011/lib/em64t
> -lmkl_em64t -lpthread
> FFT_DEFINES = -DPUBFFT
> FFT_INCLUDE =
> FFT_LIBS =
> NETCDF_HOME =
> NETCDF_DEFINES =
> NETCDF_MOD =
> NETCDF_LIBS =
> MPI_HOME = /usr/people/camm/kopposa1/mpich2-1.0.6
> MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI
> MPI_INCLUDE = -I$(MPI_HOME)/include
> MPI_LIBDIR = $(MPI_HOME)/lib
> MPI_LIBS = -L$(MPI_LIBDIR) -lmpich -lrt -luuid
> -lpthread
> DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_COMTRANS
> -DDIRFRC_NOVEC
> CPP = cpp
> CPPFLAGS = -traditional -P
> F90_DEFINES = -DFFTLOADBAL_2PROC
>
> F90 = ifort
> MODULE_SUFFIX = mod
> F90FLAGS = -c -auto
> F90_OPT_DBG = -g -traceback
> F90_OPT_LO = -tpp7 -O0
> F90_OPT_MED = -tpp7 -O2
> F90_OPT_HI = -tpp7 -xW -ip -O3
> F90_OPT_DFLT = $(F90_OPT_HI)
>
> CC = gcc
> CFLAGS =
>
> LOAD = ifort
> LOADFLAGS =
> LOADLIBS = -limf -lsvml -Wl,-rpath=$(IFORT_RPATH)
>
> ------------------------------------------------------------------
> FYI:
> 1) I have MPICH2 installation compiled with the same
> ifort compiler that I m using to compile pmemd
>
> 2) Same Ifort compiler was used to compile parallel
> Sander (Sander.MPI) which went quite smoothly without
> any problems.
>
> Thanks a lot for your help,
> Cheers,
> Sampath
>
>
>
> ____________________________________________________________________________________
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Received on Sun Dec 09 2007 - 06:07:26 PST
