AMBER Archive (2009)

Subject: Re: Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9

From: Jason Swails (jason.swails_at_gmail.com)
Date: Wed Nov 25 2009 - 10:50:41 CST

Kito,

You want to be careful here. Run the tests to make sure it worked.
However, that is not what I suggested. try using this config.h file
instead:

MATH_DEFINES =

MATH_LIBS =

IFORT_RPATH = /opt/gridengine/lib/lx26-
amd64:/usr/lib/perl5/5.8.8

MATH_DEFINES = -DMKL

MATH_LIBS = -L$(MKL_HOME)/lib/em64t -lguide -lpthread -lmkl_core
-lmkl_sequential -lmkl_intel_lp64

FFT_DEFINES = -DPUBFFT

FFT_INCLUDE =

FFT_LIBS =

NETCDF_HOME =

NETCDF_DEFINES =

NETCDF_MOD =

NETCDF_LIBS =

MPI_HOME = /opt/mpi/openmpi/1.3.3/intel/

MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI

MPI_INCLUDE = -I$(MPI_HOME)/include

MPI_LIBDIR = $(MPI_HOME)/lib

MPI_LIBS = -L$(MPI_LIBDIR)

DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC

CPP = /lib/cpp

CPPFLAGS = -traditional -P

F90_DEFINES = -DFFTLOADBAL_2PROC

F90 = mpif90

MODULE_SUFFIX = mod

F90FLAGS = -c

F90_OPT_DBG = -g -traceback

F90_OPT_LO = -O0

F90_OPT_MED = -O2

F90_OPT_HI = -axWPT -ip -O3

F90_OPT_DFLT = $(F90_OPT_HI)

CC = mpicc

CFLAGS =

LOAD = mpif90

LOADFLAGS =

LOADLIBS = -limf -lsvml -Wl,-rpath=$(IFORT_RPATH)

What you did was to prevent the pmemd installation from using the intel MKL
at all. However, without changing the MATH_LIBS line, you were still trying
to link to lguide (which is an MKL library). When you removed both, you
told pmemd not to use intel MKL. However, the intel MKL performs well and
will probably make your installation of pmemd faster. Also, when you start
changing preprocessor items (like removing -DMKL), you'll need to make clean
before you try to compile with the new options. Since you're not even
compiling with MKL, you should not need libguide, so linking it in the
MATH_LIBS line is unnecessary.

Try making clean and using the above config.h file and see if that works.
Also, don't forget to run the test cases to make sure you have a working
executable.

Good luck!
Jason

On Wed, Nov 25, 2009 at 3:12 AM, Kito <kitobhai_at_rediffmail.com> wrote:

> I was able to solve the problem
>
> "/usr/lib64/libguide.so: no version information available (required by
> ./pmemd)"
>
> It looked like the "no version information available" means that the
> library version number is lower on the shared object so I created a soft
> link of /opt/intel/Compiler/11.1/046/lib/intel64/libguide.so in /usr/lib64
> and it worked.
>
>
>
> Thanks all
>
>
>
>
>
>
>
> On Wed, 25 Nov 2009 13:21:41 +0530 wrote
>
> >Thanks Jason,
>
>
>
> When I changed MATH_DEFINES = -DMKL
>
>
>
> to MATH_DEFINES =
>
>
>
> it worked and I was able to link the object files.
>
>
>
> But on checking library dependencies, I have problem with libguide.so
> (first line on the output below)
>
>
>
>
>
>
>
> $> ldd pmemd
>
>
>
> ./pmemd: /usr/lib64/libguide.so: no version information available (required
> by ./pmemd)
>
>
>
> libguide.so => /usr/lib64/libguide.so (0x00002b1a6e4ca000)
>
>
>
> libpthread.so.0 => /lib64/libpthread.so.0 (0x00000032fdc00000)
>
>
>
> libimf.so => /usr/lib64/libimf.so (0x00002b1a6e607000)
>
>
>
> libsvml.so => /usr/lib64/libsvml.so (0x00002b1a6e89f000)
>
>
>
> libmpi_f90.so.0 => /opt/mpi/openmpi/1.3.3/intel/lib/libmpi_f90.so.0
> (0x00002b1a6e9e1000)
>
>
>
> libmpi_f77.so.0 => /opt/mpi/openmpi/1.3.3/intel/lib/libmpi_f77.so.0
> (0x00002b1a6ebe4000)
>
>
>
> libmpi.so.0 => /opt/mpi/openmpi/1.3.3/intel/lib/libmpi.so.0
> (0x00002b1a6ee1c000)
>
>
>
> libopen-rte.so.0 => /opt/mpi/openmpi/1.3.3/intel/lib/libopen-rte.so.0
> (0x00002b1a6f0ec000)
>
>
>
> libopen-pal.so.0 => /opt/mpi/openmpi/1.3.3/intel/lib/libopen-pal.so.0
> (0x00002b1a6f34c000)
>
>
>
> libdl.so.2 => /lib64/libdl.so.2 (0x00000032fd800000)
>
>
>
> libnsl.so.1 => /lib64/libnsl.so.1 (0x0000003300400000)
>
>
>
> libutil.so.1 => /lib64/libutil.so.1 (0x000000330a600000)
>
>
>
> libm.so.6 => /lib64/libm.so.6 (0x00000032fd400000)
>
>
>
> libc.so.6 => /lib64/libc.so.6 (0x00000032fd000000)
>
>
>
> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x000000330ee00000)
>
>
>
> /lib64/ld-linux-x86-64.so.2 (0x00000032fcc00000)
>
>
>
> libirc.so => /usr/lib64/libirc.so (0x00002b1a6f5e8000)
>
>
>
> libifport.so.5 =>
> /opt/intel/Compiler/11.1/046/lib/intel64/libifport.so.5 (0x00002b1a6f71e000)
>
>
>
> libifcoremt.so.5 =>
> /opt/intel/Compiler/11.1/046/lib/intel64/libifcoremt.so.5
> (0x00002b1a6f857000)
>
>
>
> libintlc.so.5 => /opt/intel/Compiler/11.1/046/lib/intel64/libintlc.so.5
> (0x00002b1a6fafb000)
>
>
>
>
>
>
>
> Thanks again
>
>
>
> Kito
>
>
>
>
>
>
>
> On Wed, 25 Nov 2009 12:34:22 +0530 wrote
>
>
>
> >This appears to be an MKL issue. What version of MKL are you using? It
>
>
>
> would appear like the MKL libraries you're linking to no longer contain
>
>
>
> vd___MATHFUNCTION__ functions/subroutines anymore, so you have to find
> which
>
>
>
> library is missing and link to that one as well. You can try adding
>
>
>
> -lmkl_intel_lp64 -lmkl_core and/or -lmkl_sequential to the MATH_LIBS line.
>
>
>
> I believe those are the only three libraries that pmemd will need, but this
>
>
>
> is for Intel MKL 10 or 11. For older MKL versions, the config file you have
>
>
>
> above should work...
>
>
>
>
>
>
>
> I just now tried compiling pmemd9 with the ifort11 compiler and MKL 11. It
>
>
>
> failed with the default config.h file (slightly different errors than
> yours,
>
>
>
> but still MKL-related). Adding the three above -lmkl... statements above to
>
>
>
> MATH_LIBS fixed the problems.
>
>
>
>
>
>
>
> Again, though, this is dependent on the version of MKL that you're using.
>
>
>
>
>
>
>
> Good luck, and I'd be interested to hear any success/failure (along with
>
>
>
> which MKL you have installed :) )
>
>
>
>
>
>
>
> All the best,
>
>
>
> Jason
>
>
>
>
>
>
>
> On Wed, Nov 25, 2009 at 1:39 AM, Kito wrote:
>
>
>
>
>
>
>
> > Hi Amber Experts/Users,
>
>
>
> >
>
>
>
> >
>
>
>
> >
>
>
>
> > I am having difficulties with pmemd installation
>
>
>
> >
>
>
>
> > My h/w and s/w configuration is
>
>
>
> >
>
>
>
> > Linux Enterprise, OpenMPI, AMD x86_64, Intel Compiliers
>
>
>
> >
>
>
>
> >
>
>
>
> >
>
>
>
> > My config.h file is
>
>
>
> >
>
>
>
> >
>
>
>
> >
>
>
>
> > MATH_DEFINES =
>
>
>
> >
>
>
>
> > MATH_LIBS =
>
>
>
> >
>
>
>
> > IFORT_RPATH = /opt/gridengine/lib/lx26-amd64:/usr/lib/perl5/5.8.8
>
>
>
> >
>
>
>
> > MATH_DEFINES = -DMKL
>
>
>
> >
>
>
>
> > MATH_LIBS = -L$(MKL_HOME)/lib/em64t -lguide -lpthread
>
>
>
> >
>
>
>
> > FFT_DEFINES = -DPUBFFT
>
>
>
> >
>
>
>
> > FFT_INCLUDE =
>
>
>
> >
>
>
>
> > FFT_LIBS =
>
>
>
> >
>
>
>
> > NETCDF_HOME =
>
>
>
> >
>
>
>
> > NETCDF_DEFINES =
>
>
>
> >
>
>
>
> > NETCDF_MOD =
>
>
>
> >
>
>
>
> > NETCDF_LIBS =
>
>
>
> >
>
>
>
> > MPI_HOME = /opt/mpi/openmpi/1.3.3/intel/
>
>
>
> >
>
>
>
> > MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI
>
>
>
> >
>
>
>
> > MPI_INCLUDE = -I$(MPI_HOME)/include
>
>
>
> >
>
>
>
> > MPI_LIBDIR = $(MPI_HOME)/lib
>
>
>
> >
>
>
>
> > MPI_LIBS = -L$(MPI_LIBDIR)
>
>
>
> >
>
>
>
> > DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
>
>
>
> >
>
>
>
> > CPP = /lib/cpp
>
>
>
> >
>
>
>
> > CPPFLAGS = -traditional -P
>
>
>
> >
>
>
>
> > F90_DEFINES = -DFFTLOADBAL_2PROC
>
>
>
> >
>
>
>
> > F90 = mpif90
>
>
>
> >
>
>
>
> > MODULE_SUFFIX = mod
>
>
>
> >
>
>
>
> > F90FLAGS = -c
>
>
>
> >
>
>
>
> > F90_OPT_DBG = -g -traceback
>
>
>
> >
>
>
>
> > F90_OPT_LO = -O0
>
>
>
> >
>
>
>
> > F90_OPT_MED = -O2
>
>
>
> >
>
>
>
> > F90_OPT_HI = -axWPT -ip -O3
>
>
>
> >
>
>
>
> > F90_OPT_DFLT = $(F90_OPT_HI)
>
>
>
> >
>
>
>
> > CC = mpicc
>
>
>
> >
>
>
>
> > CFLAGS =
>
>
>
> >
>
>
>
> > LOAD = mpif90
>
>
>
> >
>
>
>
> > LOADFLAGS =
>
>
>
> >
>
>
>
> > LOADLIBS = -limf -lsvml -Wl,-rpath=$(IFORT_RPATH)
>
>
>
> >
>
>
>
> >
>
>
>
> >
>
>
>
> > The error I get is
>
>
>
> >
>
>
>
> >
>
>
>
> >
>
>
>
> > mpif90 -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/opt/intel/Compiler/11.1/046/mkl//lib/em64t -lguide -lpthread
>
>
>
> > -L/opt/mpi/openmpi/1.3.3/intel//lib -limf -lsvml
>
>
>
> > -Wl,-rpath=/opt/gridengine/lib/lx26-amd64:/usr/lib/perl5/5.8.8
>
>
>
> >
>
>
>
> > gb_ene.o: In function `gb_ene_mod_mp_gb_ene_':
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x19de): undefined reference to `vdinvsqrt_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x1c93): undefined reference to `vdinv_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x1cac): undefined reference to `vdinv_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x1fde): undefined reference to `vdln_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x1ff7): undefined reference to `vdln_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x3b98): undefined reference to `vdinv_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x3dd9): undefined reference to `vdexp_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x4254): undefined reference to `vdinvsqrt_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x4289): undefined reference to `vdinv_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x43df): undefined reference to `vdexp_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x43fc): undefined reference to `vdinvsqrt_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x5403): undefined reference to `vdinvsqrt_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x55b1): undefined reference to `vdinv_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x55ca): undefined reference to `vdinv_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x57b2): undefined reference to `vdln_'
>
>
>
> >
>
>
>
> > gb_ene.o: In function `gb_ene_mod_mp_calc_born_radii_':
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x678a): undefined reference to `vdinvsqrt_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x6a3f): undefined reference to `vdinv_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x6a58): undefined reference to `vdinv_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x6d8a): undefined reference to `vdln_'
>
>
>
> >
>
>
>
> > gb_ene.f90:(.text+0x6da3): undefined reference to `vdln_'
>
>
>
> >
>
>
>
> > make[1]: *** [pmemd] Error 1
>
>
>
> >
>
>
>
> > make[1]: Leaving directory `/opt/apps/amber/9/intel-mkl/src/pmemd/src'
>
>
>
> >
>
>
>
> > make: *** [all] Error 2
>
>
>
> >
>
>
>
> >
>
>
>
> >
>
>
>
> > Please help... I have gone through the archives and got similar problems
>
>
>
> > but their said solution's doesnt seems to help.
>
>
>
> >
>
>
>
> >
>
>
>
> >
>
>
>
> > Thanks in advance
>
>
>
> >
>
>
>
> > Kito
>
>
>
> > _______________________________________________
>
>
>
> > AMBER mailing list
>
>
>
> > AMBER_at_ambermd.org
>
>
>
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> >
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
>
>
>
> ---------------------------------------
>
>
>
> Jason M. Swails
>
>
>
> Quantum Theory Project,
>
>
>
> University of Florida
>
>
>
> Ph.D. Graduate Student
>
>
>
> 352-392-4032
>
>
>
> _______________________________________________
>
>
>
> AMBER mailing list
>
>
>
> AMBER_at_ambermd.org
>
>
>
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
>
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>
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>
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>
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> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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