Hello,
My comments are below
On Fri, Dec 10, 2010 at 2:05 PM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> snip
>
> --------------------------------------------------------------------------
> It looks like MPI_INIT failed for some reason; your parallel process is
> likely to abort. There are many reasons that a parallel process can
> fail during MPI_INIT; some of which are due to configuration or environment
> problems. This failure appears to be an internal failure; here's some
> additional information (which may only be relevant to an Open MPI
> developer):
>
> snip
>
This is an OpenMPI problem, and is system-dependent. The newest version of
AmberTools (which I suggest installing) contains a configure_openmpi script
that will ensure that your OpenMPI installation is done with the same
settings as Amber. In any case, you need to fix your installation of
OpenMPI (or use a different MPI if this is a cluster to which you don't have
administrative privileges, in which case you should recruit your sysadmin's
help)
> during the compilation I get some warnings like this
>
> In file runmd.f90:1925
>
> if (abs(biga) - abs(a(ij))) 15, 20, 20
> 1
> Warning: Obsolete: arithmetic IF statement at (1)
> In file runmd.f90:1934
>
> snip
>
That is because arithmetic if statements were obsolete-ed in F90 (
http://en.wikipedia.org/wiki/Arithmetic_IF). In my opinion (and clearly the
compilers' opinions as well), arithmetic ifs are a horrid construct :).
There is nothing inherently *wrong* about them, and it does serve to make
some specific blocks of code shorter and arguably more succinct, which is
why it's simply a *warning* and not an error.
furthermore it does not move the executable to exe or bin but stays in
> pmemd?
>
It can do this depending on your method of install. For the versions of
Amber I am familiar with (9 a long time ago, 10, and 11), the make install
automatically moved pmemd into $AMBERHOME/bin if run from
$AMBERHOME/src/pmemd (for amber 9, 10) or $AMBERHOME/src (for amber11).
One other tip: it may be worth trying to test your OpenMPI installation if
such a test exists. The OpenMPI website should have information about this.
Good luck!
Jason
>
> On Fri, Dec 10, 2010 at 6:55 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > Hello,
> >
> > Remove the -DMKL. This, I think, will make it look for MKL libraries,
> which
> > you aren't linking to (a blank MATH_LIBS line). Don't forget to do a
> make
> > clean before you retry the install.
> >
> > Good luck,
> > Jason
> >
> > On Fri, Dec 10, 2010 at 12:53 PM, Jorgen Simonsen <jorgen589.gmail.com
> >wrote:
> >
> >> hi all
> >>
> >> I am trying to compile pmemd with gcc I was able to do it with intel
> >> compiler but with gcc I get the following error Warning: Obsolete:
> >> arithmetic IF statement at (1)
> >> /lib/cpp -traditional -P -I/usr/mpi/gcc/openmpi-1.3.2-qlc/include
> >> -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> >> -DFFTLOADBAL_2PROC veclib.fpp veclib.f90
> >> mpif90 -c -O3 veclib.f90
> >> mpicc -c pmemd_clib.c
> >> /lib/cpp -traditional -P -I/usr/mpi/gcc/openmpi-1.3.2-qlc/include
> >> -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> >> -DFFTLOADBAL_2PROC gb_alltasks_setup.fpp gb_alltasks_setup.f90
> >> mpif90 -c -O3 gb_alltasks_setup.f90
> >> /lib/cpp -traditional -P -I/usr/mpi/gcc/openmpi-1.3.2-qlc/include
> >> -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> >> -DFFTLOADBAL_2PROC pme_alltasks_setup.fpp pme_alltasks_setup.f90
> >> mpif90 -c -O3 pme_alltasks_setup.f90
> >> /lib/cpp -traditional -P -I/usr/mpi/gcc/openmpi-1.3.2-qlc/include
> >> -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> >> -DFFTLOADBAL_2PROC pme_setup.fpp pme_setup.f90
> >> mpif90 -c -O3 pme_setup.f90
> >> /lib/cpp -traditional -P -I/usr/mpi/gcc/openmpi-1.3.2-qlc/include
> >> -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> >> -DFFTLOADBAL_2PROC get_cmdline.fpp get_cmdline.f90
> >> mpif90 -c -O3 get_cmdline.f90
> >> /lib/cpp -traditional -P -I/usr/mpi/gcc/openmpi-1.3.2-qlc/include
> >> -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> >> -DFFTLOADBAL_2PROC master_setup.fpp master_setup.f90
> >> mpif90 -c -O3 master_setup.f90
> >> /lib/cpp -traditional -P -I/usr/mpi/gcc/openmpi-1.3.2-qlc/include
> >> -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> >> -DFFTLOADBAL_2PROC pmemd.fpp pmemd.f90
> >> mpif90 -c -O3 pmemd.f90
> >> /lib/cpp -traditional -P -I/usr/mpi/gcc/openmpi-1.3.2-qlc/include
> >> -DPUBFFT -DMPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> >> -DFFTLOADBAL_2PROC erfcfun.fpp erfcfun.f90
> >> mpif90 -c -O3 erfcfun.f90
> >> mpif90 -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/usr/mpi/gcc/openmpi-1.3.2-qlc/lib64
> >> gb_ene.o: In function `__gb_ene_mod__calc_born_radii':
> >> gb_ene.f90:(.text+0xe15): undefined reference to `vdinvsqrt_'
> >> gb_ene.f90:(.text+0x1174): undefined reference to `vdinv_'
> >> gb_ene.f90:(.text+0x118b): undefined reference to `vdinv_'
> >> gb_ene.f90:(.text+0x1287): undefined reference to `vdln_'
> >> gb_ene.f90:(.text+0x129e): undefined reference to `vdln_'
> >> gb_ene.o: In function `__gb_ene_mod__gb_ene':
> >> gb_ene.f90:(.text+0x29e7): undefined reference to `vdinv_'
> >> gb_ene.f90:(.text+0x2a72): undefined reference to `vdexp_'
> >> gb_ene.f90:(.text+0x2b61): undefined reference to `vdinvsqrt_'
> >> gb_ene.f90:(.text+0x2b94): undefined reference to `vdinvsqrt_'
> >> gb_ene.f90:(.text+0x344a): undefined reference to `vdinv_'
> >> gb_ene.f90:(.text+0x34c0): undefined reference to `vdexp_'
> >> gb_ene.f90:(.text+0x390c): undefined reference to `vdinvsqrt_'
> >> gb_ene.f90:(.text+0x3b37): undefined reference to `vdinv_'
> >> gb_ene.f90:(.text+0x3b4e): undefined reference to `vdinv_'
> >> gb_ene.f90:(.text+0x3bd7): undefined reference to `vdln_'
> >> collect2: ld returned 1 exit status
> >> make[1]: *** [pmemd] Error 1
> >> make[1]: Leaving directory `/people/disk2/hbohr/amber10/src/pmemd/src'
> >> make: *** [all] Error 2
> >>
> >> my config.h file looks like this
> >>
> >>
> >> MATH_DEFINES =
> >> MATH_LIBS =
> >> MATH_DEFINES = -DMKL
> >> FFT_DEFINES = -DPUBFFT
> >> FFT_INCLUDE =
> >> FFT_LIBS =
> >> NETCDF_HOME =
> >> NETCDF_DEFINES =
> >> NETCDF_MOD =
> >> NETCDF_LIBS =
> >> MPI_HOME =/usr/mpi/gcc/openmpi-1.3.2-qlc
> >> MPI_DEFINES = -DMPI
> >> MPI_INCLUDE = -I$(MPI_HOME)/include
> >> MPI_LIBDIR = $(MPI_HOME)/lib64
> >> MPI_LIBS = -L$(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 = -O3
> >> F90_OPT_DFLT = $(F90_OPT_HI)
> >>
> >> CC = mpicc
> >> CFLAGS =
> >>
> >> LOAD = mpif90
> >> LOADFLAGS =
> >>
> >> I have removed some of the optimization flags from the intel file.
> >>
> >> Have I removed too much?
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.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.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
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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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Received on Fri Dec 10 2010 - 11:30:12 PST
