AMBER Archive (2007)

Subject: Re: AMBER: problem in installing amber9

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Jun 13 2007 - 14:11:40 CDT

Guys - If you force two underscores for incoming c objects (ie., c object names that the fortran will link to), then you also have to be sure to define
DBL_C_UNDERSCORE when compiling pmemd_clib.c. That is why all the get_bytesize* and get_walltime* names are not being resolved - these two names come from the pmemd C library, and must be kept in sync with any name mangling convention changes by using the appropriate define. You still are missing a system library somewhere for the pthread stuff. Once again, just do a
'mpif77 -link_info' to find out what system libraries are needed (and their locations) for mpi.
Regards - Bob

----- Original Message -----
  From: Ross Walker
  To: amber_at_scripps.edu
  Sent: Wednesday, June 13, 2007 2:29 PM
  Subject: RE: AMBER: problem in installing amber9

  Hi Henk,

  So it appears that assuming two underscores fixes the MPI linking problem but breaks other libraries that only have one underscore :-(.

  One other thing to try is to take a freshly created pmemd config.h file and replace F90 = ifort with F90 = mpif90_i. You can then likely blank out the MPI_LIBDIR and MPI_LIBS line since the mpif90_i wrapper should take care of it. This is essentially what worked for regular AMBER yes? You used mpif90_i in place of ifort?

  Thus try the same with pmemd, it is possible that the mpif90_i script will take care of the different naming conventions in the various library files.

  All the best
  Ross
  /\
  \/
  |\oss Walker

  | HPC Consultant and Staff Scientist |
  | San Diego Supercomputer Center |
  | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
  | http://www.rosswalker.co.uk | PGP Key available on request |

  Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.

----------------------------------------------------------------------------
    From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Henk Meij
    Sent: Wednesday, June 13, 2007 10:31
    To: amber_at_scripps.edu
    Subject: Re: AMBER: problem in installing amber9

got both on board.

[root_at_swallowtail pmemd]# nm /usr/local/topspin/mpi/mpich/lib64/libmpichf90_i.so | grep mpi_bcast
0000000000020c8c T mpi1__complex4_s_mp_mpi_bcast_t_
...other lines, then...
                 U mpi_bcast_
[root_at_swallowtail pmemd]# nm /usr/local/topspin/mpi/mpich/lib64/libmpich.so | grep mpi_bcast
000000000004e45c T mpi_bcast__

i'm running with MKL_HOME='' to simplify

./configure linux_em64t ifort mpich
Intel ifort compiler found; version information:
Version 9.1
Use Intel MKL? (better performance) (answer yes or no):
no
File config_data/fft.pubfft being used...
File config_data/linux_em64t.ifort being used...
File config_data/interconnect.mpich being used...
configure assumes mpich files are in /usr/local/topspin/mpi/mpich.
PMEMD Configurate successfully completed.

putting either 2underscores|nounderscore only makes a difference in the type of error i get. with noundeescores i get a very long list of undefined references as previously stated. with 2underscores i get the ouput below.

here are some relevent lines from my config.h

IFORT_RPATH = /usr/local/topspin/lib64:/share/apps/intel/fce/9.1.043/lib:/share/apps/intel/cce/9.1.047/lib

MPI_HOME = /usr/local/topspin/mpi/mpich
MPI_INCLUDE = -I$(MPI_HOME)/include
MPI_LIBDIR = $(MPI_HOME)/lib64
MPI_LIBS = -L$(MPI_LIBDIR) -lmpich

F90FLAGS = -assume 2underscores -c -auto
LOADFLAGS = -assume 2underscores

ifort -assume 2underscores -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/local/topspin/mpi/mpich/lib64 -lmpich -limf -lsvml -Wl,-rpath=/usr/local/topspin/lib64:/share/apps/intel/fce/9.1.043/lib:/share/apps/intel/cce/9.1.047/lib
prmtop_dat.o(.text+0x479): In function `prmtop_dat_mod_mp_bcast_prmtop_dat__':
: undefined reference to `get_bytesize__'
prmtop_dat.o(.text+0x4df): In function `prmtop_dat_mod_mp_bcast_prmtop_dat__':
: undefined reference to `get_bytesize__'
prmtop_dat.o(.text+0x549): In function `prmtop_dat_mod_mp_bcast_prmtop_dat__':
: undefined reference to `get_bytesize__'
dynamics_dat.o(.text+0x19a): In function `dynamics_dat_mod_mp_bcast_dynamics_dat__':
: undefined reference to `get_bytesize__'
dynamics_dat.o(.text+0x203): In function `dynamics_dat_mod_mp_bcast_dynamics_dat__':
: undefined reference to `get_bytesize__'
loadbal.o(.text+0x10): In function `loadbal_mod_mp_start_loadbal_timer__':
: undefined reference to `get_wall_time__'
loadbal.o(.text+0x2b): In function `loadbal_mod_mp_update_loadbal_timer__':
: undefined reference to `get_wall_time__'
runmin.o(.text+0x337f): In function `runmin_mod_mp_runmin_master__':
: undefined reference to `get_wall_time__'
runmin.o(.text+0x3f40): In function `runmin_mod_mp_printe__':
: undefined reference to `get_wall_time__'
runfiles.o(.text+0x3c68): In function `runfiles_mod_mp_prntmd__':
: undefined reference to `get_wall_time__'
pmemd.o(.text+0xd9): In function `MAIN__':
: undefined reference to `unlimit_stack__'
/usr/local/topspin/lib64/libmosal.so: undefined reference to `pthread_create'
/usr/local/topspin/lib64/libmosal.so: undefined reference to `pthread_cancel'
/usr/local/topspin/lib64/libmosal.so: undefined reference to `sem_wait'
/usr/local/topspin/lib64/libmosal.so: undefined reference to `sem_post'
/usr/local/topspin/lib64/libmosal.so: undefined reference to `sem_init'
/usr/local/topspin/lib64/libmosal.so: undefined reference to `sem_trywait'
/usr/local/topspin/lib64/libmosal.so: undefined reference to `pthread_mutex_trylock'
/usr/local/topspin/lib64/libmosal.so: undefined reference to `pthread_join'
make[1]: *** [pmemd] Error 1Dear Henk,

      I'm glad you managed to get sander working. For pmemd can you try the following:

      nm /usr/local/topspin/mpi/mpich/lib64/libmpichf90_i.so | grep mpi_bcast

      and if that doesn't show anything then:

      nm /usr/local/topspin/mpi/mpich/lib64/libmpich.so | grep mpi_bcast

      I am guessing that the symbols defined in the mpich libraries will either have no trailing underscores or two trailing underscores, as opposed to the single trailing underscore that the linker is looking for below.

      If the grep above shows no final underscore then on the F90FLAGS line and the LOADFLAGS line in config.h append:

      -assume nounderscore

      if the grep above shows two trailing underscores then try adding:

      -assume 2underscores

      Then make clean, make

      Hopefully this will then link okay.

      All the best
      Ross

      /\
      \/
      |\oss Walker

      | HPC Consultant and Staff Scientist |
      | San Diego Supercomputer Center |
      | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
      | http://www.rosswalker.co.uk | PGP Key available on request |

      Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.

------------------------------------------------------------------------
        From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Henk Meij
        Sent: Wednesday, June 13, 2007 06:41
        To: amber_at_scripps.edu
        Subject: Re: AMBER: problem in installing amber9

        (reposting, archive does not show this response arrived...)

        Ross, thanks for all your help. i made links for libvapi and libmosal in lib64 pointing to the /usr/local/topspin/lib64 copies. we have binaries! way confusing, but we're there.

        pmemd however still fails. same environment. do you have any clues on were all these undefined reference are hiding?

        -Henk

[root_at_swallowtail src]# ldd /share/apps/amber/9_ifort/exe/sander.MPI
        libmpichf90_i.so => /usr/local/topspin/mpi/mpich/lib64/libmpichf90_i.so (0x0000002a95576000)
        libmpich_i.so => /usr/local/topspin/mpi/mpich/lib64/libmpich_i.so (0x0000002a956d4000)
        libmpichfsup_i.so => /usr/local/topspin/mpi/mpich/lib64/libmpichfsup_i.so (0x0000002a978f3000)
        libmpich.so => /usr/local/topspin/mpi/mpich/lib64/libmpich.so (0x0000002a979f6000)
        libvapi.so => /usr/local/topspin/lib64/libvapi.so (0x0000002a99c17000)
        libmosal.so => /usr/local/topspin/lib64/libmosal.so (0x0000002a99d37000)
        libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x0000003684400000)
        libdl.so.2 => /lib64/libdl.so.2 (0x0000003684000000)
        libvml.so => /share/apps/intel/cmkl/9.1/lib/em64t/libvml.so (0x0000002a99e47000)
        libmkl_lapack.so => /share/apps/intel/cmkl/9.1/lib/em64t/libmkl_lapack.so (0x0000002a99fdc000)
        libmkl.so => /share/apps/intel/cmkl/9.1/lib/em64t/libmkl.so (0x0000002a9a74a000)
        libguide.so => /share/apps/intel/cmkl/9.1/lib/em64t/libguide.so (0x0000002a9a8ca000)
        libm.so.6 => /lib64/tls/libm.so.6 (0x00000034d3600000)
        libc.so.6 => /lib64/tls/libc.so.6 (0x0000003683b00000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003687b00000)
        libg2c.so.0 => /usr/lib64/libg2c.so.0 (0x0000002a9aa2d000)
        /lib64/ld-linux-x86-64.so.2 (0x0000003683900000)

[root_at_swallowtail pmemd]# /share/apps/amber/9_ifort/exe/sander.MPI --help
Can't read MPIRUN_HOST

[root_at_swallowtail pmemd]# ./configure linux_em64t ifort mpich

Intel ifort compiler found; version information:
Version 9.1
configure assumes Intel MKL is installed in /share/apps/intel/cmkl/9.1
File config_data/fft.pubfft being used...
File config_data/linux_em64t.ifort being used...
File config_data/interconnect.mpich being used...
configure assumes mpich files are in /usr/local/topspin/mpi/mpich.
PMEMD Configurate successfully completed.

[root_at_swallowtail pmemd]# make install > /tmp/log 2>&1

first error:
IPO link: can not find -lmpich
ifort: error: problem during multi-file optimization compilation (code 1)

changed config.h
#MPI_LIBDIR = $(MPI_HOME)/lib
MPI_LIBDIR = $(MPI_HOME)/lib64

...remaking - no errors this far...
/lib/cpp -traditional -P -I/usr/local/topspin/mpi/mpich/include -DPUBFFT -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL -DFFTLOADBAL_2PROC erfcfun.fpp erfcfun.f90
ifort -c -auto -tpp7 -xW -ip -O3 erfcfun.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/share/apps/intel/cmkl/9.1/lib/em64t -lmkl_em64t -lpthread -L/usr/local/topspin/mpi/mpich/lib64 -lmpich -limf -lsvml -Wl,-rpath=/share/apps/intel/cmkl/9.1/lib/em64t:/share/apps/intel/mpi/3.0.043/lib64:/share/apps/intel/fce/9.1.043/lib:/share/apps/intel/cce/9.1.047/lib:/opt/lava/6.1/linux2.6-glibc2.3-ia32e/lib:/opt/lava/6.1/linux2.6-glibc2.3-ia32e/lib:/share/
 apps/openmpi-1.2/lib
parallel_dat.o(.text+0x40): In function `parallel_dat_mod_mp_mexit_':
: undefined reference to `mpi_group_free_'
parallel_dat.o(.text+0x53): In function `parallel_dat_mod_mp_mexit_':
: undefined reference to `mpi_finalize_'
parallel_dat.o(.text+0xad): In function `parallel_dat_mod_mp_mexit_':
: undefined reference to `mpi_abort_'
mdin_ctrl_dat.o(.text+0x842a): In function `mdin_ctrl_dat_mod_mp_bcast_mdin_ctrl_dat_':
: undefined reference to `mpi_bcast_'
mdin_ctrl_dat.o(.text+0x8451): In function `mdin_ctrl_dat_mod_mp_bcast_mdin_ctrl_dat_':
: undefined reference to `mpi_bcast_'

-these undefined references continue for awhile, then-

/share/apps/intel/cmkl/9.1/lib/em64t/libmkl_em64t.a(vml_threading_service.o)(.text+0x2b): In function `mkl_vml_service_threader_s_min':
: undefined reference to `omp_in_parallel'
/share/apps/intel/cmkl/9.1/lib/em64t/libmkl_em64t.a(vml_threading_service.o)(.text+0x167): In function `CalculateLogicConsts':
: undefined reference to `omp_get_num_procs'

- and lots of those -

btw,

[root_at_swallowtail pmemd]# mpif90 -link_info
ln -s /usr/local/topspin/mpi/mpich//include/mpif.h mpif.h
ifort -I/usr/local/topspin/mpi/mpich//include -L/usr/local/topspin/mpi/mpich//lib -lmpichf90_i -lmpich_i -lmpichfsup_i -L /usr/local/topspin/lib64 -L /usr/local/topspin/mpi//mpich/lib64 -lmpich -lvapi -lmosal -Bdynamic -lpthread -ldl
rm mpif.h

so i now made a link in
/usr/local/topspin/mpi/mpich
pointing lib/ to lib64/
did not help

    Hi Syed,

I think you are seeing the same problem that is mentioned in some of the
links to the amber mailing list archive. I don't think we have ever been
able to locate what causes this problem however...

One option would be to try changing the c compiler. If you have the Intel
compilers installed (ifort / icc) then try, assuming you have an x86_64
machine and the 64 bit version of the compilers (fce/cce) and OS installed:

./configure -static -nopar ifort_x86_64

Then edit config.h and change gcc to icc and g++ to icpc.

Then make clean, make

See if xleap then works in this situation.

All the best
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

  -----Original Message-----
From: owner-amber_at_scripps.edu
[mailto:owner-amber_at_scripps.edu] On Behalf Of Syed Tarique Moin
Sent: Tuesday, June 12, 2007 01:05
To: amber_at_scripps.edu
Subject: Re: AMBER: problem in installing amber9

Hi

Thanks for you kind suggestion,

But i want to update with amber9, so plz guide me for
the installation,

I have compiler g98 and the Hardware is Intel Xeon
dual processor.

Regard
--- "David A. Case" <case_at_scripps.edu> wrote:

    On Fri, Jun 01, 2007, Syed Tarique Moin wrote:

      I installed amber9 but not looking fine, i have a
problem in xleap, that when i make initial files,
        like
      using the command

solvatebox or addions the solvent surrounding the
solute not well file (file attached name as
amber9.jpg)

but its looking right with amber7.jpg (for the
comparison) surrounding the solute very well by
        the
      solvent.

        Please see if this helps:

   
http://amber.ch.ic.ac.uk/archive/200406/0298.html

or this:

   http://amber.ch.ic.ac.uk/archive/200503/0122.html

or this:

   http://amber.ch.ic.ac.uk/archive/200610/0205.html

Since Amber 7 works, you can still use that, I would
imagine. You might
provide details about your compiler and what
architecture (emt64?) you are
using.

....dac

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      Syed Tarique Moin,
Junior Research Fellow,
H.E.J. Research Institute of Chemistry,
International Center for Chemical and Biological Sciences,
University of Karachi, Karachi-75720, Pakistan

tarisyed_at_yahoo.com
tarisyed_at_hotmail.com

       
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