got both on board.
[root.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.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 1
> Dear 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.rosswalker.co.uk |
> | http://www.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.scripps.edu [mailto:owner-amber.scripps.edu]
> *On Behalf Of *Henk Meij
> *Sent:* Wednesday, June 13, 2007 06:41
> *To:* amber.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.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.swallowtail pmemd]# /share/apps/amber/9_ifort/exe/sander.MPI --help
> Can't read MPIRUN_HOST
>
> [root.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.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.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.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.scripps.edu
>>> [mailto:owner-amber.scripps.edu] On Behalf Of Syed Tarique Moin
>>> Sent: Tuesday, June 12, 2007 01:05
>>> To: amber.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.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
>>>>
>>>>
>>>>
>>> --------------------------------------------------------------
>>> ---------
>>>
>>>> The AMBER Mail Reflector
>>>> To post, send mail to amber.scripps.edu
>>>> To unsubscribe, send "unsubscribe amber" to
>>>> majordomo.scripps.edu
>>>>
>>>>
>>> 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.yahoo.com
>>> tarisyed.hotmail.com
>>>
>>>
>>>
>>> ______________________________________________________________
>>> ______________________
>>> Get the Yahoo! toolbar and be alerted to new email wherever
>>> you're surfing.
>>> http://new.toolbar.yahoo.com/toolbar/features/mail/index.php
>>> --------------------------------------------------------------
>>> ---------
>>> The AMBER Mail Reflector
>>> To post, send mail to amber.scripps.edu
>>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>>
>>>
>>
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>
>>
>
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Received on Sun Jun 17 2007 - 06:07:10 PDT
