root.swallowtail bin]# ./mpif77.i -link_info
ifort -I/usr/local/topspin/mpi/mpich//include
-L/usr/local/topspin/mpi/mpich//lib -lmpich_i -L
/usr/local/topspin/lib64 -L /usr/local/topspin/mpi//mpich/lib64 -lmpich
-lvapi -lmosal -Bdynamic -lpthread -ldl
-Henk
> 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 <mailto:ross.rosswalker.co.uk>
> *To:* amber.scripps.edu <mailto:amber.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.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 10:31
> *To:* amber.scripps.edu
> *Subject:* Re: AMBER: problem in installing amber9
>
> 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 - 06:07:13 PDT
