(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
>>
>>
>>
>> ______________________________________________________________
>> ______________________
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>> you're surfing.
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>> ---------
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>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>
>>
>
>
> -----------------------------------------------------------------------
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>
>
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Received on Sun Jun 17 2007 - 06:07:08 PDT
