AMBER Archive (2007)

Subject: Re: AMBER: amber9 compile problem

From: Henk Meij (hmeij_at_wesleyan.edu)
Date: Tue Jun 12 2007 - 13:30:54 CDT

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

...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 Henk,
>
> For some reason it looks like your mpi libraries are distributed in
> two directories, /usr/local/topspin/mpi/mpich/lib64 and
> /usr/local/topspin/lib64/. The mpif90_i script should have taken care
> of this though. For some reason here though it isn't picking up the
> second search path. In your config.h file can you try specifying
> -L/usr/local/topspin/lib64/ before the -lvapi or alternatively try
> creating a link to libvapi.a and libvapi.so in
> /usr/local/topspin/mpi/mpich/lib64. Same for any other libraries in
> /usr/local/topspin/lib64/ that it can't find. I know this is a bit of
> a hack but hopefully it will work and get you a compiled executable.
>
> 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 <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:* Tuesday, June 12, 2007 07:13
> *To:* amber_at_scripps.edu
> *Subject:* Re: AMBER: amber9 compile problem
>
> Ross, with link in place
> -Henk
>
> [root_at_swallowtail src]# make clean
> [root_at_swallowtail src]# ./configure -mpich ifort_x86_64
>
> AMBERHOME is set to /share/apps/amber/9_ifort
> Setting up Amber configuration file for architecture: ifort_x86_64
> Using parallel communications library: mpich
> MPI_HOME is set to /usr/local/topspin/mpi/mpich
> MKL_HOME is set to /share/apps/intel/cmkl/9.1
> Using MKL libraries from /share/apps/intel/cmkl/9.1/lib/em64t
>
> The configuration file, config.h, was successfully created.
>
> [root_at_swallowtail src]# which mpif90
> /usr/local/topspin/mpi/mpich/bin/mpif90
> [root_at_swallowtail src]# which ifort
> /share/apps/intel/fce/9.1.043/bin/ifort
>
> [root_at_swallowtail src]# make parallel
>
> first error when compiling sander.MPI
> IPO link: can not find -lmpif90_i
> ifort: error: problem during multi-file optimization compilation (code 1)
>
> so i changed config.h
> #LOADLIB= -L/usr/local/topspin/mpi/mpich/lib -lmpichf90_i ...
> LOADLIB= -L/usr/local/topspin/mpi/mpich/lib64 -lmpichf90_i ...
>
> reran, and now have error
> IPO link: can not find -lvapi
> ifort: error: problem during multi-file optimization compilation (code 1)
>
> [root_at_swallowtail src]# file /usr/local/topspin/lib64/libvapi.*
> /usr/local/topspin/lib64/libvapi.a: current ar archive
> /usr/local/topspin/lib64/libvapi.so: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped
>
>
>
>
>
>> Hi Henk,
>>
>> Can you create a symbolic link that points
>> /usr/local/topspin/mpi/mpich/bin/mpif90 to
>> /usr/local/topspin/mpi/mpich/bin/mpif90.i
>>
>> And then try running configure again and then make clean / make
>> parallel.
>>
>> Configure calls mpif90 as part of the configuration to find out
>> where all the libraries are and below it didn't manage to run it
>> because your mpif90 is actually called mpif90.i
>>
>> Then get back to me with the next problem and we can work from there.
>>
>> 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 <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:* Monday, June 11, 2007 12:04
>> *To:* amber_at_scripps.edu
>> *Subject:* Re: AMBER: amber9 compile problem
>>
>> Ross, here it is.
>> -Henk
>>
>>
>> 1001 cd /share/apps/amber/
>> 1002 mkdir 9_ifort
>> 1003 cd 9_ifort/
>> 1004 tar zxf /share/apps/src/amber9.tgz
>> 1005 mv amber9/* .
>> 1006 rmdir amber9/
>> 1007 sh < /share/apps/src/amber9_bugfix.cmd
>> 1008 cd src
>> 1009 export PATH=/usr/local/topspin/mpi/mpich/bin:$PATH
>> 1010 export MPI_HOME=/usr/local/topspin/mpi/mpich
>> 1011 export AMBERHOME=/share/apps/amber/9_ifort
>> 1012 export MKL_HOME=/share/apps/intel/cmkl/9.1
>>
>> [root_at_swallowtail]# which mpif90.i
>> /usr/local/topspin/mpi/mpich/bin/mpif90.i
>> [root_at_swallowtail]# which ifort
>> /share/apps/intel/fce/9.1.043/bin/ifort
>>
>> [root_at_swallowtail]# ./configure -mpich ifort_x86_64
>>
>> AMBERHOME is set to /share/apps/amber/9_ifort
>> Setting up Amber configuration file for architecture: ifort_x86_64
>> Using parallel communications library: mpich
>> MPI_HOME is set to /usr/local/topspin/mpi/mpich
>> ./configure: line 300: /usr/local/topspin/mpi/mpich/bin/mpif90: No such file or directory
>> MKL_HOME is set to /share/apps/intel/cmkl/9.1
>> Using MKL libraries from /share/apps/intel/cmkl/9.1/lib/em64t
>>
>> "make parallel" yields an error when compiling
>> "ifort -FR -o sander.MPI evb_vars.o ..."
>>
>> evb_init.o(.text+0x69e): In function `evb_init_':
>> : undefined reference to `mpi_bcast_'
>> -lots of these-
>>
>> i've seen dac's fix for this but adding -fsecond-underscore does not fix the problem.
>> meaning i have to have clean source code for topspin and compile with -fno-secoond-underscore?
>>
>> -Henk
>>
>>
>>
>

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