Folks,
I have compiled parallel AMBER 10 using openmpi-1.2.8 and intel compilers.
Here are some records of what's defined on my system.
ifort -V
Intel(R) Fortran Compiler for applications running on Intel(R) 64, Version 10.0 Build 20070426 Package ID: l_fc_p_10.0.023
Copyright (C) 1985-2007 Intel Corporation. All rights reserved.
FOR NON-COMMERCIAL USE ONLY
icc -V
Intel(R) C Compiler for applications running on Intel(R) 64, Version 10.1 Build 20070913 Package ID: l_cc_p_10.1.008
Copyright (C) 1985-2007 Intel Corporation. All rights reserved.
FOR NON-COMMERCIAL USE ONLY
gcc -v
Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.6/specs
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-java-awt=gtk --host=x86_64-redhat-linux
Thread model: posix
gcc version 3.4.6 20060404 (Red Hat 3.4.6-3)
cat /etc/redhat-release
Red Hat Enterprise Linux AS release 4 (Nahant Update 4)
uname -a
Linux hpcc2-head1.mdc.musc.edu 2.6.9-42.ELsmp #1 SMP Wed Jul 12 23:32:02 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux
cat /proc/cpuinfo
.
.
.
cpu family : 6
model : 15
model name : Intel(R) Xeon(R) CPU E5345 . 2.33GHz
.
.
.
echo $MKL_HOME
/opt/intel/mkl/10.0..011
which mpirun
/share/apps/openmpi-1.2.8/bin/mpirun
mpif90 -show
ifort -I/share/apps/openmpi-1.2.8/include -pthread -I/share/apps/openmpi-1.2.8/lib -L/share/apps/openmpi-1.2.8/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil
cd $AMBERHOME/src/pmemd/
then
./configure linux_em64t ifort lam fftw bintraj
I edited config.h following
http://archive.ambermd.org/200805/0617.html
Then at the end of compiling pmemd I find these errors:
.
.
.
ifort: command line remark #10148: option '-tp' not supported
mpif90 -o pmemd gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o inpcrd_dat.o dynamics_dat.o img.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o dihedrals.o extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.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 pme_alltasks_setup.o pme_setup.o ene_frc_splines.o gb_alltasks_setup.o nextprmtop_section.o -L/share/apps/libraries/fftw/fftw-3.2/lib -lfftw3 /home/hazards/COMPILE/amber10/src/netcdf/lib/libnetcdf.a /opt/intel/mkl/10.0.011/lib/em64t/libmkl_intel_lp64.a /opt/intel/mkl/10.0.011/lib/em64t/libmk!
l_!
core.a /opt/intel/mkl/10.0.011/lib/em64t/libmkl_sequential.a -L/share/apps/openmpi-1.2.8/lib -limf -lsvml -Wl,-rpath=/opt/intel/cce/10.1.008/lib:/opt/intel/fce/10.0.023/lib:/opt/intel/mkl/10.0.011/lib/em64t:/share/apps/ccp4-6.0.2/lib:/opt/openmpi/1.1.4/lib:/opt/lava/6.1/linux2.6-glibc2.3-ia32e/lib
prmtop_dat.o(.text+0xfe7): In function `prmtop_dat_mod_mp_bcast_amber_prmtop_dat_':
: undefined reference to `get_bytesize_'
prmtop_dat.o(.text+0x104b): In function `prmtop_dat_mod_mp_bcast_amber_prmtop_dat_':
: undefined reference to `get_bytesize_'
prmtop_dat.o(.text+0x10ab): In function `prmtop_dat_mod_mp_bcast_amber_prmtop_dat_':
: undefined reference to `get_bytesize_'
fft1d.o(.text+0x1da): In function `fft1d_mod_mp_fft1d_back_':
: undefined reference to `dfftw_execute_dft_'
fft1d.o(.text+0x1ee): In function `fft1d_mod_mp_fft1d_forward_':
: undefined reference to `dfftw_execute_dft_'
fft1d.o(.text+0x1ff): In function `fft1d_mod_mp_fft1d_destroy_':
: undefined reference to `dfftw_destroy_plan_'
fft1d.o(.text+0x20d): In function `fft1d_mod_mp_fft1d_destroy_':
: undefined reference to `dfftw_destroy_plan_'
fft1d.o(.text+0x35a): In function `fft1d_mod_mp_fft1d_create_':
: undefined reference to `dfftw_plan_dft_1d_'
fft1d.o(.text+0x37f): In function `fft1d_mod_mp_fft1d_create_':
: undefined reference to `dfftw_plan_dft_1d_'
extra_pnts_nb14.o(.text+0x6037): In function `extra_pnts_nb14_mod_mp_bcast_extra_pnts_nb14_dat_':
: undefined reference to `get_bytesize_'
loadbal.o(.text+0x42e1): In function `loadbal_mod_mp_update_loadbal_timer_':
: undefined reference to `get_wall_time_'
loadbal.o(.text+0x4348): In function `loadbal_mod_mp_start_loadbal_timer_':
: undefined reference to `get_wall_time_'
runmin.o(.text+0x34fa): In function `runmin_mod_mp_printe_':
: undefined reference to `get_wall_time_'
runfiles.o(.text+0x691): In function `runfiles_mod_mp_prntmd_':
: undefined reference to `get_wall_time_'
pmemd_clib.o(.eh_frame+0x12): undefined reference to `__gxx_personality_v0'
pmemd.o(.text+0x95): In function `MAIN__':
: undefined reference to `unlimit_stack_'
make[1]: *** [pmemd] Error 1
make[1]: Leaving directory `COMPILE/amber10/src/pmemd/src'
make: *** [all] Error 2
It looks like it got close and then gave up. What am I doing wrong?
Starr
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Received on Fri Dec 05 2008 - 16:24:25 PST
