AMBER Archive (2008)

Subject: AMBER: compiling PMEMD with MKL10.0

From: Alessandro Nascimento (al.s.nascimento_at_gmail.com)
Date: Tue Feb 26 2008 - 04:20:47 CST

Hi amber users/developers/gurus,

I tried recently to compile amber 9 using icc (10.1), ifort (10.1) and mkl(
10.0.1) and found the errors shown below.
sander and other amber programs compile okay. However, PMEMD couldn't be
compiled.

It seems that mkl libraries are not being correctly used during compilation
(the amber developers mailing list had something in this way)
Wihtou MKL, I can compile PMEMD, but since it seems to improve the
performance, it would be nice to have them compiled in.
Any suggestion on how to fix it?

thanks a lot

(...)
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/opt/intel/mkl/10.0.1.014/lib/em64t
-lmkl_em64t -lpthread -limf -lsvml
-Wl,-rpath=/opt/intel/cce/10.1.012/lib:/opt/intel/fce/10.1.012/lib
/opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_intel_thread.a(vml_threading_templates.o):
In function `mkl_vml_service_threader_z_1i_c_1o':
_tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x5a):
undefined reference to `__kmpc_global_thread_num'
_tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x131):
undefined reference to `__kmpc_ok_to_fork'
_tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x156):
undefined reference to `__kmpc_push_num_threads'
_tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x1b6):
undefined reference to `__kmpc_fork_call'
_tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x1d4):
undefined reference to `__kmpc_serialized_parallel'
_tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x251):
undefined reference to `__kmpc_end_serialized_parallel'

(...)

/opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_intel_thread.a(mkl_threading.o):
In function `MKL_Get_Max_Threads':
__tmp_mkl_threading.c:(.text+0x55): undefined reference to `omp_in_parallel'
__tmp_mkl_threading.c:(.text+0x77): undefined reference to
`omp_get_max_threads'
/opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_intel_thread.a(mkl_threading.o):
In function `MKL_Domain_Get_Max_Threads':
__tmp_mkl_threading.c:(.text+0x857): undefined reference to
`omp_in_parallel'
__tmp_mkl_threading.c:(.text+0x878): undefined reference to
`omp_get_max_threads'
make[1]: *** [pmemd] Error 1
make[1]: Leaving directory `/usr/local/amber9/src/pmemd/src'
make: *** [all] Error 2

My architecture:

~ $ uname -a
Linux protoss 2.6.20-gentoo-r8 #24 SMP Thu Jun 21 11:23:54 GMT 2007 x86_64
Intel(R) Core(TM)2 Quad CPU @ 2.40GHz GenuineIntel GNU/Linux 

-- 
[ ]s

--alessandro

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