AMBER Archive (2009)

Subject: Re: [AMBER] pmemd compilation/make failed -mkl_vml_service_threader_z_1i_c_1o

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Apr 06 2009 - 09:25:14 CDT

Okay, I don't have one of these machines handy, but there are two problems
here, at least:
1) you specified the use of fftw, but you don't have it (or at least not the
necessary info to find the libraries)
2) you specified MKL - not a problem in itself - but with MKL 10, the
library layout has been completely whacked by our dear friends at intel, and
we need to change the library linkage info.

So first of all, fftw really does not help much, if at all, especially on
more than one processor, so just configure for my public fft's:

./configure sgi_altix ifort mpi pubfft

Secondly, we need to change the mkl linkage info (you could also just opt to
not use mkl, and as long as you are not running generalized Born
simulations, it won't matter much - you decide not to use mkl as part of the
"configure" dialog):

Anyway, best current guess for mkl linkage info, assuming you want MKL, is:

MATH_LIBS = -L$MKL_HOME/lib/64/ -Wl,--start-group
$MKL_HOME/lib/64/libmkl_intel.a $MKL_HOME/lib/64/libmkl_sequential.a
$MKL_HOME/lib/64/libmkl_core.a -Wl,--end-group -lpthread

(so you need to substitute in this line for the $MKL_HOME variable, and
stick the result in config.h in place of the current definition of
MATH_LIBS)

I have no reason to believe that the 3 lines you added at the end of
config.h are doing you any good.

Regards - Bob Duke

----- Original Message -----
From: "Vijay Manickam Achari" <vjrajamany_at_yahoo.com>
To: "Amber mailing List" <AMBER_at_ambermd.org>
Sent: Monday, April 06, 2009 3:27 AM
Subject: [AMBER] pmemd compilation/make
failed -mkl_vml_service_threader_z_1i_c_1o

Hi,
I am configuring pmemd in SMP machine SGI Altix 4700 itanium 128 cores (SLES
10.2 IA64 Intel compilers & MKL version 10.0.010) as below:
/usr/local/amber9/src/pmemd # ./configure sgi_altix ifort mpi fftw

But the compilation failed, as errors below:

fft1d.f90:(.text+0x8c2): undefined reference to `dfftw_destroy_plan_'
fft1d.o: In function `fft1d_mod_mp_fft1d_create_':
fft1d.f90:(.text+0xbc2): undefined reference to `dfftw_plan_dft_1d_'
fft1d.f90:(.text+0xbf2): undefined reference to `dfftw_plan_dft_1d_'
/opt/intel/mkl/10.0.010/lib/64/libmkl_intel_thread.a(vml_threading_templates.o):
In function `mkl_vml_service_threader_z_1i_c_1o':
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x92):
undefined reference to `__kmpc_global_thread_num'
/opt/intel/mkl/10.0.010/lib/64/libmkl_intel_thread.a(vml_threading_templates.o):
In function `L_mkl_vml_service_threader_z_1i_c_1o_2325__par_loop0_2$0':
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x442):
undefined reference to `__kmpc_ok_to_fork'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x472):
undefined reference to `__kmpc_push_num_threads'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x4e2):
undefined reference to `__kmpc_fork_call'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x502):
undefined reference to `__kmpc_serialized_parallel'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x582):
undefined reference to `__kmpc_end_serialized_parallel'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x6f2):
undefined reference to `__kmpc_for_static_init_4'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x852):
undefined reference to `__kmpc_for_static_fini'
/opt/intel/mkl/10.0.010/lib/64/libmkl_intel_thread.a(vml_threading_templates.o):
In function `mkl_vml_service_threader_z_1i_2o':
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x9c2):
undefined reference to `__kmpc_global_thread_num'
/opt/intel/mkl/10.0.010/lib/64/libmkl_intel_thread.a(vml_threading_templates.o):
In function `L_mkl_vml_service_threader_z_1i_2o_2299__par_loop1_2$1':
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0xd52):
undefined reference to `__kmpc_ok_to_fork'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0xd82):
undefined reference to `__kmpc_push_num_threads'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0xdf2):
undefined reference to `__kmpc_fork_call'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0xe12):
undefined reference to `__kmpc_serialized_parallel'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0xe92):
undefined reference to `__kmpc_end_serialized_parallel'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0xff2):
undefined reference to `__kmpc_for_static_init_4'
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x1162):
undefined reference to `__kmpc_for_static_fini'
/opt/intel/mkl/10.0.010/lib/64/libmkl_intel_thread.a(vml_threading_templates.o):
In function `mkl_vml_service_threader_z_2i_1o':
_tmp/treading_linux64_intel_thread/vml_threading_templates.c:(.text+0x1282):
undefined reference to `__kmpc_global_thread_num'
/opt/intel/mkl/10.0.010/lib/64/libmkl_intel_thread.a(vml_threading_templates.o):
In function `L_mkl_vml_service_threader_z_2i_1o_2273__par_loop2_2$2':

Attached is the config.h file for your review. Please assist me in this.
Thanks.

Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
 vjramana_at_gmail.com

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