Re: [AMBER] compiling pmemd in amber9

From: Vijay Manickam Achari <>
Date: Wed, 7 Dec 2011 03:22:30 +0000 (GMT)


Thanks for the tips.

During the configure part it asks to enter MKL directory and give option yes / no to continue. Upon chosing "no" the compilation run and stop in short while with out any error. I give the last few lines of that compilation below:

ifort -c -auto -tpp7 -xW -ip -O3 erfcfun.f90
ifort: command line remark #10148: option '-tp' not supported
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     -limf -lsvml
make[1]: Leaving directory `/usr/local/amber9/src/pmemd/src'

Because this is serial compilation, and there is no error I expect a pmemd executable might present in /usr/local/amber9/exe/ directory but non exist.


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

 From: David A Case <>
To: Vijay Manickam Achari <>; AMBER Mailing List <>
Sent: Tuesday, 6 December 2011, 21:41
Subject: Re: [AMBER] compiling pmemd in amber9
On Tue, Dec 06, 2011, Vijay Manickam Achari wrote:
> ./configure linux_em64t ifort nopar
> this also fails to compile as below::
> .....
> .....
> .....
> /mnt/data/cluster/intel/mkl/10.0.010/lib/em64t/libmkl_intel_thread.a(vml_threading_templates.o): In function `mkl_vml_service_openmp_get_num_procs':
> _tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x5022): undefined reference to `omp_get_num_procs'
> /mnt/data/cluster/intel/mkl/10.0.010/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'
> make[1]: *** [pmemd] Error 1
> make[1]: Leaving directory `/usr/local/amber9/src/pmemd/src'
> make: *** [all] Error 2
> ptmlxclus:/usr/local/amber9/src/pmemd # 

You should undefine MKL_HOME from your environment, to compile pmemd without
MKL support.  Amber9 was released before MKL version 10 was, so things won't
necessarily work.  Further, you don't get much speedup by using MKL anyway,
so the simplest thing is not to try.

...good luck....dac

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Received on Tue Dec 06 2011 - 19:30:06 PST
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