AMBER Archive (2008)

Subject: RE: AMBER: PMEMD installation problem.

From: Cenk \(Jenk\) Andac (
Date: Mon Sep 08 2008 - 04:16:38 CDT

Hi Ross,

Thanks for replying.

I have only mpif77 in .../lam7.1.4/bin directory
So I changed ifort to mpif77 and made MPI_LIBS look like
MPI_LIBS = -L$(MPI_LIBDIR) -ldl -lpthread
in config.h

pmemd installation did not give any error messages this time. However, it is OK to use mpif77 instead of mpif90?



--- On Mon, 9/8/08, Ross Walker <> wrote:
From: Ross Walker <>
Subject: RE: AMBER: PMEMD installation problem.
Date: Monday, September 8, 2008, 3:21 AM


Hi Cenk,


This likely comes from the wrong MPI libraries being linked in. Try
editing the config.h file and change all instances of ifort to mpif90. Also
take out the libraries specified on the MPI_LIBS directory. Then recompile and
see if this works.


All the best



From: [] On Behalf Of Cenk
(Jenk) Andac

Sent: Sunday, September 07, 2008 11:59 PM


Subject: AMBER: PMEMD installation problem.


  Hi all,


  I have been trying to install PMEMD using the ifort v9.1, intel-MKL v9.1, lam
  v7.1.4 and pubfft libraries on the server (2 X intel Xeon Dual-Core 2.6 GHz
  em64t) of a dedicated cluster computer system (76 nodes and 2 X intel Xeon
  Dual-Core 2.6 GHz em64t/node).


  I got the following error message during the installation:


  pmemd.fpp pmemd.f90

  ifort -c -auto -tpp7 -xP -ip -O3 pmemd.f90

  /lib/cpp -traditional -P  -I/home_palamut2/software/library/lam/include

  ifort -c -auto -tpp7 -xP -ip -O3 erfcfun.f90

  ifort  -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 
  /home_palamut2/software/application/amber10/src/netcdf/lib/libnetcdf.a /opt/exp_soft/64/intel/mkl/lib/em64t/libmkl_em64t.a
  -L/opt/exp_soft/64/intel/mkl/lib/em64t -lguide -lpthread
  -L/home_palamut2/software/library/lam/lib -llamf77mpi -lmpi -llam -ldl
  -lpthread -limf -lsvml

  /home_palamut2/software/library/lam/lib/ undefined reference to

  make[1]: *** [pmemd] Error 1

  make[1]: Leaving directory

  make: *** [install] Error 2


  I will appreciate it if someone let me know how to overcome the installation


  Thanks in advance,




  P.S. Currently we have PMEMD installed with mpich2 libraries. We also would
  like to install PMEMD with lam7.1.4 libraries.
  Cenk Andac, M.S., Ph.D. Candidate

  School of Pharmacy at

  Gazi University-Ankara Turkiye
  Address: Bandirma Sok. No:6
  Etiler, Ankara, 06330 Turkey
  Cell: +90-(536)-4813012



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