AMBER Archive (2008)

Subject: AMBER: PMEMD installation problem.

From: Cenk \(Jenk\) Andac (
Date: Mon Sep 08 2008 - 01:58:42 CDT

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:



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
-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 `openpty'

make[1]: *** [pmemd] Error 1

make[1]: Leaving directory `/home_palamut2/software/application/amber10/src/pmemd/src'

make: *** [install] Error 2

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

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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