AMBER Archive (2008)

Subject: Re: AMBER: PMEMD installation problem.

From: Robert Duke (
Date: Mon Sep 08 2008 - 07:20:15 CDT

That should work fine. PMEMD only requires mpif77-level functionality - we don't use any f90 modules stuff as it relates to mpi.
Regards - Bob Duke
  ----- Original Message -----
  From: Cenk (Jenk) Andac
  Sent: Monday, September 08, 2008 5:16 AM
  Subject: RE: AMBER: PMEMD installation problem.

        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:
                ifort -c -auto -tpp7 -xP -ip -O3 pmemd.f90
                /lib/cpp -traditional -P -I/home_palamut2/software/library/lam/include -DPUBFFT -DBINTRAJ -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL -DFFTLOADBAL_2PROC erfcfun.fpp erfcfun.f90
                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 -Wl,-rpath=/lib64:/usr/lib64:/opt/exp_soft/64/intel/lib:/opt/exp_soft/64/intel/mkl/lib/em64t:/home_palamut2/software/library/lam/lib/:home_palamut2/software/application/amber10/src/netcdf/lib/:/opt/d-cache/dcap/lib:/opt/glite/lib:/opt/globus/lib:/opt/lcg/lib:/opt/log4cxx/lib/:/opt/xerces-c/lib/:/opt/c-ares/lib
                /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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