AMBER Archive (2008)

Subject: Re: AMBER: PMEMD installation problem.

From: Cenk \(Jenk\) Andac (cenk_andac_at_yahoo.com)
Date: Mon Sep 08 2008 - 07:46:19 CDT

Thank you all.

I really appreciated the help.

Best regards,

Jenk

--- On Mon, 9/8/08, Robert Duke <rduke_at_email.unc.edu> wrote:
From: Robert Duke <rduke_at_email.unc.edu>
Subject: Re: AMBER: PMEMD installation problem.
To: amber_at_scripps.edu
Date: Monday, September 8, 2008, 7:20 AM

 
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
  To: amber_at_scripps.edu
  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?

regards,

Jenk

        
        
        
        

---
        On Mon, 9/8/08, Ross Walker <ross_at_rosswalker.co.uk>
        wrote:

        From:
          Ross Walker <ross_at_rosswalker.co.uk>
Subject: RE: AMBER: PMEMD
          installation problem.
To: amber_at_scripps.edu
Date: Monday,
          September 8, 2008, 3:21 AM

          
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          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
          Ross
           
          
          
          
          From:
          owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
          Of Cenk (Jenk) Andac
Sent: Sunday, September 07, 2008
          11:59 PM
To: amber_at_scripps.edu
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:
 
 RFRC_EFS -DDIRFRC_COMTRANS
                -DDIRFRC_NOVEC -DMKL -DFFTLOADBAL_2PROC pmemd.fpp
                pmemd.f90
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/liblam.so:
                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,

Jenk

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
                
                E-Mail:cenk_andac_at_yahoo.com
           

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