RE: AMBER: PMEMD installation problem.

From: Cenk \(Jenk\) Andac <"Cenk>
Date: Mon, 8 Sep 2008 02:16:38 -0700 (PDT)

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.rosswalker.co.uk> wrote:
From: Ross Walker <ross.rosswalker.co.uk>
Subject: RE: AMBER: PMEMD installation problem.
To: amber.scripps.edu
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

Ross

  







From:
owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of Cenk
(Jenk) Andac

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

To: amber.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.yahoo.com
  
  
  
  
  
 


  





 


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo.scripps.edu
Received on Wed Sep 10 2008 - 06:07:19 PDT
Custom Search