AMBER Archive (2008)

Subject: RE: AMBER: PMEMD installation problem.

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Sep 08 2008 - 03:21:17 CDT

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/int
el/mkl/lib/em64t:/home_palamut2/software/library/lam/lib/:home_palamut2/soft
ware/application/amber10/src/netcdf/lib/:/opt/d-cache/dcap/lib:/opt/glite/li
b:/opt/globus/lib:/opt/lcg/lib:/opt/log4cxx/lib/:/opt/xerces-c/lib/:/opt/c-a
res/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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