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
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Received on Wed Sep 10 2008 - 06:07:19 PDT
