Thank you all.
I really appreciated the help.
Best regards,
Jenk
--- On Mon, 9/8/08, Robert Duke <rduke.email.unc.edu> wrote:
From: Robert Duke <rduke.email.unc.edu>
Subject: Re: AMBER: PMEMD installation problem.
To: amber.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.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.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
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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.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 - 06:07:22 PDT
