AMBER Archive (2009)

Subject: RE: [AMBER] Need help for PMEMD 10 installation

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jul 13 2009 - 14:18:26 CDT

Hi Jun,

I don't think there was ever an openmpi configure script for PMEMD, largely
because the openMPI performance is pretty awful compared infiniband tuned
libraries such as MVAPICH. Nevertheless it should be fairly easy to get to
work. Just open your config.h file and make the edits I suggested in the
earlier mail.

1) Change all ifort to mpif90, all icc to mpcc

2) Remove the references to the mpi libraries since these will be handled by
mpif90.

3) make clean; make

This should like okay this time.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Jun Dong
> Sent: Monday, July 13, 2009 11:11 AM
> To: AMBER Mailing List
> Subject: RE: [AMBER] Need help for PMEMD 10 installation
>
> Dear Ross,
> I recompile openmpi-1.3.2 using ifort. Then use its mpif90 and mpicc to
> compile pmemd,
> ./configure linux_em64t ifort mpich
> make
> /lib/cpp -traditional -P -I/raid/1/software/AMBER/openmpiifort/include
> -DPUBFFT -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -
> DDIRFRC_NOVEC -DMKL -DFFTLOADBAL_2PROC get_cmdline.fpp get_cmdline.f90
> mpif90 -c -auto -tpp7 -xP -ip -O3 get_cmdline.f90
> ifort: command line remark #10148: option '-tp' not supported
> /lib/cpp -traditional -P -I/raid/1/software/AMBER/openmpiifort/include
> -DPUBFFT -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -
> DDIRFRC_NOVEC -DMKL -DFFTLOADBAL_2PROC master_setup.fpp
> master_setup.f90
> mpif90 -c -auto -tpp7 -xP -ip -O3 master_setup.f90
> ifort: command line remark #10148: option '-tp' not supported
> /lib/cpp -traditional -P -I/raid/1/software/AMBER/openmpiifort/include
> -DPUBFFT -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -
> DDIRFRC_NOVEC -DMKL -DFFTLOADBAL_2PROC pmemd.fpp pmemd.f90
> mpif90 -c -auto -tpp7 -xP -ip -O3 pmemd.f90
> ifort: command line remark #10148: option '-tp' not supported
> /lib/cpp -traditional -P -I/raid/1/software/AMBER/openmpiifort/include
> -DPUBFFT -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_EFS -DDIRFRC_COMTRANS -
> DDIRFRC_NOVEC -DMKL -DFFTLOADBAL_2PROC erfcfun.fpp erfcfun.f90
> mpif90 -c -auto -tpp7 -xP -ip -O3 erfcfun.f90
> ifort: command line remark #10148: option '-tp' not supported
> mpif90 -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
> /raid/1/software/linux/compiler/mkl/9.1.023/lib/em64t/libmkl_em64t.a -
> L/raid/1/software/linux/compiler/mkl/9.1.023/lib/em64t -lguide -
> lpthread -L/raid/1/software/AMBER/openmpiifort/lib -lmpich -limf -lsvml
> -Wl,-
> rpath=/raid/1/software/linux/compiler/mkl/9.1.023/lib/em64t:/raid/1/sof
> tware/AMBER/openmpiifort/lib:/raid/1/software/linux/compiler/lfc64/lib
> ld: cannot find -lmpich
> make[1]: *** [pmemd] Error 1
> make[1]: Leaving directory
> `/raid/1/software/AMBER/amber10/src/pmemd/src'
> make: *** [all] Error 2
>
> I just wonder if there is a precompiled pmemd for linux 64 bit with
> openmpi that can be downloaded. Since it is not so easy to compile.
> Many thanks,
> Jun
>
>
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