AMBER Archive (2009)

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

From: Giorgos Lamprinidis (lamprinidis_at_pharm.uoa.gr)
Date: Tue Jul 14 2009 - 02:29:09 CDT

Ross,

You mean that using mvapich i get faster calculations compared to openmpi,
when runing pmemd or sander.MPI ?

Regards

George Lamprinidis PhD
School of Pharmacy
University of Athens
Greece

----- Original Message -----
From: "Ross Walker" <ross_at_rosswalker.co.uk>
To: <jun_at_strubi.ox.ac.uk>; "'AMBER Mailing List'" <amber_at_ambermd.org>
Sent: Monday, July 13, 2009 10:18 PM
Subject: RE: [AMBER] Need help for PMEMD 10 installation

> 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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