Re: [AMBER] Passing the free-format flag to files in sander and nmode

From: Michael Sternberg <sternberg.anl.gov>
Date: Thu, 10 Nov 2011 02:03:25 -0600

On Nov 9, 2011, at 23:51 , Jason Swails wrote:

> One thing that may complicate things here. The flag names and ordering changed significantly between AmberTools 1.4/Amber 11 release and AmberTools 1.5 release. The result was that a script had to be written to patch up the config.h file created by AT 1.5 to get it to compile Amber 11. This is the AT15_Amber11.py script in $AMBERHOME. You need to run this script after each time you run configure in order to compile the Amber portion.

Sure, I read and followed the instructions. I'm following David's suggestion with GNU compilers ...

Here's a snippet from my build script. Are you saying I need to re-run AT15_Amber11.py right before step (4)?

==============================================
    # (1) AmberTools serial
    cd $prefix/AmberTools/src
    #./configure intel
    ./configure gnu
    make install

    # (2) Amber main serial; first apply AmberTools patch
    cd $prefix
    python $build_root/patched/amber11/AT15_Amber11.py
    cd $prefix/src
    make serial

exit

    # (3) AmberTools parallel
    # "you must first configure and build a serial AmberTools."

    # for parallel, give access to newly provided byacc (and whatever else)
    export PATH=$prefix/bin:$PATH

    cd $prefix/AmberTools/src
    make clean
    #./configure -mpi intel
    ./configure -mpi gnu
    make install

    # (4) Amber main parallel
    cd $prefix/src
    make parallel
==============================================

The first time around (with all steps and using intel) I only got sander.MPI and sander.LES.MPI compiled, followed by this:

...
make -C src/ parallel
make[2]: Entering directory `/opt/soft/amber-11-1/src/pmemd/src'
cpp -traditional -DMPI -P -DMKL -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT master_setup.fpp master_setup.f90
mpif90 -ipo -O3 -no-prec-div -xHost -c master_setup.f90
cpp -traditional -DMPI -P -DMKL -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT pmemd.fpp pmemd.f90
mpif90 -ipo -O3 -no-prec-div -xHost -c pmemd.f90
pmemd.f90(92): error #6404: This name does not have a type, and must have an explicit type. [MYTASKID]
  call mstartup(mytaskid, numtasks)
----------------^
pmemd.f90(92): error #6404: This name does not have a type, and must have an explicit type. [NUMTASKS]
  call mstartup(mytaskid, numtasks)
--------------------------^
pmemd.f90(229): error #6404: This name does not have a type, and must have an explicit type. [GBL_MY_ATM_LST]
               gbl_my_atm_lst)
---------------^
pmemd.f90(228): error #6784: The number of actual arguments cannot be greater than the number of dummy arguments. [RUNMD]
    call runmd(natom, atm_crd, atm_mass, atm_frc, atm_vel, atm_last_vel, &
---------^
pmemd.f90(240): error #6404: This name does not have a type, and must have an explicit type. [NOTDONE]
    notdone = 0
----^
pmemd.f90(241): error #6404: This name does not have a type, and must have an explicit type. [MPI_INTEGER]
    call mpi_bcast(notdone, 1, mpi_integer, 0, mpi_comm_world, err_code_mpi)
-------------------------------^
pmemd.f90(241): error #6404: This name does not have a type, and must have an explicit type. [MPI_COMM_WORLD]
    call mpi_bcast(notdone, 1, mpi_integer, 0, mpi_comm_world, err_code_mpi)
-----------------------------------------------^
pmemd.f90(241): error #6404: This name does not have a type, and must have an explicit type. [ERR_CODE_MPI]
    call mpi_bcast(notdone, 1, mpi_integer, 0, mpi_comm_world, err_code_mpi)
---------------------------------------------------------------^
compilation aborted for pmemd.f90 (code 1)
make[2]: *** [pmemd.o] Error 1

Looks like mpi.h was not passed ...


With best regards,
Michael

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 10 2011 - 00:30:02 PST
Custom Search