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
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Received on Thu Nov 10 2011 - 00:30:02 PST
