CHARMM
Background
Building CHARMM
Instructions for instrumenting CHARMM with TAU:
1. My gfortran compiler had problems with some WRITE commands in source/nbond/enbips.src so I commented out line 3288 and 3301.
2. CHARMM finds MPI via environment variables so:
%> export MPI_INCLUDE=<mpi include dir> %> export MPI_LIB=<mpi include dir>
3. I started with source based instrumentation (via PDT), notice the use of a selective instrumentation file to tune instrumentation:
%> export TAU_MAKEFILE=<tau home>/<arch>/lib/Makefile.tau-mpi-pdt %> export TAU_OPTIONS='-optKeepFiles -optVerbose -optTauSelectFile=<full path to select.tau>'
%> cat select.tau BEGIN_EXCLUDE_LIST # omit this routine, TAU has problems this some CONTINUE statements MASTER.0.TIMRB::TIMRB # omit these low level routine that contribute to excessive instrumentation # overhead ERFCD EXCH5 GAUSSI MPI_Irecv() MPI_Isend() NINDX OLDRANDOM ORDER5 PATOM PMEUTIL::CFFTB PMEUTIL::CFFTB1 PMEUTIL::CFFTF PMEUTIL::CFFTF1 PMEUTIL::FILL_BSPLINE PMEUTIL::PASSB2 PMEUTIL::PASSB4 PMEUTIL::PASSF2 PMEUTIL::PASSF4 PROCATOMS RANDOM ATOMID CHARMM => ATOMID CHARMM => CMAPSPI CHARMM => GENIC::SUB600 CHARMM => GETRES CHARMM => GETSEG CHARMM => HYDROG CHARMM => INITIA CHARMM => LONE CHARMM => MATOM CHARMM => WRNDIE CMAPSPI CNVTUC EQST EQSTA GENIC::SUB600 GETRES GETSEG HYDROG INITIA LONE MATOM TRIME WRNDIE # new routines CHARMM => EQSTWC CHARMM => EQSTWC::SUB10 EQSTWC EQSTWC::SUB10 MPI_Comm_rank() MPI_Comm_size() PMEUTIL::XY_ZX_TR_RCV PMEUTIL::ZX_TRANS_RECV END_EXCLUDE_LIST
4. Now I need to override the default mpif90 compiler with TAU's tau_f90.sh wrapper script. The easiest way to do this was with global replace in install.com (you may want to backup this file so you can compile CHARMM without TAU):
%> sed -i 's/mpif90/tau_f90.sh/g' install.com
and compile with the xlarge version with MPI:
%> ./install.com gnu xlarge NOLOG M
Now when you run a simulation you will get TAU profile.* files in your current directory.