[gentoo-commits] gentoo-x86 commit in sci-chemistry/cns/files: cns_solve_env_sh 1.2.1-allow-gcc-openmp.patch

[Donnie Berkholz (dberkholz)]

dberkholz    08/08/03 07:54:01

  Added:                cns_solve_env_sh 1.2.1-allow-gcc-openmp.patch
  Log:
  Bump. Keyword ~amd64; add OpenMP support for parallel refinement; (#209805) Fix a number of environment variables and cns_ functions to work properly.
  (Portage version: 2.2_rc5/cvs/Linux 2.6.26 x86_64)

Revision  Changes    Path
1.1                  sci-chemistry/cns/files/cns_solve_env_sh

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/files/cns_solve_env_sh?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/files/cns_solve_env_sh?rev=1.1&content-type=text/plain

Index: cns_solve_env_sh
===================================================================
#!/bin/sh
#
# This file sets up the appropriate environmental variables and paths
# for CNSsolve. In the case of the same machines with different versions
# of the OS, backward compatibility is assumed - ie. a later version will
# be setup for a previous version of the OS if nothing else is available.
#
#   written by: Paul Adams
#
#   copyright Yale University
#
# ==========================================================================
#
# >>>>>> Important: define the location of the CNSsolve directory <<<<<<
#
# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY

	CNS_SOLVE=_CNSsolve_location_
	
#
# ==========================================================================
#
# full expansion of the CNS_SOLVE variable prior to use.
#
export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE
#
# ==========================================================================
#
# set the number of threads for SGI multiprocessors
# if this causes a problem on other systems it can be commented out
#
export MP_SET_NUMTHREADS; MP_SET_NUMTHREADS=1
#
# ==========================================================================
#
# get the machine architecture
#
if [ -d $CNS_SOLVE ]; then
  if [ ! "$CNS_ARCH" ]; then
    export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch`
  fi
else
  export CNS_ARCH; CNS_ARCH='unknown'
fi
#
# ==========================================================================
#
# general environmental variables
#
export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries
export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules
export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar
export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb
export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal
export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr
export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray
export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal
export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr
export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib
#
# general user aliases
#
cns_web () { $CNS_SOLVE/bin/cns_web; }
cns_header () { $CNS_SOLVE/bin/cns_header; }
cns_info () { cat $CNS_SOLVE/bin/cns_info; }
cns_transfer () { $CNS_SOLVE/bin/cns_transfer; }
if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then
  cns_edit () { $CNS_SOLVE/bin/cns_edit_local; }
else
  cns_edit () { $CNS_SOLVE/bin/cns_edit; }
fi
run_tutorial () { "csh -f tutorial.csh"; }
#
# g77 compilation and use
#
g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; }
g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; }
#
# developer aliases
#
run_tests () { $CNS_SOLVE/bin/run_tests; }
run_diffs () { $CNS_SOLVE/bin/run_diffs; }
maketar () { $CNS_SOLVE/bin/maketar; }
create_patch () { $CNS_SOLVE/bin/create_patch; }
#
#
# ==========================================================================
#
# to do expansions - unset noglob just in case user has it otherwise
#
set +f
#
# try to set up appropriate path
#
# first strip off any trailing information (eg. _g77)
#
CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'`
#
cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'`
cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'`
cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'`
cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'`
cns_minor=`echo $cns_major | sed -e 's/\./ /g'`
#
# if we are looking for a specific type of setup then limit search
#
cns_dirs=""
if [ ! "$CNS_G77" ]; then
  if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then
    cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`"
  fi
else
  CNS_ARCH="${CNS_ARCH}_g77"
  if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then
    cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`"
  fi
fi
#
# first look for an exact match (with os version)
#
#
cns_found=0
if [ -n "$cns_dirs" ]; then
  for cns_dir in $cns_dirs ; do
    cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'`
    if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
      if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \
           $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ]; then
        cns_archenv=$cns_dir
        cns_found=1
      fi
    fi
  done
#
#
# now look for an exact match (without os version)
#
  if [ $cns_found -eq 0 ]; then
    for cns_dir in $cns_dirs ; do
      if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
        if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \
             $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then
          cns_archenv=$cns_dir
          cns_found=1
        fi
      fi
    done
  fi
#
# now look for a backwards compatible match (with os version major/minor)
#
  if [ $cns_found -eq 0 ]; then
    for cns_dir in $cns_dirs ; do
      if [ $cns_found -eq 0 ]; then
        cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'`
        if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
          if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then
	    osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'`
            if [ $osv_test -eq 1 ]; then
              cns_archenv=$cns_dir
	      cns_found=1
            fi
          fi
        fi
      fi
    done
  fi
#
# now look for a wildcard match on cpu
#
  if [ $cns_found -eq 0 ]; then
    cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'`
    cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'`
    for cns_dir in $cns_dirs ; do
      if [ $cns_found -eq 0 ]; then
        cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'`
        cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'`
        if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
          if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \
               $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then
  	    cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'`
            if [ $cpu_test -eq 1 ]; then
              cns_archenv=$cns_dir
	      cns_found=1
            fi
          fi
        fi
      fi
    done
  fi
fi
#
# if found set environment
#
if [ $cns_found -eq 1 ]; then
  #
  # set installation and source directory
  #
  export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv
  export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source
  #
  # path for CNSsolve utility programs
  #
  if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then
    export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils`
  fi
  #
  # path for CNSsolve executable if installed
  #
  if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then
    export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin`
  fi
fi
#
unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor
unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same
unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test
#



1.1                  sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch?rev=1.1&content-type=text/plain

Index: 1.2.1-allow-gcc-openmp.patch
===================================================================
--- source/xfft.f.orig	2008-08-03 00:36:52.000000000 -0700
+++ source/xfft.f	2008-08-03 00:37:06.000000000 -0700
@@ -514,7 +514,7 @@
       LOGICAL QHERM
       DOUBLE PRECISION XRCELL(9), MAPR
 C local
-!$    integer omp_get_max_threads, kmp_get_stacksize
+!$    integer omp_get_max_threads
       LOGICAL DONE
       DOUBLE PRECISION ZERO
       PARAMETER (ZERO=0.0D0)
@@ -537,7 +537,7 @@
       NBPP=1
 ! The following command is only relevant for the ifort compiler (if -openmp option is used).
 ! If your compiler is not ifort, and gives an error, just comment the next line out:
-!$      if (kmp_get_stacksize().lt.2**23) call kmp_set_stacksize(2**23)
+!       if (kmp_get_stacksize().lt.2**23) call kmp_set_stacksize(2**23)
 ! Explanation: the default KMP_STACKSIZE of ifort is 2**21 bytes (2Mb) for 32bit, 
 ! and 2**22 bytes (4Mb) for 64bit.
 ! This may be low for big structures, which leads to segmentation faults!