| 1 |
jlec 10/11/25 13:35:42 |
| 2 |
|
| 3 |
Added: cns_solve_env_sh-1.3_p3 1.3_p3-delete.patch |
| 4 |
1.3_p3-gentoo.patch |
| 5 |
Removed: 1.3-delete.patch 1.3-gentoo.patch |
| 6 |
cns_solve_env_sh-1.3 |
| 7 |
Log: |
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Version Bump, thanks alexxy telling me this; fix for correct linking |
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|
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(Portage version: 2.2.0_alpha5/cvs/Linux x86_64) |
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|
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Revision Changes Path |
| 13 |
1.1 sci-chemistry/cns/files/cns_solve_env_sh-1.3_p3 |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p3?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p3?rev=1.1&content-type=text/plain |
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|
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Index: cns_solve_env_sh-1.3_p3 |
| 19 |
=================================================================== |
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#!/bin/sh |
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# |
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# This file sets up the appropriate environmental variables and paths |
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# for CNSsolve. In the case of the same machines with different versions |
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# of the OS, backward compatibility is assumed - ie. a later version will |
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# be setup for a previous version of the OS if nothing else is available. |
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# |
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# written by: Paul Adams |
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# |
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# copyright Yale University |
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# |
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# ========================================================================== |
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# |
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# >>>>>> Important: define the location of the CNSsolve directory <<<<<< |
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# |
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# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY |
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|
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CNS_SOLVE=_CNSsolve_location_ |
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|
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# |
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# ========================================================================== |
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# |
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# full expansion of the CNS_SOLVE variable prior to use. |
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# |
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export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE |
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# |
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# ========================================================================== |
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# |
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# get the machine architecture |
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# |
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if [ -d $CNS_SOLVE ]; then |
| 51 |
if [ ! "$CNS_ARCH" ]; then |
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export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch` |
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fi |
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else |
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export CNS_ARCH; CNS_ARCH='unknown' |
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fi |
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# |
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# ========================================================================== |
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# |
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# system variables for OpenMP |
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# |
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# The default stack sizes are usually insufficient, especially when |
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# CNS is compiled using OpenMP. If the stack sizes are too |
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# small segfaults may occur. Recommended setting for "stacksize": |
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limit stacksize unlimited |
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# |
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# KMP_STACKSIZE is specific for Intel ifort, icc: |
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##setenv KMP_STACKSIZE 256m |
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# |
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# OMP_STACKSIZE is used by all compilers: |
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setenv OMP_STACKSIZE 256m |
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# |
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# Uncomment the following line and change as appropriate to set the number |
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# of processors (threads) to use. |
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###setenv OMP_NUM_THREADS 4 |
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# |
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# ========================================================================== |
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# |
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# general environmental variables |
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# |
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export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries |
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export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules |
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export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar |
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export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb |
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export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal |
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export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr |
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export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray |
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export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal |
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export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr |
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export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib |
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# |
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# general user aliases |
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# |
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cns_web () { $CNS_SOLVE/bin/cns_web; } |
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cns_header () { $CNS_SOLVE/bin/cns_header; } |
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cns_info () { cat $CNS_SOLVE/bin/cns_info; } |
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cns_transfer () { $CNS_SOLVE/bin/cns_transfer; } |
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if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then |
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cns_edit () { $CNS_SOLVE/bin/cns_edit_local; } |
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else |
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cns_edit () { $CNS_SOLVE/bin/cns_edit; } |
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fi |
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# |
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# g77 compilation and use |
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# |
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g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; } |
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g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; } |
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# |
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# developer aliases |
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# |
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run_tests () { $CNS_SOLVE/bin/run_tests; } |
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run_diffs () { $CNS_SOLVE/bin/run_diffs; } |
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maketar () { $CNS_SOLVE/bin/maketar; } |
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create_patch () { $CNS_SOLVE/bin/create_patch; } |
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# |
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# |
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# ========================================================================== |
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# |
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# to do expansions - unset noglob just in case user has it otherwise |
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# |
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set +f |
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# |
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# try to set up appropriate path |
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# |
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# first strip off any trailing information (eg. _g77) |
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# |
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CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'` |
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# |
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cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'` |
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cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'` |
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cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'` |
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cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'` |
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cns_minor=`echo $cns_major | sed -e 's/\./ /g'` |
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# |
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# if we are looking for a specific type of setup then limit search |
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# |
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cns_dirs="" |
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if [ ! "$CNS_G77" ]; then |
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if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then |
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cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" |
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fi |
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else |
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CNS_ARCH="${CNS_ARCH}_g77" |
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if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then |
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cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" |
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fi |
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fi |
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# |
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# first look for an exact match (with os version) |
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# |
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# |
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cns_found=0 |
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if [ -n "$cns_dirs" ]; then |
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for cns_dir in $cns_dirs ; do |
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cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'` |
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if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then |
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if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \ |
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$cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ]; then |
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cns_archenv=$cns_dir |
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cns_found=1 |
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fi |
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fi |
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done |
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# |
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# |
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# now look for an exact match (without os version) |
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# |
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if [ $cns_found -eq 0 ]; then |
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for cns_dir in $cns_dirs ; do |
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if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then |
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if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \ |
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$cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then |
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cns_archenv=$cns_dir |
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cns_found=1 |
| 175 |
fi |
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fi |
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done |
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fi |
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# |
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# now look for a backwards compatible match (with os version major/minor) |
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# |
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if [ $cns_found -eq 0 ]; then |
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for cns_dir in $cns_dirs ; do |
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if [ $cns_found -eq 0 ]; then |
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cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'` |
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if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then |
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if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then |
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osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'` |
| 189 |
if [ $osv_test -eq 1 ]; then |
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cns_archenv=$cns_dir |
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cns_found=1 |
| 192 |
fi |
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fi |
| 194 |
fi |
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fi |
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done |
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fi |
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# |
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# now look for a wildcard match on cpu |
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# |
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if [ $cns_found -eq 0 ]; then |
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cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'` |
| 203 |
cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'` |
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for cns_dir in $cns_dirs ; do |
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if [ $cns_found -eq 0 ]; then |
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cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'` |
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cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'` |
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if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then |
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if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \ |
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$cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then |
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cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'` |
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if [ $cpu_test -eq 1 ]; then |
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cns_archenv=$cns_dir |
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cns_found=1 |
| 215 |
fi |
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fi |
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fi |
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fi |
| 219 |
done |
| 220 |
fi |
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fi |
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# |
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# if found set environment |
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# |
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if [ $cns_found -eq 1 ]; then |
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# |
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# set installation and source directory |
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# |
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export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv |
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export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source |
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# |
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# path for CNSsolve utility programs |
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# |
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if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then |
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export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils` |
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fi |
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# |
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# path for CNSsolve executable if installed |
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# |
| 240 |
if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then |
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export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin` |
| 242 |
fi |
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fi |
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# |
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unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor |
| 246 |
unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same |
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unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test |
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# |
| 249 |
|
| 250 |
|
| 251 |
|
| 252 |
1.1 sci-chemistry/cns/files/1.3_p3-delete.patch |
| 253 |
|
| 254 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/cns/files/1.3_p3-delete.patch?rev=1.1&view=markup |
| 255 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/cns/files/1.3_p3-delete.patch?rev=1.1&content-type=text/plain |
| 256 |
|
| 257 |
Index: 1.3_p3-delete.patch |
| 258 |
=================================================================== |
| 259 |
diff --git a/utils/cluster_struc.cpp b/utils/cluster_struc.cpp |
| 260 |
index b64467a..5f727db 100644 |
| 261 |
--- a/utils/cluster_struc.cpp |
| 262 |
+++ b/utils/cluster_struc.cpp |
| 263 |
@@ -173,7 +173,7 @@ int main(int argc, char *argv[]) { |
| 264 |
for (int i = 0; i < nrstruc; i++) { |
| 265 |
delete[] neighbor[i]; |
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} |
| 267 |
- delete[] neighbor, neighborcount; |
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+ delete[] neighbor, delete[] neighborcount; |
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return 5; |
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} |
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if (rmsd < cutoff) { |
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|
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|
| 274 |
|
| 275 |
1.1 sci-chemistry/cns/files/1.3_p3-gentoo.patch |
| 276 |
|
| 277 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/cns/files/1.3_p3-gentoo.patch?rev=1.1&view=markup |
| 278 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/cns/files/1.3_p3-gentoo.patch?rev=1.1&content-type=text/plain |
| 279 |
|
| 280 |
Index: 1.3_p3-gentoo.patch |
| 281 |
=================================================================== |
| 282 |
diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto |
| 283 |
index 0d0dd3e..dd4b680 100644 |
| 284 |
--- a/instlib/source/Makefile.proto |
| 285 |
+++ b/instlib/source/Makefile.proto |
| 286 |
@@ -11,6 +11,8 @@ |
| 287 |
|
| 288 |
SHELL=/bin/sh |
| 289 |
|
| 290 |
+cns_string=`date "+%y%m%d%H%M"` |
| 291 |
+ |
| 292 |
# commands |
| 293 |
RM = /bin/rm |
| 294 |
|
| 295 |
@@ -19,32 +21,26 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o |
| 296 |
|
| 297 |
# the default is to make the cns executable |
| 298 |
cns_solve: |
| 299 |
- @ make -k printflags F77BUG="$(debug)" DEBUG="$(debug)" |
| 300 |
- @ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" |
| 301 |
- @ make -k exepurge |
| 302 |
+ @ make printflags F77BUG="$(debug)" DEBUG="$(debug)" |
| 303 |
+ @ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" |
| 304 |
+ @ make exepurge |
| 305 |
|
| 306 |
# rule for the fortran routines |
| 307 |
$(OBJS): |
| 308 |
- @ echo "compiling: $(@:.o=.f)"; \ |
| 309 |
- $(F77) -c $(F77FLAGS) $(@:.o=.f) |
| 310 |
+ $(F77) -c $(F77FLAGS) $(@:.o=.f) |
| 311 |
|
| 312 |
# rule for the dynamic memory allocation C routines |
| 313 |
dmemory.o: dmemory.c |
| 314 |
- @ echo ; echo "compiling: $?" |
| 315 |
- @ $(CC) -c $(CCFLAGS) $? |
| 316 |
+ $(CC) -c $(CCFLAGS) $? |
| 317 |
|
| 318 |
# rule for the machine specific C routines |
| 319 |
machine_c.o: machine_c.c |
| 320 |
- @ echo ; echo "compiling: $?" |
| 321 |
- @ $(CC) -c $(CCFLAGS) $? |
| 322 |
+ $(CC) -c $(CCFLAGS) $? |
| 323 |
|
| 324 |
# rule for the executable itself |
| 325 |
../bin/cns_solve: $(DEPENDS) |
| 326 |
- @ echo ; echo "linking: cns_solve"; echo |
| 327 |
- @ cns_string=`date "+%y%m%d%H%M"`; \ |
| 328 |
- $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ |
| 329 |
- $(LDFLAGS) \ |
| 330 |
- $(CNS_FFTDIR) $(CNS_FFTLIB); \ |
| 331 |
+ $(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ |
| 332 |
+ $(CNS_FFTDIR) $(CNS_FFTLIB) $(OMPLIB); \ |
| 333 |
if [ -x cns_solve-$$cns_string.exe ]; \ |
| 334 |
then echo "created executable file cns_solve-$$cns_string.exe"; \ |
| 335 |
echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \ |
| 336 |
@@ -59,7 +55,7 @@ printflags: |
| 337 |
@ echo; echo "flags:"; \ |
| 338 |
echo " fortran -> [$(F77)] $(F77FLAGS)"; \ |
| 339 |
echo " c -> [$(CC)] $(CCFLAGS)"; \ |
| 340 |
- echo " link -> [$(LD)] $(LDFLAGS) $(CNS_FFTDIR) $(CNS_FFTLIB)"; \ |
| 341 |
+ echo " link -> [$(LD)] $(LDFLAGS) $(CNS_FFTDIR) $(CNS_FFTLIB) $(OMP_LIB)"; \ |
| 342 |
echo |
| 343 |
|
| 344 |
# regenerate makefiles |
| 345 |
diff --git a/instlib/utils/Makefile b/instlib/utils/Makefile |
| 346 |
index 98de84f..4f32b34 100644 |
| 347 |
--- a/instlib/utils/Makefile |
| 348 |
+++ b/instlib/utils/Makefile |
| 349 |
@@ -22,17 +22,17 @@ utils: |
| 350 |
make clean |
| 351 |
|
| 352 |
.f: |
| 353 |
- $(F77) -o $@ $(F77FLAGS) $(@).f $(F77LINK) |
| 354 |
+ $(F77) $(LDFLAGS) -o $@ $(F77FLAGS) $(@).f $(F77LINK) |
| 355 |
|
| 356 |
.c: |
| 357 |
- $(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK) |
| 358 |
+ $(CC) $(LDFLAGS) -o $@ $(CCFLAGS) $(@).c $(CCLINK) |
| 359 |
|
| 360 |
.cpp: |
| 361 |
- $(CPP) -o $@ $(CCFLAGS) $(@).cpp $(CCLINK) |
| 362 |
+ $(CXX) $(LDFLAGS) -o $@ $(CXXFLAGS) $(@).cpp $(CCLINK) |
| 363 |
|
| 364 |
.l: |
| 365 |
lex $(@).l |
| 366 |
- $(CC) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) |
| 367 |
+ $(CC) $(LDFLAGS) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) |
| 368 |
|
| 369 |
relink: |
| 370 |
@ cd $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile` |
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