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# ==============================================================================
# 2006-05-02 (Tuesday) 16:52 PDT
# Installing and testing lenstool with Heidi
setenv LENSTOOL_DIR $WORK_DIR/stronglensing/lenstool
cd $LENSTOOL_DIR
# This is a soft link to a web directory:
http://www.slac.stanford.edu/~pjm/lenstool/
# This is where all the files in $LENSTOOL_DIR can be viewed.
# Now, get Marusa's notes!
scp -r ki-rh14:/home/marusa/latex/students/lenstoolman .
scp -r ki-rh14:/home/marusa/cprogs/SWunitedcats/SWunited1E0657/lenstool marusa
# First is a directory containing the manual started by Marusa - print and
# absorb... Second is a directory containing notes and data files, no code. Read
# notes!
ln -s marusa/notes.sh notes-marusa.sh
# Read and absorb these too..
a2ps notes-marusa.sh
lj notes-marusa.ps
# Notes from Marusa on how to compile the code:
scp ki-rh14:/home/marusa/progs/lenstool-6/notes.sh notes-marusa-compilation.sh
a2ps notes-marusa-compilation.sh
lj notes-marusa-compilation.ps
# Download code and unpack:
wget --timestamping --continue http://www.oamp.fr/cosmology/lenstool/lenstool-6.tar.gz
tar xvzf lenstool-6.tar.gz
# Also get the manual and print it:
lj lenstool-6/doc/lenstool.ps
# lenstool needs three libraries - lets find out if we have them:
set ld_dirs = `echo $LD_LIBRARY_PATH | sed s/:/\ /g`
foreach dir ( $ld_dirs )
find $dir | grep libwcs.a
find $dir | grep libcfitsio.a
find $dir | grep longnam.h
find $dir | grep fitsio.h
find $dir | grep libpgplot.a
end
/afs/slac/g/ki/ki01/pgplot/libpgplot.a
/afs/slac/g/ki/ki01/lib/libwcs.a
/afs/slac/g/ki/ki01/lib/libcfitsio.a
# Also need these:
/afs/slac/g/ki/ki01/include/fitsio.h
/afs/slac/g/ki/ki01/include/longnam.h
# Marusa says that the SLAC installation does not work for lenstool - lets try
# it anyway!
cd lenstool-6/
./configure
# Got this message:
# ...
# checking for ffdkopn in -lcfitsio... no
# Cfitsio library >2.510 absolute path :
# /afs/slac/g/ki/ki01/lib/libcfitsio.a
# -L/afs/slac/g/ki/ki01/lib/libcfitsio.a
# checking for ffdkopn in -lcfitsio... no
# Error : with the cfitsio library. Check the cfitsio version
# Does libcfitsio have to be reinstalled? What version do we have?
more /afs/slac/g/ki/ki01/src/cfitsio/changes.txt
# Version 2.490 - 11 February 2004
# HACK: copy Marusa's cfitsio library to ~/lib and try that...
scp ki-rh14:/u1/marusa/progs/cfitsio/lib/libcfitsio.a ~/lib/
scp ki-rh14:/u1/marusa/progs/cfitsio/include/longnam.h ~/lib/
scp ki-rh14:/u1/marusa/progs/cfitsio/include/fitsio.h ~/lib/
# Re run configure, but use /u/ki/pjm/lib/libcfitsio.a
# Same problem. Re-install cfitsio!
cd ~/software
wget --timestamping --continue ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/cfitsio2510.tar.gz
# No such file, alert Jp/Eric...
wget --timestamping --continue ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/oldvers/cfitsio2510.tar.gz
# Unpack, compile, cp fil es to ~/lib:
tar xvzf cfitsio2510.tar.gz
cd cfitsio
./configure
make
cp libcfitsio.a longnam.h fitsio.h ~/lib/
# Try again:
setenv CFITSIO_DIR /u/ki/pjm/lib
setenv WCS_DIR /afs/slac/g/ki/ki01/lib
cd $LENSTOOL_DIR/lenstool-6/
./configure
# Now get this message re pgplot:
# checking for cpgend in -lcpgplot... no
# PGPLOT library absolute path : /afs/slac/g/ki/ki01/pgplot
# -L/afs/slac/g/ki/ki01/pgplot -L/usr/X11R6/lib -lX11 -lcpgplot -lpgplot
# checking for cpgend in -lcpgplot... no
# Error : with the pgplot library.
# Try pgplot library in my directory: nope.
# Try with marusa's pgplot lib:
scp ki-rh14:/u1/marusa/progs/pgplot/libcpgplot.a ~/lib/
# Nope, this didn't work either. This is weird because she claims that she can
# do this just fine... What is going on here? Alert Jp/Eric...
# Re-install pgplot!
cd ~/software
wget ftp://ftp.astro.caltech.edu/pub/pgplot/pgplot5.2.tar.gz
tar xvzf pgplot5.2.tar.gz
mkdir ~/lib/pgplot
cp pgplot/drivers.list ~/lib/pgplot/
pico ~/lib/pgplot/drivers.list
grep -v '!' ~/lib/pgplot/drivers.list
cd ~/lib/pgplot
~/software/pgplot/makemake ~/software/pgplot linux g77_gcc
make
make clean
make cpg
# OK, now try and remake lenstool! May need to reset PGPLOT environment
# variables?
setenv PGPLOT_DIR /u/ki/pjm/lib/pgplot
# STILL GET SAME ERROR!
nm ~/lib/pgplot/libcpgplot.a | grep cpgend
# cpgend.o:
# 00000000 T cpgend
# ITS THERE! ITS IN THE LIBRARY! ITS IN MARUSA'S LIBRARY!
# Something funny is going on- alert Jp/Eric...
# Found bug - 3rd argument must be g77_gcc NOT g77_gcc_aout
# Webpage gives correct options, makemake with no 3rd argument is confusing.
# lenstool makefiles are now ready!
# header files are missing!
COPYHEADERS:
cp /afs/slac/g/ki/ki01/src/wcstools-3.5.3/libwcs/wcs.h include/
cp /afs/slac/g/ki/ki01/src/wcstools-3.5.3/libwcs/wcslib.h include/
cp /afs/slac/g/ki/ki01/src/wcstools-3.5.3/libwcs/fitshead.h include/
# Actually, makefile is wrong - the -I flags need setting when header files are
# not stored with libraries...
# Executable is made, but is in src directory...
# Run example program as Marusa did...
cd examples
../src/lenstool test
# Get vi editor, edit pars then quit...
# Conversion Factor 1arcsec == 5.498 kpc
# Number of Clump used: 1
# Clump 0: truncated PIEMD Kovner: vdisp=900 rc=1.8 e_m=0.300 r_ct=0.0 r_cr=0.0
# 0 81 mag:0.00 sig:900.00 L:0.000 M/L:0.00 rc:10.000 rt:500.00
# --- Lens Tool, Jean-Paul KNEIB, July 1997 ----------------------------------
# SET: xy_grid 50
# INFO: Write the pot.dat file
# COMP1: critic and caustic lines for source plane at z=1.200
# nlens=1 npas=1024 x0=1.000 y0=0.200
# COMP2: critic and caustic lines for source plane at z=1.800
# nlens=1 npas=1024 x0=1.000 y0=0.200
# COMP3: critic and caustic lines for source plane at z=3.200
# nlens=1 npas=1024 x0=1.000 y0=0.200
# SET: sources
# READ2: source.cat:3
# READ2: image.cat:3
# COMP: shear components 0.517201
# OK 3......
# COMP: images of the sources
# COMP: grid at z=1.200 (0.623)
# COMP: 1: multiplicity: 5 at (-2.776,1.799): found 3 image(s)
# COMP: grid at z=1.200 (0.623)
# COMP: 4: multiplicity: 3 at (-1.000,1.000): found 3 image(s)
# COMP: large distorsion 4 (-1.000,1.000) (0.200,0.100,0.698)
# COMP: grid at z=1.800 (0.694)
# COMP: 2: multiplicity: 7 at (2.336,0.746): found 5 image(s)
# COMP: large distorsion 2 (2.336,0.746) (0.105,0.032,2.317)
# COMP: grid at z=1.800 (0.694)
# COMP: 5: multiplicity: 5 at (1.000,-1.000): found 5 image(s)
# COMP: large distorsion 5 (1.000,-1.000) (0.200,0.100,0.698)
# COMP: grid at z=3.200 (0.760)
# COMP: 3: multiplicity: 7 at (-1.171,0.556): found 5 image(s)
# COMP: large distorsion 3 (-1.171,0.556) (0.207,0.007,0.776)
# COMP: grid at z=3.200 (0.760)
# COMP: 6: multiplicity: 5 at (-1.000,-1.000): found 5 image(s)
# COMP: large distorsion 6 (-1.000,-1.000) (0.200,0.100,0.698)
# To do:
# Tell Jp/Eric about other problems
# Figure out how best to install lenstool globally...
cd ~/tmp
cp -r $LENSTOOL_DIR/lenstool-6/examples test
cd test
$LENSTOOL_DIR/lenstool-6/src/lenstool test
# This works - copy examples directory to local space, then add
/u/ki/pjm/public_html/lenstool/lenstool-6/src
# to your path
# ==============================================================================
# 2006-06-05 (Monday) 18:21 PDT
# Putting lenstool into cvs.
# Start with version 6, and tag as version 6. Then overwrite with version 6.1
# and tag.
# Download code and unpack:
mkdir -p cvs-setup
cd cvs-setup
wget --timestamping --continue http://www.oamp.fr/cosmology/lenstool/lenstool-6.tar.gz
tar xvzf lenstool-6.tar.gz
mv lenstool-6 lenstool
# Clean up:
cd doc
rm *.aux *.dvi *.log lenstool.ps inputfile.tex~ lenstool.tex~ lenstool.toc
# Add cvs instructions
sed s/B1608/lenstool/g $B1608_DIR/doc/instructions-cvs.txt > doc/instructions-cvs.txt
# Add lenstool to cvs repository
cvs -d:pserver:pjm@kipac.stanford.edu:/a9/cvs import \
-m "Initialisation: Version 6.0" lenstool lenstool start
# No conflicts created by this import
cd ../
mv lenstool lenstool-6
# And check out the one true version...
cvs -d:pserver:pjm@kipac.stanford.edu:/a9/cvs co lenstool
# Tag the initial version as v6.0:
cd lenstool
cvs tag "v60"
# Now download v6.1 and cp files into the lenstool module.
cd ../
wget --timestamping --continue http://www.oamp.fr/cosmology/lenstool/lenstool-6.1beta.tar.gz
tar xvfz lenstool-6.1beta.tar.gz
# Now copy the files (not the directories) into lenstool and tag it v61:
cd ../
echo "cp lenstool-6.1/* lenstool/"
foreach dir ( `\ls -l lenstool-6.1/* | grep '/' | grep -v 'rw' | cut -d':' -f1` )
echo "cp $dir/* lenstool/$dir:t/"
end
cvs add src/o_rescale.c
cvs add src/o_set_lens_bayes.c
rm src/rescale.c
cvs remove src/rescale.c
cvs add include/fitshead.h
cvs add include/wcs.h
cvs add include/wcslib.h
rm liblt/al_sq_ft.c
cvs remove liblt/al_sq_ft.c
cvs add liblt/al_sq_dbl.c
rm liblt/al_ve_ft.c
cvs remove liblt/al_ve_ft.c
cvs add liblt/al_ve_dbl.c
rm liblt/fr_sq_ft.c
cvs remove liblt/fr_sq_ft.c
cvs add liblt/fr_sq_dbl.c
cvs update
# Only M flags!
cvs ci -m "Version 6.1 beta"
cvs tag "v61"
# Now move the lenstool to replace my current version... but copy the notes
# first!
# ==============================================================================
# 2006-06-06 (Tuesday) 15:17 PDT
# Now compile new (development) version:
cd $LENSTOOL_DIR/
./configure
# Errors with autoconf and automake, check we have correct config files checked
# in... GEt 6.1beta again!
mkdir -p test
cd test
wget --timestamping --continue http://www.oamp.fr/cosmology/lenstool/lenstool-6.1beta.tar.gz
tar xvfz lenstool-6.1beta.tar.gz
cd lenstool-6.1/
./configure
make
set files = (\
Makefile\
Makefile.am\
Makefile.in\
aclocal.m4\
config.h\
config.h.in\
config.log\
config.status\
configure\
configure.in\
)
foreach file ( $files )
set n = `diff $file test/lenstool-6.1/$file | wc -l`
if ( $n > 0 ) then
echo "$file is different"
endif
end
# Hmm, investigate more:
\ls -R1 lenstool-6.1 | sed s/lenstool-6.1/lenstool/g > web.contents
\ls -R1 lenstool > cvs.contents
sdiff web.contents cvs.contents | more
# Generated files:
set genfiles = (\
Makefile\
autom4te.cache\
config.h\
config.log\
config.status\
stamp-h1\
liblt/.deps\
liblt/Makefile\
src/.deps\
src/Makefile\
src/lenstool\
table_src/.deps\
table_src/Makefile\
table_src/lenstool_tab\
utils/Histogram\
utils/Histogram2D\
utils/Makefile\
)
# Compare all files - cvs version still does not check out properly...
cd ../test
cd lenstool/
find | cut -d'/' -f 2- > ../files.list
cd ../
foreach file ( `cat files.list` )
set n = `diff lenstool/$file lenstool-6.1/$file | wc -l`
if ( $n > 0 ) then
echo "$file is different"
endif
end
# autoconf/mkinstalldirs is different
# But this has no effect anyway...
# Here's the problem:
cvs -d:pserver:pjm@kipac.stanford.edu:/a9/cvs co lenstool
./configure
make
# cd . && /bin/sh /u/ki/pjm/work/stronglensing/test/lenstool/autoconf/missing --run aclocal-1.9
# /u/ki/pjm/work/stronglensing/test/lenstool/autoconf/missing: line 46: aclocal-1.9: command not found
# WARNING: `aclocal-1.9' is missing on your system. You should only need it if
# you modified `acinclude.m4' or `configure.in'. You might want
# to install the `Automake' and `Perl' packages. Grab them from
# any GNU archive site.
# cd . && /bin/sh /u/ki/pjm/work/stronglensing/test/lenstool/autoconf/missing --run automake-1.9 --foreign
# /u/ki/pjm/work/stronglensing/test/lenstool/autoconf/missing: line 46: automake-1.9: command not found
# WARNING: `automake-1.9' is missing on your system. You should only need it if
# you modified `Makefile.am', `acinclude.m4' or `configure.in'.
# You might want to install the `Automake' and `Perl' packages.
# Grab them from any GNU archive site.
# cd . && /bin/sh /u/ki/pjm/work/stronglensing/test/lenstool/autoconf/missing --run autoconf
# configure.in:7: error: Autoconf version 2.58 or higher is required
# aclocal.m4:501: AM_INIT_AUTOMAKE is expanded from...
# configure.in:7: the top level
# autom4te: /usr/bin/m4 failed with exit status: 1
# make: *** [configure] Error 1
# Does this occur after a cvs up in $LENSTOOL_DIR?
cd $LENSTOOL_DIR
cvs up
# The only modified files are the examples/ ones...
./configure
make
make clean
make
# All this is OK!
# Something is wrong with the automake/autoconfigure - compare all files like
# this one by one between freshly checkd out version and the one that works...
set TEST_LENSTOOL_DIR = /u2/pjm/work/stronglensing/test/lenstool
set files = (\
Makefile\
config.h\
config.log\
config.status\
stamp-h1\
liblt/Makefile\
)
set files = ( $files \
INSTALL\
Makefile.am\
Makefile.in\
NEWS\
README_table\
aclocal.m4\
config.h.in\
configure\
configure.in\
)
set files = ( $files \
autoconf/config.guess\
autoconf/config.sub\
autoconf/depcomp\
autoconf/install-sh\
autoconf/ltmain.sh\
autoconf/missing\
autoconf/mkinstalldirs\
)
set files = ( $files \
liblt/Makefile.am\
liblt/Makefile.in\
liblt/al_sq_dbl.c\
liblt/al_sq_int.c\
liblt/al_ve_dbl.c\
liblt/fr_sq_dbl.c\
liblt/fr_sq_int.c\
liblt/lt.h\
liblt/nrutil.c\
liblt/polint.c\
liblt/printerror.c\
liblt/qromb.c\
liblt/rd_ipx.c\
liblt/rd_ipxs.c\
liblt/rdf_fits.c\
liblt/rdf_ipx.c\
liblt/rdf_ipxs.c\
liblt/trapzd.c\
liblt/wfits.c\
liblt/wr_ipx.c\
liblt/wr_ipxs.c\
liblt/wrf_ipx.c\
)
FILECOMPARISON:
foreach file ( $files )
set test = `diff $LENSTOOL_DIR/$file $TEST_LENSTOOL_DIR/$file |& \
grep -v 'diff:' | grep -v 'Common subdirectories' | wc -l`
if ( $test > 0 ) echo $file
end
# These files are different. Why?!
set problems = (\
Makefile\
config.log\
config.status\
liblt/Makefile\
)
PROBLEMSDIFF:
foreach file ( $problems )
echo "$file.sdiff"
sdiff -w 400 -s $LENSTOOL_DIR/$file $TEST_LENSTOOL_DIR/$file > $file.sdiff
end
# Makefile sdiff is due just to different path to local module
# config.log sdiff is due just to differnent temporary files eg /tmp/cckdG6Ii.o(.text+0x11)
# config.status sdiff is due just to different path to local module
# liblt/Makefile sdiff is due just to different path to local module
# Hmm - what about hidden files?
# Sod it - do everything...
cd $LENSTOOL_DIR
set files = `find . | cut -c 3-`
# goto FILECOMPARISON; return
# goto PROBLEMSDIFF; return
# Hmm - dependencies are different:
set problems = (\
src/.deps/tirer.Po\
src/.deps/o_run_bayes.Po\
)
# .deps/*.Po are dummy files in test directory - guess thes would be made
# properly if automake worked...
# Now repeat this exercise with test directory being the freshly downloaded
# unpacked tarball...
set TEST_LENSTOOL_DIR = /u2/pjm/work/stronglensing/test/lenstool-6.1
# Checked that confgure and make in this directory are successful...
# Needed to repeat copy done at COPYHEADERS
# Build is good. Now repeat above
# goto FILECOMPARISON; return
# Aha! Here is a genuine difference:
set problems = (\
autoconf/mkinstalldirs\
config.log\
liblt/Makefile\
src/Makefile\
table_src/Makefile\
utils/Makefile\
config.status\
Makefile\
)
# goto PROBLEMSDIFF; return
# LENSTOOL_DIR # $Id: notes-phil.txt,v 1.3 2006-07-28 12:47:07 pjm Exp $
# TEST_LENSTOOL_DIR # $Id: notes-phil.txt,v 1.3 2006-07-28 12:47:07 pjm Exp $
# ie cvs repository has a file made by me, whereas tarball has version from
# Eric. Try compiling in the test cvs directory with this mkinstalldirs!
cp $TEST_LENSTOOL_DIR/autoconf/mkinstalldirs $LENSTOOL_DIR/autoconf/mkinstalldirs
set TEST_LENSTOOL_DIR = /u2/pjm/work/stronglensing/test/lenstool
cp $LENSTOOL_DIR/autoconf/mkinstalldirs $TEST_LENSTOOL_DIR/autoconf/mkinstalldirs
cd $TEST_LENSTOOL_DIR
# Now I get a different error!
# cd . && /bin/sh /u2/pjm/work/stronglensing/test/lenstool/autoconf/missing --run autoconf
# configure.in:7: error: Autoconf version 2.58 or higher is required
# aclocal.m4:501: AM_INIT_AUTOMAKE is expanded from...
# configure.in:7: the top level
# autom4te: /usr/bin/m4 failed with exit status: 1
# make: *** [configure] Error 1
# Give up - here is a summary of the problem to email to Eric!
# The v6.1 tarball is fine - I can download it, unpack it, do ./configure
# followed by make and, since I installed the right libraries etc, it compiles
# just fine.
#
# I added the new files in v6.1 to, and removed the no longer existing ones
# from, the cvs repository and checked them in. After a cvs update
# my local copy of lenstool compiles fine.
#
# However, if I check out the current version of lenstool from elsewhere and
# attempt to compile, the configure works fine but I get automake and autoconf
# errors, namely the following:
#
# cd . && /bin/sh /u/ki/pjm/work/stronglensing/test/lenstool/autoconf/missing --run autoconf
# configure.in:7: error: Autoconf version 2.58 or higher is required
# aclocal.m4:501: AM_INIT_AUTOMAKE is expanded from...
# configure.in:7: the top level
# autom4te: /usr/bin/m4 failed with exit status: 1
# make: *** [configure] Error 1
# ==============================================================================
# 2006-07-18 (Tuesday) 15:52 PDT
#
# Priya calls asking for advice about compilation
# Mentiosn bug: chi0 does not change when ellipticity of clump is varied..
# Using verion 2 or 3(!)
# ==============================================================================
# 2006-07-28 (Friday) 13:14 BST
# Bugs in lenstool 6.2:
# Evidence not printed to screen
# Nrem set to small no if rate is high
# Seed not negative
# ==============================================================================
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