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locupe
mexec_exec
Commits
8b7ceabb
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8b7ceabb
authored
5 years ago
by
PStar User Account
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jc191
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da2f61d1
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cruisedir_setup_scripts/conf_script_jc174
cruisedir_setup_scripts/conf_script_jc174
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cruisedir_setup_scripts/conf_script_jc191
cruisedir_setup_scripts/conf_script_jc191
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cruisedir_setup_scripts/conf_script_jc174
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8b7ceabb
#!/bin/csh -f
############ names and directories ############
# The directory where your cruise processing directory lives/will live
set mexecloc = '/local/users/pstar/'
set mexecver = 'v3'
set oldcruiseloc = '/data/pstar/'
set cruise = 'jc174' #current cruise
set CRUISE = 'JC174'
set oldcruise = 'jc159'
set OLDCRUISE = 'JC159'
# Underway system and ship data remote mount points
# - on James Cook
set usys = 'techsas'
set shipudr = '/mnt/techsas/${CRUISE}/NetCDF'
set shipcdr = '/mnt/CTD/'
set shipvdr1 = '/mnt/adcp75/'
set shipvdr2 = '/mnt/adcp150/'
############ now actually set things up ############
# you shouldn't need to change anything below this
# ${mexecloc}/${cruise}/cruise will be the mexec processing directory
# so you can have other subdirectories of ${cruise}
if (! -e ${mexecloc}/${cruise}) then
mkdir -p ${mexecloc}/${cruise}
endif
mkdir -p ${mexecloc}/${cruise}/data
mkdir -p ${mexecloc}/${cruise}/sw
#link mexec processing directory for current cruise to generic "cruise"
#this is just so that you can easily make m_setup.m (for whichever cruise)
#always be on the matlab path by adding
#${mexecloc}/cruise/data/mexec_processing_scripts to the path
#in ~/matlab/startup.m
if (-e ${mexecloc}/cruise) then
/bin/rm ${mexecloc}/cruise #in case a link exists, remove it
endif
cd ${mexecloc}
ln -s ${cruise} cruise
#make links to software and scripts
ln -s ${mexecloc}/programs/general_sw ${mexecloc}/cruise/sw
ln -s ${mexecloc}/programs/mexec_v3 ${mexecloc}/cruise/sw/mexec_v3
ln -s ${mexecloc}/programs/mexec_processing_scripts_v3 ${mexecloc}/cruise/data/mexec_processing_scripts_v3
# Create srring to copy exec and templates
echo 'If not already done use thse liens to copy execs and templates'
set CopyExec = 'cp -Rp '${oldcruiseloc}/${oldcruise}'/data/exec '${mexecloc}'/cruise/data/'
echo $CopyExec
chmod -R u+x ${mexecloc}/cruise/data/exec/
set CopyTemp = 'cp -Rp '$${oldcruiseloc}/${oldcruise}'/data/templates '${mexecloc}'/cruise/data/'
echo $CopyTemp
#you may still need to edit the files in exec/ (specifically, the linkscripts) to reflect naming conventions of data files on the remote machines
#set up data directory structure--you can comment out some of the BOTTLE lines if not sampling them
cd ${mexecloc}/cruise/data
mkdir -p ctd/ASCII_FILES #ascii CTD files from ship machine will be copied here by ctd_linkscript
mkdir -p ctd/RAW_CTD_FILES #raw CTD files from ship machine will be copied here by ctd_linkscript
mkdir -p ctd/WINCH
mkdir -p ctd/BOTTLE_SAL
mkdir -p ctd/BOTTLE_OXY
mkdir -p ctd/BOTTLE_NUT
# mkdir -p ctd/BOTTLE_CO2
# mkdir -p ctd/BOTTLE_CFC
mkdir -p vmadcp/${cruise}_os75
mkdir -p vmadcp/${cruise}_os150
mkdir -p mexec_housekeeping/version
mkdir -p mexec_housekeeping/history
mkdir -p station_depths
mkdir -p collected_files
mkdir -p planning
# Underway data processing directories are created later by m_setup.m
# Mke links to underway data directory
mkdir /local/users/pstar/mounts
ln -s $shipudr /local/users/pstar/mounts/techsas
cd ${mexecloc}/cruise/data
mkdir -p techsas/netcdf_files_links #these will be to netcdf_files_rawdir
cd techsas
mkdir netcdf_files_rawdir_local #will sync everything here at end of cruise
ln -s /local/users/pstar/mounts/techsas netcdf_files_rawdir_ship
mkdir techsas_link_logs
ln -s netcdf_files_rawdir_ship netcdf_files_rawdir #but for now, point to the ship directory
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cruisedir_setup_scripts/conf_script_jc191
0 → 100755
View file @
8b7ceabb
#!/bin/csh -f
####### names and directories #######
set mexecloc = '/local/users/pstar/programs' #this is the directory containing general_sw plus mexec and mexec_processing_scripts repositories
set cruiseloc = '/local/users/pstar' #this is the directory where your cruise processing directores live
set mexecver = 'v3'
set cruise = 'jc191'
set CRUISE = 'JC191'
#underway system and ship data remote mount points
#on jcr
###set usys = 'scs'
###set shipudr = '/mnt/data/cruise/jcr/current/scs/Compress'
###set shipcdr = '/mnt/data/cruise/jcr/current/ctd/$CRUISE'
###set shipvdr = '/mnt/data/cruise/jcr/current/adcp'
###set shipldr = '/mnt/data/cruise/jcr/current/ladcp'
###set isladcp = 1
#on cook/disco
set usys = 'techsas'
set shipudr = '/mnt/techsas/$CRUISE/NetCDF'
set shipcdr = '/mnt/CTD'
####### now actually set things up #######
#shouldn't need to change anything below this
if (! -e $cruiseloc/$cruise/mcruise/data) then
mkdir -p $cruiseloc/$cruise/mcruise/data
endif
mkdir -p $cruiseloc/$cruise/mcruise/sw/general_sw
#link to generic cruise directory
#this is just so that you can have $cruiseloc/cruise/data/mexec_processing_scripts on your matlab path in ~/matlab/startup.m and be ready to run m_setup.m for the current cruise
if (-e $cruiseloc/cruise) then
/bin/rm $cruiseloc/cruise
endif
cd $cruiseloc
ln -s $cruise/mcruise cruise
#make links to software and scripts
cd $cruise/mcruise/data
ln -s $mexecloc/mexec_processing_scripts_$mexecver mexec_processing_scripts
cd ../sw
ln -s $mexecloc/mexec_$mexecver mexec
cd general_sw
foreach d1 (`ls $mexecloc/general_sw`)
ln -s $mexecloc/general_sw/$d1 $d1
end
cd ../..
echo "edit linkscripts and possibly other files in mexec-exec"
echo "edit m_setup.m to change data time origin, cruise name"
echo "and possibly some paths e.g. versions of external software packages"
#set up rest of data directory structure
cd data
mkdir -p mexec_housekeeping/version
mkdir mexec_housekeeping/history
mkdir -p collected_files/figures
mkdir -p ctd/RAW_CTD_FILES
mkdir ctd/ASCII_FILES
mkdir ctd/BOTTLE_CFC
mkdir ctd/BOTTLE_CO2
mkdir ctd/BOTTLE_NUT
mkdir ctd/BOTTLE_OXY
mkdir ctd/BOTTLE_SAL
mkdir ctd/BOTTLE_SHORE
mkdir ctd/WINCH
mkdir -p ladcp/ctd
mkdir -p ladcp/ix/checkpoints
mkdir ladcp/ix/raw
mkdir ladcp/ix/DL_GPS
mkdir ladcp/ix/DL_GPS_BT
mkdir ladcp/ix/DL_GPS_BT_SADCP
mkdir ladcp/rawdata
#mkdir -p ladcp/uh/pro
#mkdir ladcp/uh/raw
#cp $oldcruise/data/ladcp/uh/LADall ladcp/uh
mkdir plots
mkdir station_depths
mkdir -p vmadcp/mproc
mkdir -p vmadcp/postprocessing
mkdir -p vmadcp/atsea
mkdir -p vmadcp/spprocessing
#ln -s $shipudr scs_raw #flag for scs or techsas?
#mkdir scs_sed
#mkdir scs_mat
#echo "run sedexec_startall once $shipudr available"
mkdir -p techsas/netcdf_files_links
cd techsas
ln -s /local/users/pstar/mounts/techsas netcdf_files_rawdir_ship
ln -s netcdf_files_rawdir_ship netcdf_files_rawdir
ln -s netcdf_files_copy/$CRUISE/NetCDF netcdf_files_rawdir_local
mkdir techsas_link_logs
cd ..
#other directories (for processed underway data) are generated by running m_setup
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