Error in 2dx_deftilt_sub.com

[rdrighetto]

When using 2dx_ctffind3.exe on 7x7 locations to determine the tilt geometry, the following error occurs (output from using #!/bin/csh -efx ):

rm -f FASTDISK/CUT/image_2dx_7_3.mrc 
/local0/git/focus/build/scripts/proc/lin Cutting position 7,4 
rm -f SCRATCH/TMP.mrc 
rm -f FASTDISK/CUT/image_2dx_7_4.mrc 
/local0/git/focus/build/scripts/proc/lin Cutting position 7,5 
rm -f SCRATCH/TMP.mrc 
rm -f FASTDISK/CUT/image_2dx_7_5.mrc 
/local0/git/focus/build/scripts/proc/lin Cutting position 7,6 
rm -f SCRATCH/TMP.mrc 
rm -f FASTDISK/CUT/image_2dx_7_6.mrc 
/local0/git/focus/build/scripts/proc/lin Cutting position 7,7 
rm -f SCRATCH/TMP.mrc 
rm -f FASTDISK/CUT/image_2dx_7_7.mrc 
rm -f SCRATCH/TMP.mrc 
echo > 
/local0/git/focus/build/scripts/proc/linblock 2dx_deftilt_sub.com: On center of image 
set sub_tilesize = 256 
set centerX = `echo ${defocus_tiles_count} | awk '{ s = int( $1 / 2 ) + 1} END { print s }'` 
echo 7 
awk { s = int( $1 / 2 ) + 1} END { print s } 
set centerY = `echo ${defocus_tiles_count} | awk '{ s = int( $1 / 2 ) + 1} END { print s }'` 
awk { s = int( $1 / 2 ) + 1} END { print s } 
echo 7 
echo :: centerX=4 
echo :: centerY=4 
set dfdist = 10000.0 
set inoast = 0 
set drms1 = 0.0 
set newX = 4 
set newY = 4 
set refX = 0 
set refY = 0 
source /local0/git/focus/build/scripts/proc/2dx_deftilt_sub.com 
echo New coordinates = 4,4 
echo Reference coord = 0,0 
echo dfdist = 10000.0 
echo inoast = 0 
set second = 0 
echo second = 0 
if ( 1 == 0 ) then 
echo 256 
if ( 0 == 3 ) then 
set inimage = FASTDISK/CUT/image_2dx_4_4.mrc 
set outimage = CUT/image_2dx_4_4_ps.mrc 
set outlabel = CUT-PS_4,4 
endif 
if ( 0 > = 2 ) then 
if ( 2 > 1 ) then 
if ( y == y ) then 
source /local0/git/focus/build/scripts/proc/2dx_find_GPU.com 
rm -f tmp.tmp 
set counter = 2 
@ counter -= 1 
while ( 1 > = 0 ) 
set GPUload = `nvidia-smi -i ${counter} | head -n 9 | tail -n 1 | cut -c 58-66 | cut -d\% -f1 ` 
nvidia-smi -i 1 
head -n 9 
set GLUloadplus1000 = `echo ${GPUload} | awk '{ s = $1 + 1000 } END { print s }'` 
awk { s = $1 + 1000 } END { print s } 
echo 0 
echo 1000 0 
echo GPU 0 has load of 0 
@ counter -= 1 
end 
while ( -1 > = 0 ) 
sort tmp.tmp 
set next_GPU = `sort tmp.tmp | head -n 1 | cut -d\ -f2` 
sort tmp.tmp 
cut -d -f2 
head -n 1 
echo This job is for GPU 0. 
rm -f tmp.tmp 
set GPU_to_use = 0 
endif 
endif 
if ( 0 == 0 || 0 == 0 ) then 
set dfmid = `echo ${defocus} | sed 's/,/ /g' | awk '{s = ($1 + $2 ) / 2 } END {print s}'` 
echo 13939.51,14938.94,78.71 
awk {s = ($1 + $2 ) / 2 } END {print s} 
sed s/,/ /g 
set dfref = `echo ${defocus}` 
echo 13939.51,14938.94,78.71 
set dfstart = 2000.0 
set dfend = 50000.0 
set dfstep = 250.0 
set dfdast = 300.0 
else 
echo :Search range is 2000.0, 50000.0, 250.0, 300.0 
/local0/git/focus/build/scripts/proc/lin 2dx_ctffind3 - search the defocus 
rm -f SCRATCH/2dx_ctffind3_result.tmp 
rm -f CUT/image_2dx_4_4_ps.mrc 
if ( 1 == 1 ) then 
set locstepdigitizer = `echo ${stepdigitizer} | awk '{ s = 2 * $1 } END { print s }'` 
awk { s = 2 * $1 } END { print s } 
echo 5.0 
else 
if ( 0 == 0 || 0 == 0 ) then 
set inoast = 0 
else 
if ( 0 == 0 ) then 
if ( y == y ) then 
set progname = 2dx_ctffind3.exe 
else 
/local0/git/focus/build/scripts/proc/lin Calling 2dx_ctffind3.exe 
echo 
echo with: 
echo FASTDISK/CUT/image_2dx_4_4.mrc 
echo CUT/image_2dx_4_4_ps.mrc 
echo 2.0,300.0,0.0998749,50000,10 
echo 256,80.0,3.2,2000.0,50000.0,250.0,300.0 
echo 0,13939.51,14938.94,78.71,0.0 
echo 
dfref1: Undefined variable. 

When using CTFTILT or Gctf on 7x7 locations, this problem does not occur.

[sthennin]

seems to be solved now.