afni.nimh.nih.gov

Hi Rick,
I wanted to find out if the Centos 7 version is also openmp or not?

Secondly, in running 3dNwarpApply I had the following errors on the red hat system when the exact same command/files passed on my ubuntu system....any thoughts?

3dNwarpApply -interp NN -nwarp 'tmp.anat2MNI_WARP.nii tmp.anat2MNI.aff.Xat.1D anat.brain2tpl.aff6.1D INV(T2.brain2B0.aff6.1D) nl_WARP.nii' -iwarp -master B0ref_resamp.nii.gz -source ./DWI.weight+tlrc. -prefix weight22 -verb >> 3dNwarpApply_err1.txt
++ 3dNwarpApply: AFNI version=AFNI_17.1.01 (Apr 12 2017) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is 'B0ref_resamp.nii.gz'
++ opened source dataset './DWI.weight+tlrc.'
++ Processing -nwarp ++ Enter IW3D_read_nwarp_catlist( tmp.anat2MNI_WARP.nii tmp.anat2MNI.aff.Xat.1D anat.brain2tpl.aff6.1D INV(T2.brain2B0.aff6.1D) nl_WARP.nii )
+ Open dataset warp tmp.anat2MNI_WARP.nii
+ max displacments = 20.1844 14.3053 11.4142
+ Open matrix file tmp.anat2MNI.aff.Xat.1D
+ max shifts = 0.551628 2.81892 5.4792
+ Open matrix file anat.brain2tpl.aff6.1D
+ max shifts = 0.420547 2.80645 14.4052
+ Open matrix file INV(T2.brain2B0.aff6.1D)
+ max shifts = 2.08339 11.8799 32.1879
+ Open dataset warp nl_WARP.nii
+ max displacments = 5.69117 10.5456 4.94413
+ found geometry mismatch: orig=MATRIX(-1,0,0,96,0,-1,0,132,0,0,1,-93):193,231,208 new=MATRIX(1,0,0,-117.0035,0,1,0,-120.5573,0,0,1,-62.79667):230,236,173
+ --- Totalized max displacments = 28.9311 42.3562 68.4307

++ IW3D_set_geometry_nwarp_catlist: padding = 46
+ results: master_geomstring = MATRIX(1.5,0,0,-116.5035,0,1.5,0,-120.0573,0,0,1.5,-46.54667):153,153,96 actual_geomstring = MATRIX(1.5,0,0,-185.5035,0,1.5,0,-189.0573,0,0,1.5,-115.5467):245,245,188
+ -- warp #0 geometry = MATRIX(-1,0,0,96,0,-1,0,132,0,0,1,-93):193,231,208
+ regridding warp #0 to geometry = MATRIX(1.5,0,0,-185.5035,0,1.5,0,-189.0573,0,0,1.5,-115.5467):245,245,188
+ -- warp #4 geometry = MATRIX(1,0,0,-117.0035,0,1,0,-120.5573,0,0,1,-62.79667):230,236,173
+ regridding warp #4 to geometry = MATRIX(1.5,0,0,-185.5035,0,1.5,0,-189.0573,0,0,1.5,-115.5467):245,245,188
+++++ initial structure of Nwarp_catlist: Nwarp ; Matrix[1] ; Matrix[1] ; Matrix[1] ; Nwarp ;
++ -- IW3D_reduce_nwarp_catlist -- start loop
+ looking at nwc[0]
+ .. #0 and #1 are neighbors
+ looking at nwc[1]
+ .. #1 and #2 are neighbors
+ .. IW3D_reduce_nwarp_catlist: Matrix[1]-Matrix[1] ii=1 jj=2
+ looking at nwc[2]
+ .. #2 and #3 are neighbors
+ .. IW3D_reduce_nwarp_catlist: Matrix[1]-Matrix[1] ii=2 jj=3
+ looking at nwc[3]
+ .. #3 and #4 are neighbors
+ -- loop reduction operation count = 2
++ -- IW3D_reduce_nwarp_catlist -- start loop
+ looking at nwc[0]
+ .. #0 and #3 are neighbors
+ IW3D_reduce_nwarp_catlist: warp-Matrix[1] ii=0 jj=3
+ looking at nwc[3]
+ .. #3 and #4 are neighbors
+ .. IW3D_reduce_nwarp_catlist: warp-warp ii=3 jj=4
+ ii=3: geometry = MATRIX(1.5,0,0,-185.5035,0,1.5,0,-189.0573,0,0,1.5,-115.5467):245,245,188
+ jj=4: geometry = MATRIX(1.5,0,0,-185.5035,0,1.5,0,-189.0573,0,0,1.5,-115.5467):245,245,188
+ -- loop reduction operation count = 2
++ -- IW3D_reduce_nwarp_catlist -- start loop
+ nwc[0] is doubly NULL
+ nwc[1] is doubly NULL
+ nwc[2] is doubly NULL
+ nwc[3] is doubly NULL
+ -- loop reduction operation count = 0
+++++ final structure of Nwarp_catlist: (NULL) ; (NULL) ; Nwarp ;
++ Warping: [nvar=1]ab{nwarp_catlist[0] [NULL entry?] [NULL entry?] [warp]} + -- invert max|AA|=64.153511
+ - init nstep=8 qq=1/2^8=0.003906
+ - init step 1
+ - init step 2
+ - init step 3
+ - init step 4
+ - init step 5
+ - init step 6
+ - init step 7
+ - init step 8
+ - start iterations: normAA=36.756603 inewtfac=0.248055
+ - iterate 1 nrat=0.027847
+ - iterate 2 nrat=0.019870
+ - switch to inewtfac=0.306100
+ - iterate 3 nrat=0.019028
+ - iterate 4 nrat=0.013255
+ - switch to inewtfac=0.377727
+ - iterate 5 nrat=0.010855
+ - iterate 6 nrat=0.007080
+ - switch to inewtfac=0.466116
+ - iterate 7 nrat=0.005142
+ - iterate 8 nrat=0.002772
+ - switch to inewtfac=0.575187
+ - iterate 9 nrat=0.001922
+ - iterate 10 nrat=0.000805
+ - switching from linear interp
+ - iterate 11 nrat=0.000343
+ - iterate 12 nrat=0.000151
+ - switch to inewtfac=0.678901
+ - iterate 13 nrat=0.000076
+ -- iteration converged
'** ERROR: EDIT_full_copy: invalid dataset input ptr=0x6e92a00
** ERROR: Can't copy nwarp dataset #0 ?!?
** FATAL ERROR: Warping failed for some reason ((
** Program compile date = Apr 12 2017


Output of ldd on redhat ..........just as a note for linux-vdso.so.1 this is also blank on the ubuntu machine that worked.
linux-vdso.so.1 => (0x00007ffc98ff8000)
libXt.so.6 => /usr/lib64/libXt.so.6 (0x00002b2e2c23d000)
libXft.so.2 => /usr/lib64/libXft.so.2 (0x00002b2e2c4a4000)
libXp.so.6 => /usr/lib64/libXp.so.6 (0x00002b2e2c6ba000)
libXpm.so.4 => /usr/lib64/libXpm.so.4 (0x00002b2e2c8c3000)
libXext.so.6 => /usr/lib64/libXext.so.6 (0x00002b2e2cad5000)
libXmu.so.6 => /usr/lib64/libXmu.so.6 (0x00002b2e2cce7000)
libSM.so.6 => /usr/lib64/libSM.so.6 (0x00002b2e2cf02000)
libICE.so.6 => /usr/lib64/libICE.so.6 (0x00002b2e2d10a000)
libX11.so.6 => /usr/lib64/libX11.so.6 (0x00002b2e2d326000)
libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x00002b2e2d664000)
libz.so.1 => /usr/lib64/libz.so.1 (0x00002b2e2d88b000)
libm.so.6 => /usr/lib64/libm.so.6 (0x00002b2e2daa1000)
libdl.so.2 => /usr/lib64/libdl.so.2 (0x00002b2e2dda3000)
libc.so.6 => /usr/lib64/libc.so.6 (0x00002b2e2dfa7000)
libgomp.so.1 => /hpc/software/gcc/4.8.3/lib64/libgomp.so.1 (0x00002b2e2e368000)
libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00002b2e2e576000)
libfontconfig.so.1 => /usr/lib64/libfontconfig.so.1 (0x00002b2e2e792000)
libfreetype.so.6 => /usr/lib64/libfreetype.so.6 (0x00002b2e2e9cf000)
libXrender.so.1 => /usr/lib64/libXrender.so.1 (0x00002b2e2ec75000)
libXau.so.6 => /usr/lib64/libXau.so.6 (0x00002b2e2ee7f000)
libuuid.so.1 => /usr/lib64/libuuid.so.1 (0x00002b2e2f083000)
libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00002b2e2f288000)
/lib64/ld-linux-x86-64.so.2 (0x00002b2e2c01b000)
librt.so.1 => /usr/lib64/librt.so.1 (0x00002b2e2f4aa000)
libexpat.so.1 => /usr/lib64/libexpat.so.1 (0x00002b2e2f6b2000)



Edited 2 time(s). Last edit at 07/29/2017 10:23AM by AjaySK.