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revision 1.22 by dimitri, Fri Feb 6 21:12:01 2004 UTC revision 1.70 by dimitri, Thu Oct 12 05:45:52 2006 UTC
# Line 1  Line 1 
1  Instructions for setting up a cube-sphere integration with sea-ice.  Instructions for setting up a cube-sphere integration with sea-ice.
2  Date last tested: January 24, 2004.  
3  This is the code used for cube2, the second 1992-2002 510x510x6  September 28, 2006: 216-CPU code for cube38
4  cube-sphere integration.  
5    September 4, 2006
6    Modified 32*32*6*15 experiments to use grid_cs32.* files from
7     verification/tutorial_held_suarez_cs/input instead of
8     tile* files from verification/global_ocean.cs32x15/input
9    
10    August 8, 2006
11    216-CPU code and input used for integrating cube37
12    using "June 10, 2006" MITgcm code.
13    
14    for online T/S profile diagnostics all that is needed is
15      profiles_init_fixed
16      profiles_inloop
17    see pkg/ecco/ecco_cost_init_fixed.F
18        pkg/ecco/cost_averagesfields.F
19    
20    
21  ##########################################################################  ##########################################################################
22  ##########################################################################  ##########################################################################
23  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
24    #
25    
26  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack    bash or sh shell:
27  cvs login ( CVS password: cvsanon )      $ export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
28  cvs co -r hrcube_2 MITgcm_contrib/high_res_cube/README_ice      $ cvs login
29  cvs co -r hrcube_2 MITgcm_contrib/high_res_cube/code-mods        ( enter the CVS password: "cvsanon" )
30  cvs co -r hrcube_2 MITgcm_contrib/high_res_cube/matlab-grid-converter  
31  cvs co -r hrcube_2 MITgcm_contrib/high_res_cube/input    tcsh or csh shell:
32  cvs co -r hrcube_2 MITgcm_contrib/high_res_cube/results      $ setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
33  cvs co -r hrcube_2 MITgcm_code      $ cvs login
34  cvs co -r hrcube_2 MITgcm/verification/global_ocean.cs32x15        ( enter the CVS password: "cvsanon" )
35    
36    cvs co MITgcm_contrib/high_res_cube/README_ice
37    cvs co MITgcm_contrib/high_res_cube/code-mods
38    cvs co MITgcm_contrib/high_res_cube/input
39    cvs co MITgcm_contrib/high_res_cube/results
40    cvs co MITgcm_code
41    cvs co MITgcm/verification/global_ocean.cs32x15
42    cvs co MITgcm/verification/tutorial_held_suarez_cs/input
43    
44    
45  ##########################################################################  ##########################################################################
# Line 25  cvs co -r hrcube_2 MITgcm/verification/g Line 48  cvs co -r hrcube_2 MITgcm/verification/g
48    
49  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
50  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
51  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
52    cd ../build
53  cd ..  \rm *
 mkdir build  
 cd build  
54  ../../../tools/genmake2 -mods=../code  ../../../tools/genmake2 -mods=../code
55  make depend  make depend
56  make  make
   
57  cd ..  cd ..
58  mkdir run  mkdir run
59  cd run  cd run
60    \rm *
61    \cp ../../tutorial_held_suarez_cs/input/grid* .
62  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
63  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
64  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
65    
# Line 48  comparison output is in: Line 69  comparison output is in:
69  to use matlab to look at the output  to use matlab to look at the output
70  matlab  matlab
71    
72  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...
73             'QNETtave','FVtave','FUtave','EmPmRtave'}
74      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);      tmp=permute(readbin([fld{1} '.0000000020.data'],[32,6,32]),[1 3 2]);
75      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
76  end  end
77    
78  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);
79  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
80  uice=mask.*permute(readbin(['UICE.0000000020.data'],[32,6,32]),[1 3 2]);  uice=mask.*permute(readbin(['UICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
81  vice=mask.*permute(readbin(['VICE.0000000020.data'],[32,6,32]),[1 3 2]);  vice=mask.*permute(readbin(['VICEtave.0000000020.data'],[32,6,32]),[1 3 2]);
82  clf  clf
83  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
84  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
85  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
86  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
87    
88    
89  ##########################################################################  ##########################################################################
90  ##########################################################################  ##########################################################################
91  # 32*32*6*15, 2-cpu cube sphere on the altices with efc  # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
92    # requires input files in sudirectories run_template and ncep_rgau
93    # these can be obained from lou:/u/menemenl/cube
94    
95  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
96  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
97  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
98  \cp SIZE.h_mpi SIZE.h  \cp SIZE.h_216 SIZE.h
99    \cp packages.conf_hr packages.conf
100    
101    cd ../build
102    \rm *
103    ../../../tools/genmake2 -mods=../code -of
104    ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
105    make depend
106    make -j
107    
108  cd ..  cd ..
109  mkdir build  mkdir run
110  cd build  cd run
111  \rm *  \rm *
112  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  \cp ../input/* .
113    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
114    ln -sf ../../../../run_template/* .
115    \rm pickup* data.pkg data.seaice data.exf_clim data.exf data bathy_Hmin50.bin
116    \rm *192_94* *cs32* *.m lev* tren* job_c* job_altix150 job_altix92_54t
117    ln -sf ../../../../run_template/pickup.0000000216.cube38 pickup.0000000216
118    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube38 pickup_seaice.0000000216
119    \cp ../build/mitgcmuv .
120    qsub job_altix
121    
122    
123    ##########################################################################
124    ##########################################################################
125    # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
126    
127    cd MITgcm/verification/global_ocean.cs32x15/code
128    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
129    \cp ../code_alt/code.176t_8x4/* .
130    cd ../build
131    \rm *
132    ../../../tools/genmake2 -mods=../code
133  make depend  make depend
134  make  make
135    cd ..
136    mkdir run
137    cd run
138    \rm *
139    \cp ../../tutorial_held_suarez_cs/input/grid* .
140    \cp ../input/* .
141    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
142    ../build/mitgcmuv >& output.txt
143    
144    
145    ##########################################################################
146    ##########################################################################
147    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
148    
149    cd MITgcm/verification/global_ocean.cs32x15/code
150    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
151    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
152    \cp SIZE.h_mpi SIZE.h
153    
154    cd ../build
155    \rm *
156    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
157    make depend
158    make -j
159    
160  cd ..  cd ..
161  mkdir run  mkdir run
162  cd run  cd run
163  \rm *  \rm *
164    \cp ../../tutorial_held_suarez_cs/input/grid* .
165  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
166  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
167  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
168    
169    
170  ##########################################################################  ##########################################################################
171  ##########################################################################  ##########################################################################
172  # 510*510*6*50, 54-cpu cube sphere on the altices with efc  # 510*510*6*50, 54-tile, 54-cpu cube sphere on the altices with efc
173    # starting with pickup file from end of 1992
174    # requires input files in sudirectories run_template and ncep_rgau
175    
176    cd MITgcm/verification/global_ocean.cs32x15/code
177    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
178    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
179    \cp packages.conf_hr packages.conf
180    
181    cd ../build
182    \rm *
183    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
184    make depend
185    make -j
186    
187    cd ..
188    mkdir run
189    cd run
190    \rm *
191    \cp ../input/* .
192    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
193    qsub job_altix92_54t
194    
195    
196    ##########################################################################
197    ##########################################################################
198    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
199    # uses s1500t_17x51 configuration
200    
201    cd MITgcm/verification/global_ocean.cs32x15/code
202    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
203    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
204    \cp SIZE.h_150 SIZE.h
205    \cp packages.conf_hr packages.conf
206    
207    cd ../build
208    \rm *
209    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
210    make depend
211    make -j
212    
213    cd ..
214    mkdir run
215    cd run
216    \rm *
217    \cp ../input/* .
218    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
219    ln -sf ../../../../run_template/* .
220    \rm pickup*
221    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
222    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
223    \cp ../build/mitgcmuv mitgcmuv150
224    qsub job_altix150
225    
226    
227    ##########################################################################
228    ##########################################################################
229    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
230    # uses s1500t_17x51 configuration
231    # example for running on c17-c20 using arrayd
232    
233    cd MITgcm/verification/global_ocean.cs32x15/code
234    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
235    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
236    \cp SIZE.h_375 SIZE.h
237    \cp packages.conf_hr packages.conf
238    
239    cd ../build
240    \rm *
241    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
242    make depend
243    make -j
244    
245    cd ..
246    mkdir run
247    cd run
248    \rm *
249    \cp ../input/* .
250    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
251    ln -sf ../../../../run_template/* .
252    \rm pickup*
253    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
254    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
255    \cp ../build/mitgcmuv .
256    job_c20_375cpu < /dev/null >&! output.run &
257    
258    
259    ##########################################################################
260    ##########################################################################
261    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
262    # uses s1500t_17x51 configuration
263    # example for running on c17-c20 using arrayd
264    
265    cd MITgcm/verification/global_ocean.cs32x15/code
266    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
267    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
268    \cp SIZE.h_375 SIZE.h
269    \cp packages.conf_hr packages.conf
270    
271    cd ../build
272    \rm *
273    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
274    make depend
275    make -j
276    
277    cd ..
278    mkdir run
279    cd run
280    \rm *
281    \cp ../input/* .
282    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
283    ln -sf ../../../../run_template/* .
284    \rm pickup*
285    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
286    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
287    \cp ../build/mitgcmuv .
288    job_c20_375cpu < /dev/null >&! output.run &
289    
290    
291    ##########################################################################
292    ##########################################################################
293    # 510*510*6*50, 1500-tile, 500-cpu, excludes land
294    # uses s1500t_17x51 configuration
295    # example for running on c17-c20 using arrayd
296    
297    cd MITgcm/verification/global_ocean.cs32x15/code
298    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
299    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
300    \cp SIZE.h_500 SIZE.h
301    \cp packages.conf_hr packages.conf
302    
303    cd ../build
304    \rm *
305    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
306    make depend
307    make -j
308    
309    cd ..
310    mkdir run
311    cd run
312    \rm *
313    \cp ../input/* .
314    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
315    ln -sf ../../../../run_template/* .
316    \rm pickup*
317    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
318    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
319    \cp ../build/mitgcmuv .
320    job_c19_500cpu < /dev/null >&! output.run &
321    
322    
323    ##########################################################################
324    ##########################################################################
325    # 510*510*6*50, 216-cpu cube sphere on cosmos
326    
327    cd MITgcm/verification/global_ocean.cs32x15/code
328    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
329    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
330    \cp SIZE.h_216 SIZE.h
331    \cp packages.conf_hr packages.conf
332    
333    module unload latest_intel80
334    module unload mpich-gm-intel80
335    module load latest_intel81
336    module load mpich-gm-intel81
337    
338    cd ../build
339    \rm *
340    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
341    make depend
342    make -j
343    
344    cd ..
345    mkdir run
346    cd run
347    \rm *
348    \cp ../input/* .
349    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
350    ln -sf ../../../../run_template/* .
351    \rm pickup*
352    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
353    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
354    \cp ../build/mitgcmuv .
355    bsub < job_cosmos
356    
357    
358    ##########################################################################
359    ##########################################################################
360    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
361  # requires input files in sudirectories run_template and ncep_rgau  # requires input files in sudirectories run_template and ncep_rgau
362  # presently residing under orion:/tmp1/dmenem/cube  # presently residing under orion:/tmp1/dmenem/cube
363    
# Line 102  cd MITgcm/verification/global_ocean.cs32 Line 366  cd MITgcm/verification/global_ocean.cs32
366  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
367  \cp SIZE.h_54 SIZE.h  \cp SIZE.h_54 SIZE.h
368  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
 \cp mom_vi_hdissip.F_hr mom_vi_hdissip.F  
369    
370  cd ..  cd ../build
 mkdir build  
 cd build  
371  \rm *  \rm *
372  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
373  make depend  make depend
374  make  make -j
375    
376  cd ..  cd ..
377  mkdir run  mkdir run
# Line 123  qsub job_orion Line 384  qsub job_orion
384    
385  ##########################################################################  ##########################################################################
386  ##########################################################################  ##########################################################################
387  # 510*510*6*50, 216-cpu cube sphere on altix with efc  # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
388  # requires input files in sudirectories run_template and ncep_rgau  # requires input files in sudirectories run_template and ncep_rgau
389  # these can be obained from lou:/u/menemenl/cube  # presently residing under orion:/tmp1/dmenem/cube
390    
391  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
392  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
393  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
394  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_41 SIZE.h
395  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
 \cp mom_vi_hdissip.F_hr mom_vi_hdissip.F  
396    
397  cd ..  cd ../build
 mkdir build  
 cd build  
398  \rm *  \rm *
399  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
400  make depend  make depend
401  make  make -j
402    
403  cd ..  cd ..
404  mkdir run  mkdir run
# Line 148  cd run Line 406  cd run
406  \rm *  \rm *
407  \cp ../input/* .  \cp ../input/* .
408  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
409  qsub job_altix  qsub job_orion41
410    
411    
412  ##########################################################################  ##########################################################################
413  ##########################################################################  ##########################################################################
414  # matlab script for generating pChkptFreq  # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
415    # requires input files in sudirectories run_template and ncep_rgau
416    # presently residing under orion:/tmp1/dmenem/cube
417    
418  nTimeSteps=26352;  cd MITgcm/verification/global_ocean.cs32x15/code
419  for niter0=216:26352:(26352*11)  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
420   pChkptFreq=(niter0+nTimeSteps)*1200;  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
421   day=pChkptFreq/24/60/60;  \cp SIZE.h_50 SIZE.h
422   disp(['niter0=' int2str(niter0) ',day=' int2str(day) ', ' ...  \cp packages.conf_hr packages.conf
  datestr(datenum(1992,1,1)+day) ', pChkptFreq=' int2str(pChkptFreq)])  
 end  
423    
424  niter0 = 216   , day = 369 , 04-Jan-1993, pChkptFreq = 31881600  cd ../build
425  niter0 = 26568 , day = 735 , 05-Jan-1994, pChkptFreq = 63504000  \rm *
426  niter0 = 52920 , day = 1101, 06-Jan-1995, pChkptFreq = 95126400  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
427  niter0 = 79272 , day = 1467, 07-Jan-1996, pChkptFreq = 126748800  make depend
428  niter0 = 105624, day = 1833, 07-Jan-1997, pChkptFreq = 158371200  make -j
429  niter0 = 131976, day = 2199, 08-Jan-1998, pChkptFreq = 189993600  
430  niter0 = 158328, day = 2565, 09-Jan-1999, pChkptFreq = 221616000  cd ..
431  niter0 = 184680, day = 2931, 10-Jan-2000, pChkptFreq = 253238400  mkdir run
432  niter0 = 211032, day = 3297, 10-Jan-2001, pChkptFreq = 284860800  cd run
433  niter0 = 237384, day = 3663, 11-Jan-2002, pChkptFreq = 316483200  \rm *
434  niter0 = 263736, day = 4029, 12-Jan-2003, pChkptFreq = 348105600  \cp ../input/* .
435    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
436    qsub job_orion
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