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revision 1.23 by dimitri, Sat Feb 7 23:18:05 2004 UTC revision 1.61 by dimitri, Wed Dec 14 05:12:19 2005 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.  Date last updated: December 13, 2005
3  This is the code used for cube2, the second 1992-2002 510x510x6  216-CPU code and input used for integrating cube27.
 cube-sphere integration.  
4    
5    
6  ##########################################################################  ##########################################################################
7  ##########################################################################  ##########################################################################
8  # getting the code from anonymous CVS server  # getting the code from anonymous CVS server
9    
10  setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  cvs co MITgcm_contrib/high_res_cube/README_ice
11  cvs login ( CVS password: cvsanon )  cvs co MITgcm_contrib/high_res_cube/code-mods
12  cvs co -r hrcube_2 MITgcm_contrib/high_res_cube/README_ice  cvs co MITgcm_contrib/high_res_cube/input
13  cvs co -r hrcube_2 MITgcm_contrib/high_res_cube/code-mods  cvs co MITgcm_contrib/high_res_cube/results
14  cvs co -r hrcube_2 MITgcm_contrib/high_res_cube/matlab-grid-converter  cvs co MITgcm_code
15  cvs co -r hrcube_2 MITgcm_contrib/high_res_cube/input  cvs co MITgcm/verification/global_ocean.cs32x15
 cvs co -r hrcube_2 MITgcm_contrib/high_res_cube/results  
 cvs co -r hrcube_2 MITgcm_code  
 cvs co -r hrcube_2 MITgcm/verification/global_ocean.cs32x15  
16    
17    
18  ##########################################################################  ##########################################################################
# Line 25  cvs co -r hrcube_2 MITgcm/verification/g Line 21  cvs co -r hrcube_2 MITgcm/verification/g
21    
22  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
23  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
24  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
25    cd ../build
26  cd ..  \rm *
 mkdir build  
 cd build  
27  ../../../tools/genmake2 -mods=../code  ../../../tools/genmake2 -mods=../code
28  make depend  make depend
29  make  make
   
30  cd ..  cd ..
31  mkdir run  mkdir run
32  cd run  cd run
33    \rm *
34  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
35  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
36  ../build/mitgcmuv >& output.txt  ../build/mitgcmuv >& output.txt
37    
# Line 48  comparison output is in: Line 41  comparison output is in:
41  to use matlab to look at the output  to use matlab to look at the output
42  matlab  matlab
43    
44  for fld={'Eta','VICE','UICE','HEFF','AREA','Qsw','Qnet','FV','FU','EmPmR'}  for fld={'VICEtave','UICEtave','HEFFtave','AREAtave','QSWtave', ...
45             'QNETtave','FVtave','FUtave','EmPmRtave'}
46      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]);
47      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause      cx=[min(tmp(:)) max(tmp(:))]; clf, plot_cube, title(fld{1}), pause
48  end  end
49    
50  heff=permute(readbin(['HEFF.0000000020.data'],[32,6,32]),[1 3 2]);  heff=permute(readbin(['HEFFtave.0000000020.data'],[32,6,32]),[1 3 2]);
51  mask=0*heff; mask(find(heff>.001))=1;  mask=0*heff; mask(find(heff>.001))=1;
52  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]);
53  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]);
54  clf  clf
55  subplot(221), mypcolor(uice(:,:,3)'), colorbar, title('uice, tile 3')  subplot(221), mypcolor(uice(:,:,3)'); colorbar, title('uice, tile 3')
56  subplot(222), mypcolor(uice(:,:,6)'), colorbar, title('uice, tile 6')  subplot(222), mypcolor(uice(:,:,6)'); colorbar, title('uice, tile 6')
57  subplot(223), mypcolor(vice(:,:,3)'), colorbar, title('vice, tile 3')  subplot(223), mypcolor(vice(:,:,3)'); colorbar, title('vice, tile 3')
58  subplot(224), mypcolor(vice(:,:,6)'), colorbar, title('vice, tile 6')  subplot(224), mypcolor(vice(:,:,6)'); colorbar, title('vice, tile 6')
59    
60    
61  ##########################################################################  ##########################################################################
62  ##########################################################################  ##########################################################################
63  # 32*32*6*15, 2-cpu cube sphere on the altices with efc  # 32*32*6*15, 17-tile, 1-cpu cube sphere experiment
64    
65  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
66  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
67  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s12t_16x32/* .  \cp ../code_alt/code.176t_8x4/* .
68    cd ../build
69    \rm *
70    ../../../tools/genmake2 -mods=../code
71    make depend
72    make
73    cd ..
74    mkdir run
75    cd run
76    \rm *
77    \cp ../input/* .
78    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
79    ../build/mitgcmuv >& output.txt
80    
81    
82    ##########################################################################
83    ##########################################################################
84    # 32*32*6*15, 2-cpu cube sphere on the altices with ifort
85    
86    cd MITgcm/verification/global_ocean.cs32x15/code
87    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
88    \cp ../../../utils/exch2/code-mods/s12t_16x32/* .
89  \cp SIZE.h_mpi SIZE.h  \cp SIZE.h_mpi SIZE.h
90    
91  cd ..  cd ../build
 mkdir build  
 cd build  
92  \rm *  \rm *
93  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
94  make depend  make depend
95  make  make -j
96    
97  cd ..  cd ..
98  mkdir run  mkdir run
99  cd run  cd run
100  \rm *  \rm *
101  \cp ../input/* .  \cp ../input/* .
 \cp ../../../../MITgcm_contrib/high_res_cube/matlab-grid-converter/tile00* .  
102  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
103  mpirun -np 2 ../build/mitgcmuv  mpirun -np 2 ../build/mitgcmuv
104    
105    
106  ##########################################################################  ##########################################################################
107  ##########################################################################  ##########################################################################
108  # 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
109    # starting with pickup file from end of 1992
110  # requires input files in sudirectories run_template and ncep_rgau  # requires input files in sudirectories run_template and ncep_rgau
111  # presently residing under orion:/tmp1/dmenem/cube  
112    cd MITgcm/verification/global_ocean.cs32x15/code
113    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
114    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s54t_170x170/* .
115    \cp packages.conf_hr packages.conf
116    
117    cd ../build
118    \rm *
119    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
120    make depend
121    make -j
122    
123    cd ..
124    mkdir run
125    cd run
126    \rm *
127    \cp ../input/* .
128    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
129    qsub job_altix92_54t
130    
131    
132    ##########################################################################
133    ##########################################################################
134    # 510*510*6*50, 216-cpu cube sphere on altix with ifort and pkg/diagnostics
135    # requires input files in sudirectories run_template and ncep_rgau
136    # these can be obained from lou:/u/menemenl/cube
137    
138  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
139  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
140  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
141  \cp SIZE.h_54 SIZE.h  \cp SIZE.h_216 SIZE.h
142  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
143    
144    cd ../build
145    \rm *
146    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
147    make depend
148    make -j
149    
150  cd ..  cd ..
151  mkdir build  mkdir run
152  cd build  cd run
153    \rm *
154    \cp ../input/* .
155    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
156    ln -sf ../../../../run_template/* .
157    \rm pickup*
158    ln -sf ../../../../run_template/pickup.0000000216.cube27 pickup.0000000216
159    ln -sf  ../../../../run_template/pickup_seaice.0000000216.cube27 pickup_seaice.0000000216
160    \cp ../build/mitgcmuv .
161    qsub job_altix
162    
163    
164    ##########################################################################
165    ##########################################################################
166    # 510*510*6*50, 1500-tile, 150-cpu, excludes land
167    # uses s1500t_17x51 configuration
168    
169    cd MITgcm/verification/global_ocean.cs32x15/code
170    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
171    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
172    \cp SIZE.h_150 SIZE.h
173    \cp packages.conf_hr packages.conf
174    
175    cd ../build
176  \rm *  \rm *
177  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
178  make depend  make depend
179  make  make -j
180    
181  cd ..  cd ..
182  mkdir run  mkdir run
# Line 117  cd run Line 184  cd run
184  \rm *  \rm *
185  \cp ../input/* .  \cp ../input/* .
186  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
187  qsub job_orion  ln -sf ../../../../run_template/* .
188    \rm pickup*
189    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
190    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
191    \cp ../build/mitgcmuv mitgcmuv150
192    qsub job_altix150
193    
194    
195    
196    
197  ##########################################################################  ##########################################################################
198  ##########################################################################  ##########################################################################
199  # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc  # 510*510*6*50, 1500-tile, 375-cpu, excludes land
200  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
201  # presently residing under orion:/tmp1/dmenem/cube  # example for running on c17-c20 using arrayd
202    
203  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
204  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
205  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
206  \cp SIZE.h_41 SIZE.h  \cp SIZE.h_375 SIZE.h
207  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
208    
209    cd ../build
210    \rm *
211    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
212    make depend
213    make -j
214    
215  cd ..  cd ..
216  mkdir build  mkdir run
217  cd build  cd run
218    \rm *
219    \cp ../input/* .
220    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
221    ln -sf ../../../../run_template/* .
222    \rm pickup*
223    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
224    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
225    \cp ../build/mitgcmuv .
226    job_c20_375cpu < /dev/null >&! output.run &
227    
228    
229    
230    
231    
232    
233    
234    
235    
236    
237    
238    
239    ##########################################################################
240    ##########################################################################
241    # 510*510*6*50, 1500-tile, 375-cpu, excludes land
242    # uses s1500t_17x51 configuration
243    # example for running on c17-c20 using arrayd
244    
245    cd MITgcm/verification/global_ocean.cs32x15/code
246    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
247    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
248    \cp SIZE.h_375 SIZE.h
249    \cp packages.conf_hr packages.conf
250    
251    cd ../build
252  \rm *  \rm *
253  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
254  make depend  make depend
255  make  make -j
256    
257  cd ..  cd ..
258  mkdir run  mkdir run
# Line 146  cd run Line 260  cd run
260  \rm *  \rm *
261  \cp ../input/* .  \cp ../input/* .
262  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
263  qsub job_orion  ln -sf ../../../../run_template/* .
264    \rm pickup*
265    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
266    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
267    \cp ../build/mitgcmuv .
268    job_c20_375cpu < /dev/null >&! output.run &
269    
270    
271  ##########################################################################  ##########################################################################
272  ##########################################################################  ##########################################################################
273  # 510*510*6*50, 216-cpu cube sphere on altix with efc  # 510*510*6*50, 1500-tile, 500-cpu, excludes land
274  # requires input files in sudirectories run_template and ncep_rgau  # uses s1500t_17x51 configuration
275  # these can be obained from lou:/u/menemenl/cube  # example for running on c17-c20 using arrayd
276    
277    cd MITgcm/verification/global_ocean.cs32x15/code
278    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
279    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
280    \cp SIZE.h_500 SIZE.h
281    \cp packages.conf_hr packages.conf
282    
283    cd ../build
284    \rm *
285    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_ifort+mpi_altix_nas
286    make depend
287    make -j
288    
289    cd ..
290    mkdir run
291    cd run
292    \rm *
293    \cp ../input/* .
294    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
295    ln -sf ../../../../run_template/* .
296    \rm pickup*
297    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
298    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
299    \cp ../build/mitgcmuv .
300    job_c19_500cpu < /dev/null >&! output.run &
301    
302    
303    
304    
305    
306    ##########################################################################
307    ##########################################################################
308    # 510*510*6*50, 216-cpu cube sphere on cosmos
309    
310  cd MITgcm/verification/global_ocean.cs32x15/code  cd MITgcm/verification/global_ocean.cs32x15/code
311  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
# Line 161  cd MITgcm/verification/global_ocean.cs32 Line 313  cd MITgcm/verification/global_ocean.cs32
313  \cp SIZE.h_216 SIZE.h  \cp SIZE.h_216 SIZE.h
314  \cp packages.conf_hr packages.conf  \cp packages.conf_hr packages.conf
315    
316    module unload latest_intel80
317    module unload mpich-gm-intel80
318    module load latest_intel81
319    module load mpich-gm-intel81
320    
321    cd ../build
322    \rm *
323    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia32_ifort+mpi_cosmos
324    make depend
325    make -j
326    
327    cd ..
328    mkdir run
329    cd run
330    \rm *
331    \cp ../input/* .
332    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
333    ln -sf ../../../../run_template/* .
334    \rm pickup*
335    ln -sf ../../../../run_template/pickup.0000316440.cube19 pickup.0000000216
336    ln -sf  ../../../../run_template/pickup_seaice.0000316440.cube19 pickup_seaice.0000000216
337    \cp ../build/mitgcmuv .
338    bsub < job_cosmos
339    
340    
341    
342    
343    
344    
345    
346    
347    
348    
349    
350    
351    
352    
353    
354    
355    
356    
357    
358    
359    ##########################################################################
360    ##########################################################################
361    # 510*510*6*50, 216-tile, 54-cpu cube sphere on the altices with efc
362    # requires input files in sudirectories run_template and ncep_rgau
363    # presently residing under orion:/tmp1/dmenem/cube
364    
365    cd MITgcm/verification/global_ocean.cs32x15/code
366    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
367    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s216t_85x85/* .
368    \cp SIZE.h_54 SIZE.h
369    \cp packages.conf_hr packages.conf
370    
371    cd ../build
372    \rm *
373    ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
374    make depend
375    make -j
376    
377  cd ..  cd ..
378  mkdir build  mkdir run
379  cd build  cd run
380    \rm *
381    \cp ../input/* .
382    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
383    qsub job_orion
384    
385    
386    ##########################################################################
387    ##########################################################################
388    # 510*510*6*50, 205-tile, 41-cpu cube sphere on the altices with efc
389    # requires input files in sudirectories run_template and ncep_rgau
390    # presently residing under orion:/tmp1/dmenem/cube
391    
392    cd MITgcm/verification/global_ocean.cs32x15/code
393    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
394    \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s205t_85x85/* .
395    \cp SIZE.h_41 SIZE.h
396    \cp packages.conf_hr packages.conf
397    
398    cd ../build
399  \rm *  \rm *
400  ../../../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
401  make depend  make depend
402  make  make -j
403    
404  cd ..  cd ..
405  mkdir run  mkdir run
# Line 175  cd run Line 407  cd run
407  \rm *  \rm *
408  \cp ../input/* .  \cp ../input/* .
409  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .  \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
410  qsub job_altix  qsub job_orion41
411    
412    
413  ##########################################################################  ##########################################################################
414  ##########################################################################  ##########################################################################
415  # matlab script for generating pChkptFreq  # 510*510*6*50, 1500-tile, 50-cpu cube sphere on the altices with efc
416    # requires input files in sudirectories run_template and ncep_rgau
417    # presently residing under orion:/tmp1/dmenem/cube
418    
419  nTimeSteps=26352;  cd MITgcm/verification/global_ocean.cs32x15/code
420  for niter0=216:26352:(26352*11)  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/* .
421   pChkptFreq=(niter0+nTimeSteps)*1200;  \cp ../../../../MITgcm_contrib/high_res_cube/code-mods/s1500t_17x51/* .
422   day=pChkptFreq/24/60/60;  \cp SIZE.h_50 SIZE.h
423   disp(['niter0=' int2str(niter0) ',day=' int2str(day) ', ' ...  \cp packages.conf_hr packages.conf
  datestr(datenum(1992,1,1)+day) ', pChkptFreq=' int2str(pChkptFreq)])  
 end  
424    
425  niter0 = 216   , day = 369 , 04-Jan-1993, pChkptFreq = 31881600  cd ../build
426  niter0 = 26568 , day = 735 , 05-Jan-1994, pChkptFreq = 63504000  \rm *
427  niter0 = 52920 , day = 1101, 06-Jan-1995, pChkptFreq = 95126400  ../../../tools/genmake2 -mods=../code -of ../../../tools/build_options/linux_ia64_efc+mpi_altix
428  niter0 = 79272 , day = 1467, 07-Jan-1996, pChkptFreq = 126748800  make depend
429  niter0 = 105624, day = 1833, 07-Jan-1997, pChkptFreq = 158371200  make -j
430  niter0 = 131976, day = 2199, 08-Jan-1998, pChkptFreq = 189993600  
431  niter0 = 158328, day = 2565, 09-Jan-1999, pChkptFreq = 221616000  cd ..
432  niter0 = 184680, day = 2931, 10-Jan-2000, pChkptFreq = 253238400  mkdir run
433  niter0 = 211032, day = 3297, 10-Jan-2001, pChkptFreq = 284860800  cd run
434  niter0 = 237384, day = 3663, 11-Jan-2002, pChkptFreq = 316483200  \rm *
435  niter0 = 263736, day = 4029, 12-Jan-2003, pChkptFreq = 348105600  \cp ../input/* .
436    \cp ../../../../MITgcm_contrib/high_res_cube/input/* .
437    qsub job_orion
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