[ncl-talk] A Fatal Error Question: is this a bug in NCL?

Barry Lynn barry.h.lynn at gmail.com
Wed Jul 19 07:39:20 MDT 2017


Hello:

My code still runs out of memory, but not nearly as fast.  This is helpful
by itself.

I have included two version of the code for users who desire to make GEFS
mean map plots.  You have to create GEFS/GEFS_XX directories where XX is
the GEFS member.

1) Plotting sea level values of mean GEFS temperatures, humidity, winds,
and sea-level pressure.

2) 700 mb mean GEFS temperatures, humidity, winds, and height.

I have modified the code sent by Mary to skip over missing files.  This
step goes way back to a previous ncl-talk (thanks to Guido who gave a
suggestion how to skip over missing files).  Without it, the code can fail
if a file is missing.

I am not sure why the second map does not show a variable title, like the
first.  I haven't had a chance to check timings, yet.

I don't see an easy way to take the initial time in the forecast variable
"summary," include the forecast time in hours, and get the real time. So, I
still calculate times externally.  I have included "variable.file" in case
someone has a suggestion.  We would need to grab the actual time, and then
find the new time by adding the number of hours.

Barry

On Tue, Jul 18, 2017 at 6:28 PM, Mary Haley <haley at ucar.edu> wrote:

> Hi Barry,
>
> We could provide you with a profiling version of NCL, in which you run
> your script like normal, but then ncl produces a supplemental file with
> information about how long certain code segments are taking. It breaks it
> down by percentage of time spent in various sections.
>
>
> This profiling information is a bit clunky because you have to run a
> script on it and then view it from a browser, but these extra steps may be
> worth it in order to find out where the code is slow.
>
> To see a sample of how the profiler works, go to:
>
> http://www.ncl.ucar.edu/Document/Tools/Profiler/multiple_plots/
>
> and click on any one of the *.xml (the "multiple_plots_ncl__multiple_
> plots.xml
> <http://www.ncl.ucar.edu/Document/Tools/Profiler/multiple_plots/multiple_plots_ncl__multiple_plots.xml>"
> is the main one and a good place to start)
> ​.  Look for lines that are colored
>> ​in red, as these indicate where more time is being spent.
>> You can also use "get_cpu_time()" to track the timings yourself. For
> example, if you want to time how long it takes to create each set of panel
> plots, then you would have code that looks like this:
>
>   start_time = get_cpu_time()
>   plot(0) = gsn_csm_contour_map(wks,t_ave,res1)
>   plot(1) = gsn_csm_contour_map(wks,rh_ave,res2)
>   plotB   = gsn_csm_vector(wks,u_ave_new(::4,::4), \
>                             v_ave_new(::4,::4),vecres)
>   plotD   = gsn_csm_contour(wks,z_ave_new,res3)
>   overlay(plot(0),plotB)
>   overlay(plot(1),plotD)
>   gsn_panel(wks,plot,(/2,1/),resP)    ; now draw as one plot
>   end_time = get_cpu_time()
>   print("Elapsed time for plotting = " + (end_time-start_time)
>
> If you plan to do a lot of these timings, then I recommend a function.  :-)
>
> procedure print_elapsed_time(stime,etime,title)
> begin
>   print("==================================================")
>   print("Elapsed time for " + title + ": " + (etime-stime))
>   print("==================================================")
> end
>
> Then your code would be:
>
>   start_plot_time = get_cpu_time()
>   plot(0) = gsn_csm_contour_map(wks,t_ave,res1)
>   plot(1) = gsn_csm_contour_map(wks,rh_ave,res2)
>   plotB   = gsn_csm_vector(wks,u_ave_new(::4,::4), \
>                             v_ave_new(::4,::4),vecres)
>   plotD   = gsn_csm_contour(wks,z_ave_new,res3)
>   overlay(plot(0),plotB)
>   overlay(plot(1),plotD)
>   gsn_panel(wks,plot,(/2,1/),resP)    ; now draw as one plot
>   end_plot_time = get_cpu_time()
>   print_elapsed time(start_plot_time,end_plot_time,"Plotting")
>
> Note that I changed the name from "start_time/end_time to
> start_plot_time/end_plot_time. This is in case you do a bunch of these,
> then you can print all the timings at the end, and it also helps keep track
> of what timings these are associated with.
>
>   start_read_time = get_cpu_time()
>   .... Code that calls addfile and reads data
>   end_read_time = get_cpu_time()
>   ...
>   start_ave_time = get_cpu_time()
>   .... code that calls average_subset function a bunch of times
>   end_ave_time = get_cpu_time()
>   ...
>   start_plot_time = get_cpu_time()
>   ,,, code that creates and draws plots ...
>   end_plot_time = get_cpu_time()
>
>   print_elapsed time(start_read_time,end_read_time,"Reading data")
>   print_elapsed time(start_ave_time,end_ave_time,"Averages")
>   print_elapsed time(start_plot_time,end_plot_time,"Plotting")
>
> Of course, you don't have to put all the elapsed timing prints at the
> end.  You can print them out right when the code is done, so you
> immediately have the information.  It just depends on what you are
> interested in.
>
> As a side, and Dave or Rick may want to correct me on my understanding on
> this, but I think one thing that can make your code slow is that you have a
> lot of print statements. Every time you do something like this:
>
>    print("x = " + x)
>
> versus this:
>
> print(x)
>
> I believe a string gets stored somewhere in memory. If you have a lot of
> these, then NCL will get noticeably slower and slower, especially if you
> are doing this inside do loops with a lot of iterations. I don't know if
> you really have enough print statements for this to be a problem, but it's
> worth making a mental note of this issue.
>
> --Mary
>
>
> On Mon, Jul 17, 2017 at 8:06 PM, Barry Lynn <barry.h.lynn at gmail.com>
> wrote:
>
>> Dear Mary:
>>
>> Thank you. Very helpful!
>>
>> I had noticed that my code was running very, very slowly, but being
>> relatively "new" to NCL programming was not sure why.  (Also, it was, as
>> you noted, running out of memory since I "dialed back" the RAM on my
>> account.)
>>
>> I will try your code and compare, and get back to the list about the
>> timing differences.
>>
>> Barry
>>
>> On Tue, Jul 18, 2017 at 12:26 AM, Mary Haley <haley at ucar.edu> wrote:
>>
>>> Hi Barry,
>>>
>>> Rick is out this afternoon.
>>>
>>> Part of what Rick is suggesting is that if you are done with a variable,
>>> then you should delete it in order to free up memory for later
>>> calculations.
>>>
>>> If I may provide some honest comments about your script overall: if you
>>> use some simple "clean coding practices", this will make it *much* easier
>>> for you to debug your own code, and it will certainly make it easier for
>>> other people to debug it. It will also help you see where you might have
>>> some memory issues.
>>>
>>>
>>> Here are some suggestions for improving your script:
>>>
>>> *[1] Use "delete" to remove variables you don't need any more:*
>>>
>>> t_ave=t_ave-273.16  ; convert to C
>>>
>>>         z_ave=z_ave/10.  ; convert to dam
>>>
>>>         printMinMax(z_ave,False)
>>>         u = u * 3.6
>>>         v = v * 3.6
>>>         copy_VarCoords(u,u_ave)                         ; copy coord
>>> vars to speed
>>>         copy_VarCoords(v,v_ave)                         ; copy coord
>>> vars to speed
>>>         copy_VarCoords(z,z_ave)                         ; copy coord
>>> vars to speed
>>>         copy_VarCoords(t,t_ave)                         ; copy coord
>>> vars to speed
>>>         copy_VarCoords(rh,rh_ave)                         ; copy coord
>>> vars to speed
>>>
>>> If you no longer need the "u", "v", "z", etc variables, then delete them:
>>>
>>> t_ave=t_ave-273.16  ; convert to C
>>>
>>>         z_ave=z_ave/10.  ; convert to dam
>>>
>>>         printMinMax(z_ave,False)
>>>         u = u * 3.6
>>>         v = v * 3.6
>>>         copy_VarCoords(u,u_ave)                         ; copy coord
>>> vars to speed
>>>         copy_VarCoords(v,v_ave)                         ; copy coord
>>> vars to speed
>>>         copy_VarCoords(z,z_ave)                         ; copy coord
>>> vars to speed
>>>         copy_VarCoords(t,t_ave)
>>>         copy_VarCoords(rh,rh_ave)
>>>         delete([/u,v,z,t,rh/])                          ;  no longer
>>> needed
>>>
>>> *[2] You are reading several variables and not doing anything with them
>>> but printing them out. Reading them in uses memory. *
>>>
>>> If all you need to do is print them, then print them directly. An
>>> example:
>>>
>>>       lv0 = fin->lv_ISBL0
>>>       print("lv0 = " + lv0)
>>>       lv8 = fin->lv_ISBL8
>>>       print("lv8 = " + lv8)
>>>       lv10 = fin->lv_ISBL10
>>>       print("lv10 = " + lv10)
>>>
>>> Do this instead, to save memory:
>>>
>>>       print("lv0 = " + fin->lv_ISBL0)
>>>       print("lv8 = " + fin->lv_ISBL8)
>>>       print("lv10 = " + fin->lv_ISBL10)
>>>
>>>
>>> *[3] Avoid putting unchanged code inside do loops.*
>>>
>>> Your script has two do loops with a bunch of code inside of them that
>>> doesn't change.
>>>
>>> Do loops can be slow, so it's important to keep as much code *outside*
>>> of a do loop as possible.
>>>
>>> As an example, these are your two outside do loops:
>>>
>>>   do n=0,n_files -1,1
>>>     do i_dir = 0,n_dirWRF-1
>>>
>>> Inside these two loops, you have code that looks like this:
>>>
>>>        res1                     = True
>>>         res1 at mpDataBaseVersion = "Ncarg4_1"           ; choose more
>>> recent database
>>>         . . .
>>>         res1 at mpNationalLineThicknessF    = 3.0
>>>         res1 at mpGeophysicalLineThicknessF = 2.0
>>>       . . .
>>>
>>>         res1 at tiMainString         = time_var
>>>         res1 at gsnDraw             = False           ; don't draw
>>>
>>> res1 at cnLevelSelectionMode = "ExplicitLevels"    ; set explicit contour
>>> levels
>>>         . . .
>>>         res1 at cnInfoLabelOn = False                  ; turn off contour
>>> info label                                             res1 at lbAutoManage
>>>          = False          ; control label bar
>>>                         res1 at lbOrientation         = "Vertical"
>>>         . . .
>>>
>>>         res1 at lbTopMarginF = 0.001
>>>         res2                     = True
>>>         res2                     = True
>>>         .  . .
>>>         res2 at mpNationalLineThicknessF    = 3.0
>>>         res2 at mpGeophysicalLineThicknessF = 2.0
>>>         res2 at tiMainString         = time_var
>>>         res2 at gsnDraw             = False           ; don't draw
>>>
>>>         . . .
>>>         res2 at lbOrientation         = "Vertical"
>>>         res2 at pmLabelBarSide        = "Right"
>>>         res2 at lbLabelAutoStride =   True
>>>         res2 at pmLabelBarWidthF      = 0.20
>>>         res2 at pmLabelBarHeightF     = 0.7
>>>         . . .
>>>
>>> None of this code changes inside the do loops, but yet it is getting set
>>> again and again for every iteration of the two do loops. In order to speed
>>> things up, move as much code as you can to outside the do loop, and only
>>> keep things that actually change inside the do loop.
>>>
>>> I recommend creating functions to set the various resource lists:
>>> set_res1_list, set_res2_list, etc. This may not necessarily save memory,
>>> but it makes your code much cleaner.
>>>
>>> *[4] Use functions for cleaner code.*
>>>
>>> You have code that is repeated in multiple locations.  This can cause
>>> extra memory usage.  If you turn these repeated code segments into NCL
>>> functions, then this can save some memory.
>>>
>>> An example, you have:
>>>
>>>   i_loc = 1
>>>   j_loc = 1
>>>   GET_IJ::get_ij(lat2d,lon2d,lat_beg,lon_beg,i_loc,j_loc,nj,ni)
>>>   x_start = i_loc
>>>   y_start = j_loc
>>>
>>> Granted, this doesn't use a lot of memory, but every time you copy these
>>> 5 lines, it makes your script harder to read, and you will slowly use more
>>> memory if you do this kind of thing frequently.
>>>
>>> Turn the above five lines into a function:
>>>
>>> function get_ij_ncl(lat2d,lon2d,lat_beg,lon_beg)
>>> local nj, ni
>>> begin
>>>   i_loc = 1
>>>   j_loc = 1
>>>   nj = dimsizes(lat2d(:,0))
>>>   ni = dimsizes(lat2d(0,:))
>>>   GET_IJ::get_ij(lat2d,lon2d,lat_beg,lon_beg,i_loc,j_loc,nj,ni)
>>>  return([/i_loc,j_loc/])
>>> end
>>>
>>> and then call the function with:
>>>
>>> xy_start = get_ij_ncl(lat2d,lon2d,lat_beg,lon_beg)
>>>
>>> You will then need to change "x_start" to xy_start(0) and "y_start" to
>>> xy_start(1)
>>>
>>> *[5] Another place where a function would be helpful:*
>>>
>>>   u_ave_new = u_ave(xy_start(1):xy_end(1),xy_start(0):xy_end(0))
>>>   v_ave_new = v_ave(xy_start(1):xy_end(1),xy_start(0):xy_end(0))
>>>   lat2d_new = lat2d(xy_start(1):xy_end(1),xy_start(0):xy_end(0))
>>>   lon2d_new = lon2d(xy_start(1):xy_end(1),xy_start(0):xy_end(0))
>>> ; plotB   = gsn_csm_vector(wks,u_ave_new,v_ave_new,vecres)
>>>
>>> ;;;opy_VarCoords(dumb_ave,u_ave_new)
>>>
>>> ; copy_VarCoords(dumb_ave,v_ave_new)
>>>
>>>    u_ave_new!0 = "lat"
>>>    u_ave_new!1 = "lon"
>>>    u_ave_new&lat= lat(xy_start(1):xy_end(1))
>>>    u_ave_new&lon= lon(xy_start(0):xy_end(0))
>>>    v_ave_new!0 = "lat"
>>>    v_ave_new!1 = "lon"
>>>    v_ave_new&lat= lat(xy_start(1):xy_end(1))
>>>    v_ave_new&lon= lon(xy_start(0):xy_end(0))
>>>
>>> Create a function to do the subsetting and attaching of the metadata:
>>>
>>> function average_subset(x,lat,lon,xy_start,xy_end)
>>> begin
>>>   x_ave_new = x(xy_start(1):xy_end(1),xy_start(0):xy_end(0))
>>>   x_ave_new!0 = "lat"
>>>   x_ave_new!1 = "lon"
>>>   x_ave_new&lat= lat(xy_start(1):xy_end(1))
>>>   x_ave_new&lon= lon(xy_start(0):xy_end(0))
>>>   return(x_ave_new)
>>> end
>>>
>>> so now you can replace the above code with two lines:
>>>
>>>   u_ave_new = average_subset(u_ave,lat,lon,xy_start,xy_end)
>>>   v_ave_new = average_subset(v_ave,lat,lon,xy_start,xy_end)
>>>
>>> *[6] You created "lat2d_new" and "lon2d_new" but never use them. Again,
>>> this is using up memory for no purpose. Remove those two lines.*
>>>
>>> *[7] If you are propagating a smaller array to a larger array, as is the
>>> case here:*
>>>
>>>   lat2d = z
>>>   lon2d = z
>>>   do j = 0,nj-1
>>>   do i = 0,ni-1
>>>    lat2d(j,i)=lat(j)
>>>    lon2d(j,i)=lon(i)
>>>   end do
>>>   end do
>>>
>>> then use conform_dims instead of a do loop:
>>>
>>>   lat2d = conform_dims(dims2d,lat,0)
>>>   lon2d = conform_dims(dims2d,lon,1)
>>>
>>> Note that I no longer need the "lat2d = z" or "lon2d = z" code.
>>>
>>> [8] You have this code, and I'm not sure why:
>>>
>>>       a = addfile(filename,"r")
>>>       fin = a
>>>
>>> This seems like an unnecessary copy of "a".  Why not simply do:
>>>
>>>   fin = addfile(filename,"r")
>>>
>>> *[9] The "gsn_define_colormap" call should not be inside the do loop.
>>> Call this right after you call gsn_open_wks.*
>>>
>>> *[10] There's some random code I don't understand. For example:*
>>>
>>>   copy_VarCoords(z,lat2d)
>>>   copy_VarCoords(z,lon2d)
>>>
>>> lat2d and lon2d don't need to have z's coordinate arrays attached to
>>> them for any reason that I can see, so I think you can remove those two
>>> lines.
>>>
>>> *[11] Every time you have a do loop or an if statement, indent all the
>>> code inside *consistently* so you can more easily see what part of the code
>>> you're in.*
>>>
>>> *[12] Don't make extra copies of variables unless you really need to.*
>>>
>>> For example, you have:
>>>
>>>       filename = all_files(n)
>>>
>>> There's really no need to create "filename" since you can just use
>>> "all_files(n)".
>>> I've tried to clean up your code to show you what I'm talking about. The
>>> attached script likely won't run because I don't have your data to test
>>> it.  But, hopefully you can see what I'm doing and mimic this in your code.
>>>
>>> --Mary
>>>
>>>
>>>
>>> On Mon, Jul 17, 2017 at 11:40 AM, Barry Lynn <barry.h.lynn at gmail.com>
>>> wrote:
>>>
>>>> Hi Rick:
>>>>
>>>> Thank you for your suggestion.
>>>>
>>>> Could you please give me some guidelines on how to delete resources.
>>>>
>>>> I have included the script.  If you can provide an example, I can take
>>>> it from there.
>>>>
>>>> Thank you,
>>>>
>>>> Barry
>>>>
>>>> On Mon, Jul 17, 2017 at 5:22 PM, Rick Brownrigg <brownrig at ucar.edu>
>>>> wrote:
>>>>
>>>>> Hi Barry,
>>>>>
>>>>> On Linux, an errno=12 is an "out of memory" error.  I doubt that its
>>>>> related directly to the systemfunc() call, but rather due to memory being
>>>>> consumed by your script in previous iterations of the loop.  You might
>>>>> check if there are variables that can be freed (i.e., deleted()) after each
>>>>> iteration.
>>>>>
>>>>> HTH...
>>>>> Rick
>>>>>
>>>>> On Sun, Jul 16, 2017 at 8:56 PM, Barry Lynn <barry.h.lynn at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi:
>>>>>>
>>>>>> I have a program that does multiple loops.
>>>>>>
>>>>>> I had this error:
>>>>>>
>>>>>> 0) i_dir = 6
>>>>>>
>>>>>> fatal:systemfunc: cannot create child process:[errno=12]
>>>>>>
>>>>>> fatal:["Execute.c":8640]:Execute: Error occurred at or near line 84
>>>>>> in file ./plot_loop_700mb.ncl
>>>>>>
>>>>>>
>>>>>> This occurred when reading the file from the sixth directory of 20.
>>>>>>
>>>>>>
>>>>>> Here was the read from the 5th directory:
>>>>>>
>>>>>> (0) i_dir = 5
>>>>>>
>>>>>> (0) all_files(n) = /home/cust100021_vol1/barry/cu
>>>>>> st100021_vol2/GEFS/GEFS_05/gep05.t00z.pgrb2b.0p50.f084.grb
>>>>>>
>>>>>> Here is a listing of both files:
>>>>>>
>>>>>> They are both present, but the second attempted allocation/definition
>>>>>> of the file fails with the read that follows:
>>>>>>
>>>>>>
>>>>>> [barry at cust100021-login1 GEFS]$ ls -ltr
>>>>>> /home/cust100021_vol1/barry/cust100021_vol2/GEFS/GEFS_05/gep
>>>>>> 05.t00z.pgrb2b.0p50.f084.grb
>>>>>>
>>>>>> -rw-r--r-- 1 barry cust100021 78985320 Jul 16 04:58
>>>>>> /home/cust100021_vol1/barry/cust100021_vol2/GEFS/GEFS_05/gep
>>>>>> 05.t00z.pgrb2b.0p50.f084.grb
>>>>>>
>>>>>> [barry at cust100021-login1 GEFS]$ ls -ltr
>>>>>> /home/cust100021_vol1/barry/cust100021_vol2/GEFS/GEFS_06/gep
>>>>>> 06.t00z.pgrb2b.0p50.f084.grb
>>>>>>
>>>>>> -rw-r--r-- 1 barry cust100021 80466702 Jul 16 04:58
>>>>>> /home/cust100021_vol1/barry/cust100021_vol2/GEFS/GEFS_06/gep
>>>>>> 06.t00z.pgrb2b.0p50.f084.grb
>>>>>>
>>>>>> Here is the read:
>>>>>>
>>>>>>
>>>>>>   print("i_dir = " + i_dir)
>>>>>>
>>>>>>   diri = dirWRF(i_dir) + "/"
>>>>>>
>>>>>> ; define individual file read
>>>>>>
>>>>>>    all_files = systemfunc("ls " + diri + "ge*pgrb2b*grb")
>>>>>>
>>>>>>    print("all_files(n) = " + all_files(n))
>>>>>>
>>>>>>   filename = all_files(n)
>>>>>>
>>>>>>
>>>>>> Is the problem that I make this allocation multiple times, each
>>>>>> directory, each file? Perhaps I should read all files at once into a two
>>>>>> dimensional filename array?
>>>>>>
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Barry H. Lynn, Ph.D
>>>>>> Senior Lecturer,
>>>>>> The Institute of the Earth Science,
>>>>>> The Hebrew University of Jerusalem,
>>>>>> Givat Ram, Jerusalem 91904, Israel
>>>>>> Tel: 972 547 231 170
>>>>>> Fax: (972)-25662581
>>>>>>
>>>>>> C.E.O, Weather It Is, LTD
>>>>>> Weather and Climate Focus
>>>>>> http://weather-it-is.com
>>>>>> Jerusalem, Israel
>>>>>> Local: 02 930 9525
>>>>>> Cell: 054 7 231 170
>>>>>> Int-IS: x972 2 930 9525
>>>>>> US 914 432 3108 <(914)%20432-3108>
>>>>>>
>>>>>> _______________________________________________
>>>>>> ncl-talk mailing list
>>>>>> ncl-talk at ucar.edu
>>>>>> List instructions, subscriber options, unsubscribe:
>>>>>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Barry H. Lynn, Ph.D
>>>> Senior Lecturer,
>>>> The Institute of the Earth Science,
>>>> The Hebrew University of Jerusalem,
>>>> Givat Ram, Jerusalem 91904, Israel
>>>> Tel: 972 547 231 170
>>>> Fax: (972)-25662581
>>>>
>>>> C.E.O, Weather It Is, LTD
>>>> Weather and Climate Focus
>>>> http://weather-it-is.com
>>>> Jerusalem, Israel
>>>> Local: 02 930 9525
>>>> Cell: 054 7 231 170
>>>> Int-IS: x972 2 930 9525
>>>> US 914 432 3108 <(914)%20432-3108>
>>>>
>>>> _______________________________________________
>>>> ncl-talk mailing list
>>>> ncl-talk at ucar.edu
>>>> List instructions, subscriber options, unsubscribe:
>>>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>>>>
>>>>
>>>
>>
>>
>> --
>> Barry H. Lynn, Ph.D
>> Senior Lecturer,
>> The Institute of the Earth Science,
>> The Hebrew University of Jerusalem,
>> Givat Ram, Jerusalem 91904, Israel
>> Tel: 972 547 231 170
>> Fax: (972)-25662581
>>
>> C.E.O, Weather It Is, LTD
>> Weather and Climate Focus
>> http://weather-it-is.com
>> Jerusalem, Israel
>> Local: 02 930 9525
>> Cell: 054 7 231 170
>> Int-IS: x972 2 930 9525
>> US 914 432 3108 <(914)%20432-3108>
>>
>
>


-- 
Barry H. Lynn, Ph.D
Senior Lecturer,
The Institute of the Earth Science,
The Hebrew University of Jerusalem,
Givat Ram, Jerusalem 91904, Israel
Tel: 972 547 231 170
Fax: (972)-25662581

C.E.O, Weather It Is, LTD
Weather and Climate Focus
http://weather-it-is.com
Jerusalem, Israel
Local: 02 930 9525
Cell: 054 7 231 170
Int-IS: x972 2 930 9525
US 914 432 3108
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