Re: [GRASS-dev] Unable to rename cell/null file - NULL file messed up

2015-12-03 Thread Anna Petrášová 
On Dec 2, 2015 11:17 PM, "Glynn Clements"  wrote:
>
>
> Paulo van Breugel wrote:
>
> > Can't answer that, but I see that a related (?) ticket
>
> #2434 isn't related to #2712. #2712 relates specifically to the null
> file compression changes. #2434 was opened a year before those changes
> were started.
>
> > https://trac.osgeo.org/grass/ticket/2434 was retargeted to 7.03? From
the
> > description that issue seems to be very similar to the problem described
> > above?
>
> The problem described above:
>
> > > > WARNING: Unable to rename cell file
> > > > 'C:\GIS\GrassJvdS/latlong/YLD_NUT/.tmp/unknown/3988.0' to
> > > > 'C:\GIS\GrassJvdS/latlong/YLD_NUT/fcell/Shan3_CA_Renyi_0_0': File
exists
> > > > WARNING: Unable to rename null file
> > > > 'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/.tmp/unknown/4100.1' to
> > > >
'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/cell_misc/Shan3_CA_Renyi_1_0/null':
> > > > File exists
>
> doesn't match the symptoms of either #2434 or #2712. In both of those
> cases, the rename() fails with EACCESS ("Permission denied"), which is
> symptomatic of the file being open.
>
> This case fails with EEXIST ("File exists"), which suggests that the
> destination file wasn't deleted first. On Unix, deleting the original
> isn't required (or even desired); rename() will atomically remove any
> existing file. Windows generates an error if the destination exists.
> So we (try to) remove it first (on all platforms).
>
> remove(path);
> if (rename(fcb->temp_name, path)) {
> G_warning(_("Unable to rename cell file '%s' to '%s': %s"),
>   fcb->temp_name, path, strerror(errno));
> stat = -1;
> }
>
> (close_new() in lib/raster/close.c).
>
> The warning suggests that the file exists and remove() failed to
> remove it. On Windows, that can happen if the file is open.
>
Glynn, any insights about #2434? I remember looking at the code of
v.surf.bspline but I haven't found any obvious  differences between it and
other modules which use segment library.

Thanks,

Anna
> And looking at r.biodiversity.py, I notice:
>
> grass.mapcalc("$outl = -1 * $outl",
>   outl=out_renyi,
>   overwrite=True,
>   quiet=True)
>
> I.e. it's running r.mapcalc with the same map as both input and
> output. That isn't guaranteed to work. And in fact it doesn't, because
> the close_maps() function (which closes all of the input maps) is
> never actually called.
>
> So when it tries to close the output maps, which involves renaming the
> new cell/fcell/null files into place, the original cell/fcell/null
> files are still open for reading, meaning that the remove() will fail,
> as will the subsequent rename().
>
> Having r.mapcalc close the input maps would avoid that, and should be
> done, but ultimately that's fixing the symptoms. r.biodiversity
> shouldn't be trying to modify out_renyi "in-place". It should create a
> new map then, if necessary, replace the original using g.remove and
> g.rename.
>
> One problem with in-place modification is that closing an output map
> writes a number of support files (history, range, quant, cats,
> histogram). But after closing the output maps, r.mapcalc will
> sometimes copy some of the metadata (cats, colors, history) from the
> input map. Currently, it only does this if the entire expression is
> just a map with optional modifiers, but it may get more "intelligent"
> in the future. Clearly, that's a problem if the input map has already
> been replaced.
>
> --
> Glynn Clements 
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Re: [GRASS-dev] Unable to rename cell/null file - NULL file messed up

2015-12-02 Thread Glynn Clements 

Paulo van Breugel wrote:

> Can't answer that, but I see that a related (?) ticket

#2434 isn't related to #2712. #2712 relates specifically to the null
file compression changes. #2434 was opened a year before those changes
were started.

> https://trac.osgeo.org/grass/ticket/2434 was retargeted to 7.03? From the
> description that issue seems to be very similar to the problem described
> above?

The problem described above:

> > > WARNING: Unable to rename cell file
> > > 'C:\GIS\GrassJvdS/latlong/YLD_NUT/.tmp/unknown/3988.0' to
> > > 'C:\GIS\GrassJvdS/latlong/YLD_NUT/fcell/Shan3_CA_Renyi_0_0': File exists
> > > WARNING: Unable to rename null file
> > > 'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/.tmp/unknown/4100.1' to
> > > 'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/cell_misc/Shan3_CA_Renyi_1_0/null':
> > > File exists

doesn't match the symptoms of either #2434 or #2712. In both of those
cases, the rename() fails with EACCESS ("Permission denied"), which is
symptomatic of the file being open.

This case fails with EEXIST ("File exists"), which suggests that the
destination file wasn't deleted first. On Unix, deleting the original
isn't required (or even desired); rename() will atomically remove any
existing file. Windows generates an error if the destination exists. 
So we (try to) remove it first (on all platforms).

remove(path);
if (rename(fcb->temp_name, path)) {
G_warning(_("Unable to rename cell file '%s' to '%s': %s"),
  fcb->temp_name, path, strerror(errno));
stat = -1;
}

(close_new() in lib/raster/close.c).

The warning suggests that the file exists and remove() failed to
remove it. On Windows, that can happen if the file is open.

And looking at r.biodiversity.py, I notice:

grass.mapcalc("$outl = -1 * $outl", 
  outl=out_renyi,
  overwrite=True,
  quiet=True)

I.e. it's running r.mapcalc with the same map as both input and
output. That isn't guaranteed to work. And in fact it doesn't, because
the close_maps() function (which closes all of the input maps) is
never actually called.

So when it tries to close the output maps, which involves renaming the
new cell/fcell/null files into place, the original cell/fcell/null
files are still open for reading, meaning that the remove() will fail,
as will the subsequent rename().

Having r.mapcalc close the input maps would avoid that, and should be
done, but ultimately that's fixing the symptoms. r.biodiversity
shouldn't be trying to modify out_renyi "in-place". It should create a
new map then, if necessary, replace the original using g.remove and
g.rename.

One problem with in-place modification is that closing an output map
writes a number of support files (history, range, quant, cats,
histogram). But after closing the output maps, r.mapcalc will
sometimes copy some of the metadata (cats, colors, history) from the
input map. Currently, it only does this if the entire expression is
just a map with optional modifiers, but it may get more "intelligent"
in the future. Clearly, that's a problem if the input map has already
been replaced.

-- 
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Re: [GRASS-dev] Unable to rename cell/null file - NULL file messed up

2015-12-02 Thread Paulo van Breugel 



On 03-12-15 05:15, Glynn Clements wrote:

Paulo van Breugel wrote:


Can't answer that, but I see that a related (?) ticket

#2434 isn't related to #2712. #2712 relates specifically to the null
file compression changes. #2434 was opened a year before those changes
were started.


https://trac.osgeo.org/grass/ticket/2434 was retargeted to 7.03? From the
description that issue seems to be very similar to the problem described
above?

The problem described above:


WARNING: Unable to rename cell file
'C:\GIS\GrassJvdS/latlong/YLD_NUT/.tmp/unknown/3988.0' to
'C:\GIS\GrassJvdS/latlong/YLD_NUT/fcell/Shan3_CA_Renyi_0_0': File exists
WARNING: Unable to rename null file
'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/.tmp/unknown/4100.1' to
'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/cell_misc/Shan3_CA_Renyi_1_0/null':
File exists

doesn't match the symptoms of either #2434 or #2712. In both of those
cases, the rename() fails with EACCESS ("Permission denied"), which is
symptomatic of the file being open.

This case fails with EEXIST ("File exists"), which suggests that the
destination file wasn't deleted first. On Unix, deleting the original
isn't required (or even desired); rename() will atomically remove any
existing file. Windows generates an error if the destination exists.
So we (try to) remove it first (on all platforms).

remove(path);
if (rename(fcb->temp_name, path)) {
G_warning(_("Unable to rename cell file '%s' to '%s': %s"),
  fcb->temp_name, path, strerror(errno));
stat = -1;
}

(close_new() in lib/raster/close.c).

The warning suggests that the file exists and remove() failed to
remove it. On Windows, that can happen if the file is open.

And looking at r.biodiversity.py, I notice:

 grass.mapcalc("$outl = -1 * $outl",
   outl=out_renyi,
   overwrite=True,
   quiet=True)

I changed that already, now output is different from any of the input layers


I.e. it's running r.mapcalc with the same map as both input and
output. That isn't guaranteed to work. And in fact it doesn't, because
the close_maps() function (which closes all of the input maps) is
never actually called.

So when it tries to close the output maps, which involves renaming the
new cell/fcell/null files into place, the original cell/fcell/null
files are still open for reading, meaning that the remove() will fail,
as will the subsequent rename().

Having r.mapcalc close the input maps would avoid that, and should be
done, but ultimately that's fixing the symptoms. r.biodiversity
shouldn't be trying to modify out_renyi "in-place". It should create a
new map then, if necessary, replace the original using g.remove and
g.rename.


Thanks for the detailed explanation. After I changed the r.mapcalc 
statement the script also works on Windows, but it is good to know 
better the underlying problem.




One problem with in-place modification is that closing an output map
writes a number of support files (history, range, quant, cats,
histogram). But after closing the output maps, r.mapcalc will
sometimes copy some of the metadata (cats, colors, history) from the
input map. Currently, it only does this if the entire expression is
just a map with optional modifiers, but it may get more "intelligent"
in the future. Clearly, that's a problem if the input map has already
been replaced.



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Re: [GRASS-dev] Unable to rename cell/null file - NULL file messed up

2015-12-02 Thread Paulo van Breugel 



On 01-12-15 14:51, Paulo van Breugel wrote:



On Tue, Dec 1, 2015 at 2:04 PM, Helmut Kudrnovsky > wrote:


pvanbosgeo wrote
> When running a script (r.biodiversity) in GRASS 7.0 for Windows, I am
> getting the warning:
>
> WARNING: Unable to rename cell file
> 'C:\GIS\GrassJvdS/latlong/YLD_NUT/.tmp/unknown/3988.0' to
> 'C:\GIS\GrassJvdS/latlong/YLD_NUT/fcell/Shan3_CA_Renyi_0_0':
File exists
> WARNING: Unable to rename null file
> 'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/.tmp/unknown/4100.1' to
>
'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/cell_misc/Shan3_CA_Renyi_1_0/null':
> File exists

tested here:

r.biodiversity -r --verbose
input=spec1@data,spec2@data,spec3@data,spec4@data,spec5@data
output=renyi
alpha=0,1,2
WARNING: Unable to rename null file
'C:\grassdata/test3035/data/.tmp/unknown/1680.1' to
'C:\grassdata/test3035/data/cell_misc/renyi_Renyi_0_0/null': File
exists
WARNING: Unable to rename cell file
'C:\grassdata/test3035/data/.tmp/unknown/1680.0' to
'C:\grassdata/test3035/data/fcell/renyi_Renyi_0_0': File exists
WARNING: Unable to rename null file
'C:\grassdata/test3035/data/.tmp/unknown/8936.1' to
'C:\grassdata/test3035/data/cell_misc/renyi_Renyi_1_0/null': File
exists
WARNING: Unable to rename cell file
'C:\grassdata/test3035/data/.tmp/unknown/8936.0' to
'C:\grassdata/test3035/data/fcell/renyi_Renyi_1_0': File exists
WARNING: Unable to rename null file
'C:\grassdata/test3035/data/.tmp/unknown/9328.1' to
'C:\grassdata/test3035/data/cell_misc/renyi_Renyi_2_0/null': File
exists
WARNING: Unable to rename cell file
'C:\grassdata/test3035/data/.tmp/unknown/9328.0' to
'C:\grassdata/test3035/data/fcell/renyi_Renyi_2_0': File exists

is there some overwriting of existing files in the script? AFAIR
there may
be some issues with overwriting existing files in windows os.

Thanks Helmut. Yes, the script does also overwrite some intermediate 
files (with r.mapcalc). I will look into that and see how to change that.


Hi Helmut, you were absolutely right, the problem was with r.mapcalc 
overwriting some intermediate files, so I changed that. I don't have 
Windows myself, but had a quick try on my colleagues computer, and it 
seems to work now.  Thanks for your help.




I wonder though, if I use overwrite on the command line, there is no 
problem. So than that would be a problem specific to 
grass.script.mapcalc ?




-
best regards
Helmut
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[GRASS-dev] Unable to rename cell/null file - NULL file messed up

2015-12-01 Thread Paulo van Breugel 
When running a script (r.biodiversity) in GRASS 7.0 for Windows, I am
getting the warning:

WARNING: Unable to rename cell file
'C:\GIS\GrassJvdS/latlong/YLD_NUT/.tmp/unknown/3988.0' to
'C:\GIS\GrassJvdS/latlong/YLD_NUT/fcell/Shan3_CA_Renyi_0_0': File exists
WARNING: Unable to rename null file
'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/.tmp/unknown/4100.1' to
'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/cell_misc/Shan3_CA_Renyi_1_0/null':
File exists

The script does create the output files, but the NULL file seems to be
messed up, as large parts of the map are rendered as no-data. Removing and
then recreating the null file seems to solve the problem.

However, there still is another issue: r.info shows that the range of
values is e.g., min = -0  max = 2.98928848941905. This is as expected. Yet,
when clicking on the map with the query button, the query results show
negative values.

I thought this was related to g.rename, but that function runs without
problems. Perhaps something with permission: to run the script I just
copied it to the script folder
(c:/users/user1/appdata/roaming/grass7/addons/bin) (I did not install with
g.extension because that does not seem to work for GRASS at the moment).

Running the same on Linux results in the correct map, with none of the
problems listed above. Any idea what I am doing wrong / how this can be
solved?

Paulo
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Re: [GRASS-dev] Unable to rename cell/null file - NULL file messed up

2015-12-01 Thread Helmut Kudrnovsky 
> (I did not install with g.extension because that does not seem to work for
GRASS at the moment).

testedt here with

System Info 
GRASS version: 7.0.2
GRASS SVN Revision: 66861   
Build Date: 2015-11-19  
Build Platform: i686-pc-mingw32 
GDAL/OGR: 1.11.3
PROJ.4: 4.8.0   
GEOS: 3.5.0 
SQLite: 3.7.17  
Python: 2.7.4   
wxPython: 2.8.12.1  
Platform: Windows-7-6.1.7601-SP1 (OSGeo4W)  

g.extension extension=r.biodiversity
svnurl=http://svn.osgeo.org/grass/grass-addons/grass7
Downloading precompiled GRASS Addons ...
Updating addons metadata file...
Installation of  successfully finished



-
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Helmut
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Re: [GRASS-dev] Unable to rename cell/null file - NULL file messed up

2015-12-01 Thread Helmut Kudrnovsky 
pvanbosgeo wrote
> When running a script (r.biodiversity) in GRASS 7.0 for Windows, I am
> getting the warning:
> 
> WARNING: Unable to rename cell file
> 'C:\GIS\GrassJvdS/latlong/YLD_NUT/.tmp/unknown/3988.0' to
> 'C:\GIS\GrassJvdS/latlong/YLD_NUT/fcell/Shan3_CA_Renyi_0_0': File exists
> WARNING: Unable to rename null file
> 'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/.tmp/unknown/4100.1' to
> 'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/cell_misc/Shan3_CA_Renyi_1_0/null':
> File exists

tested here:

r.biodiversity -r --verbose
input=spec1@data,spec2@data,spec3@data,spec4@data,spec5@data output=renyi
alpha=0,1,2
WARNING: Unable to rename null file
'C:\grassdata/test3035/data/.tmp/unknown/1680.1' to
'C:\grassdata/test3035/data/cell_misc/renyi_Renyi_0_0/null': File exists
WARNING: Unable to rename cell file
'C:\grassdata/test3035/data/.tmp/unknown/1680.0' to
'C:\grassdata/test3035/data/fcell/renyi_Renyi_0_0': File exists
WARNING: Unable to rename null file
'C:\grassdata/test3035/data/.tmp/unknown/8936.1' to
'C:\grassdata/test3035/data/cell_misc/renyi_Renyi_1_0/null': File exists
WARNING: Unable to rename cell file
'C:\grassdata/test3035/data/.tmp/unknown/8936.0' to
'C:\grassdata/test3035/data/fcell/renyi_Renyi_1_0': File exists
WARNING: Unable to rename null file
'C:\grassdata/test3035/data/.tmp/unknown/9328.1' to
'C:\grassdata/test3035/data/cell_misc/renyi_Renyi_2_0/null': File exists
WARNING: Unable to rename cell file
'C:\grassdata/test3035/data/.tmp/unknown/9328.0' to
'C:\grassdata/test3035/data/fcell/renyi_Renyi_2_0': File exists

is there some overwriting of existing files in the script? AFAIR there may
be some issues with overwriting existing files in windows os.



-
best regards
Helmut
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Re: [GRASS-dev] Unable to rename cell/null file - NULL file messed up

2015-12-01 Thread Paulo van Breugel 
On Tue, Dec 1, 2015 at 3:28 PM, Markus Neteler  wrote:

> On Tue, Dec 1, 2015 at 1:44 PM, Paulo van Breugel
>  wrote:
> > When running a script (r.biodiversity) in GRASS 7.0 for Windows, I am
> > getting the warning:
> >
> > WARNING: Unable to rename cell file
> > 'C:\GIS\GrassJvdS/latlong/YLD_NUT/.tmp/unknown/3988.0' to
> > 'C:\GIS\GrassJvdS/latlong/YLD_NUT/fcell/Shan3_CA_Renyi_0_0': File exists
> > WARNING: Unable to rename null file
> > 'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/.tmp/unknown/4100.1' to
> >
> 'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/cell_misc/Shan3_CA_Renyi_1_0/null':
> > File exists
> >
> > The script does create the output files, but the NULL file seems to be
> > messed up, as large parts of the map are rendered as no-data. Removing
> and
> > then recreating the null file seems to solve the problem.
>
> Looks like:
> https://trac.osgeo.org/grass/ticket/2712
>
> Was the fix backported? According to a local diff, r65775 was not
> backported but the ticket closed.
>
> ?
>

Can't answer that, but I see that a related (?) ticket
https://trac.osgeo.org/grass/ticket/2434 was retargeted to 7.03? From the
description that issue seems to be very similar to the problem described
above?


>
> Markus
>
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Re: [GRASS-dev] Unable to rename cell/null file - NULL file messed up

2015-12-01 Thread Paulo van Breugel 
On Tue, Dec 1, 2015 at 2:04 PM, Helmut Kudrnovsky  wrote:

> pvanbosgeo wrote
> > When running a script (r.biodiversity) in GRASS 7.0 for Windows, I am
> > getting the warning:
> >
> > WARNING: Unable to rename cell file
> > 'C:\GIS\GrassJvdS/latlong/YLD_NUT/.tmp/unknown/3988.0' to
> > 'C:\GIS\GrassJvdS/latlong/YLD_NUT/fcell/Shan3_CA_Renyi_0_0': File exists
> > WARNING: Unable to rename null file
> > 'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/.tmp/unknown/4100.1' to
> >
> 'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/cell_misc/Shan3_CA_Renyi_1_0/null':
> > File exists
>
> tested here:
>
> r.biodiversity -r --verbose
> input=spec1@data,spec2@data,spec3@data,spec4@data,spec5@data output=renyi
> alpha=0,1,2
> WARNING: Unable to rename null file
> 'C:\grassdata/test3035/data/.tmp/unknown/1680.1' to
> 'C:\grassdata/test3035/data/cell_misc/renyi_Renyi_0_0/null': File exists
> WARNING: Unable to rename cell file
> 'C:\grassdata/test3035/data/.tmp/unknown/1680.0' to
> 'C:\grassdata/test3035/data/fcell/renyi_Renyi_0_0': File exists
> WARNING: Unable to rename null file
> 'C:\grassdata/test3035/data/.tmp/unknown/8936.1' to
> 'C:\grassdata/test3035/data/cell_misc/renyi_Renyi_1_0/null': File exists
> WARNING: Unable to rename cell file
> 'C:\grassdata/test3035/data/.tmp/unknown/8936.0' to
> 'C:\grassdata/test3035/data/fcell/renyi_Renyi_1_0': File exists
> WARNING: Unable to rename null file
> 'C:\grassdata/test3035/data/.tmp/unknown/9328.1' to
> 'C:\grassdata/test3035/data/cell_misc/renyi_Renyi_2_0/null': File exists
> WARNING: Unable to rename cell file
> 'C:\grassdata/test3035/data/.tmp/unknown/9328.0' to
> 'C:\grassdata/test3035/data/fcell/renyi_Renyi_2_0': File exists
>
> is there some overwriting of existing files in the script? AFAIR there may
> be some issues with overwriting existing files in windows os.
>
> Thanks Helmut. Yes, the script does also overwrite some intermediate files
(with r.mapcalc). I will look into that and see how to change that.

I wonder though, if I use overwrite on the command line, there is no
problem. So than that would be a problem specific to grass.script.mapcalc ?

>
>
> -
> best regards
> Helmut
> --
> View this message in context:
> http://osgeo-org.1560.x6.nabble.com/Unable-to-rename-cell-null-file-NULL-file-messed-up-tp5239350p5239357.html
> Sent from the Grass - Dev mailing list archive at Nabble.com.
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Re: [GRASS-dev] Unable to rename cell/null file - NULL file messed up

2015-12-01 Thread Markus Neteler 
On Tue, Dec 1, 2015 at 1:44 PM, Paulo van Breugel
 wrote:
> When running a script (r.biodiversity) in GRASS 7.0 for Windows, I am
> getting the warning:
>
> WARNING: Unable to rename cell file
> 'C:\GIS\GrassJvdS/latlong/YLD_NUT/.tmp/unknown/3988.0' to
> 'C:\GIS\GrassJvdS/latlong/YLD_NUT/fcell/Shan3_CA_Renyi_0_0': File exists
> WARNING: Unable to rename null file
> 'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/.tmp/unknown/4100.1' to
> 'C:\GIS\GrassJvdS/latlong_2005/YLD_NUT/cell_misc/Shan3_CA_Renyi_1_0/null':
> File exists
>
> The script does create the output files, but the NULL file seems to be
> messed up, as large parts of the map are rendered as no-data. Removing and
> then recreating the null file seems to solve the problem.

Looks like:
https://trac.osgeo.org/grass/ticket/2712

Was the fix backported? According to a local diff, r65775 was not
backported but the ticket closed.

?

Markus
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